t e c h n ic a l r e p o r t s

ReaChR: a red-shifted variant of channelrhodopsin
enables deep transcranial optogenetic excitationnpg© 2013 Nature America, Inc. All rights reserved.

John Y Lin1,5, Per Magne Knutsen2,5, Arnaud Muller2, David Kleinfeld2,3 & Roger Y Tsien1,4
Channelrhodopsins (ChRs) are used to optogeneticallydepolarize neurons. We engineered a variant of ChR, denoted
red-activatable ChR (ReaChR), that is optimally excited withorange to red light (l ~590–630 nm) and offers improved
membrane trafficking, higher photocurrents and faster kinetics
compared to existing red-shifted ChRs. Red light is lessscattered by tissue and is absorbed less by blood than the blue
to green wavelengths that are required by other ChR variants.
We used ReaChR expressed in the vibrissa motor cortex todrive spiking and vibrissa motion in awake mice when excitedwith red light through intact skull. Precise vibrissa movements
were evoked by expressing ReaChR in the facial motor nucleus
in the brainstem and illumination with red light through theexternal auditory canal. Thus, ReaChR enables transcranial
optical activation of neurons in deep brain structures without
the need to surgically thin the skull, form a transcranial
window or implant optical fibers.
ChRs are light-gated, non-specific cation channels that allow theselective depolarization of genetically targeted cells 1–6. However,currently available ChRs are limited by action spectra that typicallypeak at 450–545 nm7–11. In mammalian systems, such blue-green
wavelengths have limited penetration depths into neural tissue12, as
they are strongly absorbed by endogenous chromophores such as flavins, hemoglobin and melanin, and they are scattered more strongly
than yellow-red wavelengths. A common means to circumvent thisattenuation and achieve deep ChR excitation is to insert a thin opticalfiber into the target neural tissue13. However, this invasive procedurerequires precise stereotaxic positioning that may be difficult to perform when ChR is expressed in subcortical nuclei, and the fiber may
damage neuronal and/or vascular structures en route to the target. The
practical issue of efficient light delivery can be solved by creating a
red-shifted ChR with spectral peaks near or above 600 nm, where lightabsorption by hemes and scattering cross-sections drop off steeply12.
Such ChRs could facilitate the stimulation of deep structures with alight source placed outside the tissue or region of interest and thus
mitigate the need for invasive stimulation.
In this study, we engineered a new variant of ChR that we
named ReaChR for red-activatable ChR. Compared to the previously described ChRs with red spectral shifts VChR1 (ref. 14) andC1V1E122T (ref. 11), ReaChR has improved membrane trafficking

and expression in mammalian cells, a more robust spectral response
above 600 nm and an enhanced steady-state response to light withwavelengths longer than 600 nm. When ReaChR was expressed in
the mouse vibrissae motor cortex (vM1), we could trigger temporally
precise neuronal responses by illumination of the cortical surface
with 617 nm light through a transcranial window or evoke vibrissae
movements through the intact skin and bone at wavelengths ranging
from 470 to 655 nm. Expression of ReaChR in the facial motor nucleusof the brainstem allowed us to reliably activate vibrissa motoneurons
with wavelengths up to 655 nm through the non-invasive placementof a light-emitting diode (LED) at the opening of the external auditory
canal. Thus, ReaChR enables effective and temporally precise noninvasive stimulation of deep brain structures with ChR technology.
RESULTS
Development of a red-activatable ChR
The red-shifted ChR VChR1 (ref. 14), which has minimal trafficking
to the membrane as well as poor expression in mammalian cells11,15,
served as a template to engineer an efficient red light–activated ChR.
To improve membrane trafficking, we examined the superior membrane trafficking of the variant ChIEF7, which gives almost exclusive
plasma membrane expression with minimal cytosolic aggregation in
mammalian cells without the need for additional trafficking signals,
unlike many other ChR variants (Supplementary Fig. 1)15. We thus
replaced the N terminus of VChR1 before the first transmembrane
domain with the corresponding ChIEF sequence. The new construct,denoted C-VChR1, had considerably improved membrane trafficking15 (P < 0.001 for VChR1 compared to C-VChR1). To increase theexpression level, we replaced transmembrane domain F of VChR1
with the corresponding VChR2 helix, a strategy that has been shown
previously to increase the expression level of ChR in ChR1-ChR2
chimeras16. This new variant, named VCOMET for VChR optimized
for membrane expression and trafficking, had a red-shifted response
spectra similar to that of C-VChR1 or VChR115, with spectral peaks
at 590 and 530 nm for the maximum and steady-state (also called
plateau) responses, respectively (Supplementary Fig. 2b). VCOMET
expressed strongly in mammalian cells and retained robust membranetrafficking (Supplementary Fig. 1). It also yielded greater photocurrent in HEK293 cells (39 ± 8 pA pF−1 (mean ± s.e.m.), n = 13)
compared to C-VChR1 (6.9 ± 1.0 pA pF−1, n = 13; P < 0.01) andcomparable photocurrents to mammalian codon–optimized ChEF

1Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 2Department of Physics, University of California, San Diego, La Jolla,
California, USA. 3Section of Neurobiology, University of California, San Diego, La Jolla, California, USA. 4Howard Hughes Medical Institute, La Jolla, California, USA.
5These authors contributed equally to this work. Correspondence should be addressed to J.Y.L. (j8lin@ucsd.edu).

Received 3 June; accepted 29 July; published online 1 September 2013; doi:10.1038/nn.3502

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NFigure 1 Basic properties of ReaChR compared
Extracellular side
to those of C-VChR1 (VChR1 with the ChIEF
E122T
C1V1
N terminus) and C1V1E122T. (a) Schematic
ChEF/ChIEF
design of ReaChR. ReaChR consists of the
VChR1
VChR2
A B C D E F G
N terminus of the ChEF (or ChIEF) variant
Citrine (YFP)(ChEF/ChIEF), transmembrane domains A–E and
L171l
ReaChR
G of VChR1, transmembrane domain F of VChR2
Cytoplasm
and the L171I point mutation. (b) Examples ofC1V1E122T and ReaChR expression in HEK293
***
*
***
***
**
cells as visualized by the fluorescence of fused
**
**
**
*
Citrine. Much of the ReaChR expression was*****at the plasma membrane, whereas C1V1E122T
200
1.0
40
expression was more intracellular, with strong
0.5
100
20
aggregation. Scale bar, 20 µm. (c) The relativeplasma membrane expression level (left) and000
the ratio of plasma membrane to intracellular
fluorescence (right) of VChR1 (n = 19),
C-VChR1 (n = 29), C1V1 (n = 26), C1V1E122T(n = 16) and ReaChR (n = 21) as measured
with Citrine fluorescence. AU, arbitrary units.
610 nm
470 nm
650 nm
630 nm
590 nm
410 nm(d) The mean photocurrent amplitudes of
C-VChR1
0
C-VChR1 (n = 13), C1V1 (n = 10), C1V1E122T(n = 10), VCOMET (n = 13) and ReaChR–200(n = 9) recorded from HEK293 cells. The
current amplitudes were measured at theC1V1E122T0wavelengths that evoked the greatest responsein each variant and were normalized to cell
capacitance. The data in c and d are shown–100
as the mean ± s.e.m. *P < 0.05, **P < 0.01,
ReaChR***P < 0.001, Kruskal-Wallis test with0
post-hoc Dunn’s test performed on all pairs ofvariants (only significant differences detected–400
500 mswith Dunn’s tests with VCOMET or ReaChR
are shown; the statistical tests shown in d also
1.0
1.0
C-VChR1
include comparison to oChEF (n = 12) andC1V1E122T
oChIEF (n = 7)). H = 31.63, k = 5, P < 0.0001
ReaChR(c, left); H = 41.28, k = 5, P < 0.0001
0.5
0.5(c, right); H = 48.02, k = 7, P < 0.0001 (d).
(e) The responses of C-VChR1 (top), C1V1E122T(middle) and ReaChR (bottom) to 650, 630,
0
0
400
500
600
400
500
600
610, 590, 470 and 410 nm light of the same
Wavelength (nm)Wavelength(nm)
photon flux (5.1 × 1016 photon mm−2 s−1).
(f) The spectra of the maximum response (left)
and steady-state (plateau) response (right) of C-VChR1 (n = 7), C1V1E122T (n = 8) and ReaChR (n = 7). The responses were normalized to the maximum
response of each cell. The gray regions highlight the response above 600 nm. The data in f are shown as the mean ± s.e.m.

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fNormalized response© 2013 Nature America, Inc. All rights reserved.

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Plasma membrane/
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fluorescence

Plasma membrane
fluorescence (AU)c(oChEF; 48 ± 8 pA pF−1, n = 12; Supplementary Fig. 2a) and mammalian codon–optimized ChIEF (oChIEF; 52 ± 7 pA pF−1, n = 7).
VCOMET had a reversal potential (12 ± 2 mV (mean ± s.e.m.),n = 8) that was significantly higher than that of oChIEF (4 ± 1 mV,
n = 5; P < 0.05) but not that of the calcium-translocating ChRs,
CatChs17 (5 ± 1 mV, n = 6) in physiological saline (H = 10.39, k = 4,
P = 0.0155 for comparisons between VCOMET, ChIEF, CatCh and
ReaChR) and a reduced inward rectification similar to that of oChIEF(Supplementary Fig. 2c)7.
Although VCOMET responded strongly to light above 600 nm(Supplementary Fig. 2b), the responses at these longer wavelengths
were desensitizing and did not recover completely in the dark without
reconditioning with 410 nm light (Supplementary Fig. 3). We thussought to reduce the desensitization of VCOMET to light above 600 nm
through known point mutations of ChRs. The ChETA mutation17 did
not red shift or reduce the desensitization of VCOMET. The corres­
ponding H134R mutation of ChR2 (ref. 18) slowed the channel kinetics and thus degraded the temporal fidelity of the ChR. One mutation,
L171I (Fig. 1a), which corresponds to the same position of the ChIEF
mutation7, increased the amplitude of the photoresponse at both

610 and 630 nm light through reduced desensitization while retaining the membrane trafficking and expression of VCOMET (Figs. 1
and 2 and Supplementary Fig. 4) and thus led to an increase in thesteady-state (plateau) spectral peak at 630 nm (Fig. 1f). This formed
ReaChR, the new ChR. ReaChR retained the reversal potential(7 ± 4 mV, n = 6), reduced inward rectification and photocurrent
amplitude (34 ± 4 pA pF−1, n = 9) of VCOMET (Fig. 1b–d). The one
limitation of ReaChR relative to C-VChR1 was the slower channel
closure rate after termination of the light pulse: τ1/e = 137 ± 7 ms
(mean ± s.e.m. n = 11) for ReaChR compared to τ1/e = 85 ± 4 ms
(n = 9) for C-VChR1 (P < 0.05) (Fig. 2d and Table 1).

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Comparisons of red-shifted ChR variants in cell culture
The ChR variant C1V1E122T has been shown to excite the neuronalmembrane potential with 630 nm light that is pulsed for 50 ms11.
To gauge the potential benefit of ReaChR over C1V1 and related
constructs, we characterized the attributes of ReaChR in comparison to those of C1V1, C1V1E122T and VCOMET (Table 1). C1V1
and C1V1E122T both expressed strongly in HEK293 cells as visualizedwith Citrine19 fluorescence of the C-terminal fusion protein. However,nature NEUROSCIENCE

t e c h n ic a l r e p o r t s

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C1V1E122T

ReaChR

610 nm
light

0

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–100
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C-VChR1C1V1E122T

ReaChR

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–100
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C-VChR1
E122T
C1V1
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610 nm light400

0.08 mW mm
0.19 mW mm–2
0.34 mW mm–20.74 mW mm–2
1.93 mW mm–2
4.09 mW mm–27.65 mW mm–2
11.75 mW mm–2

–400

–50

Channel on rate (ms)c–2Channel off rate (ms)

630 nmlight

Photocurrent (pA)b

Photocurrent (pA)

C-VChR1

C

ea

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C

hR

1.0
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1.0
10.0
membrane as well as ReaChR or VCOMET–2–2
Light intensity (mW mm )Light intensity (mW mm )in these cells, and they both showed highamounts of intracellular aggregation andstrong cytosolic fluorescence (Fig. 1b,c). The mean photocurrent of Supplementary Fig. 4). As ReaChR has improved membrane traffickC1V1 expressed in HEK293 cells (13 ± 3 pA pF−1, n = 10) was smaller ing, greater photocurrents and faster kinetics compared to C1V1E122T,
than those for VCOMET and ReaChR (Fig. 1d), possibly because of we propose that ReaChR is a robust means to stimulate neurons with
reduced efficiency in trafficking to the plasma membrane (Fig. 1c). red-orange to red light.
Introduction of the E122T mutation to form C1V1E122T reduced theC1V1 photocurrent ~66% (4 ± 1 pA pF−1, n = 10; Fig. 1d), although Comparison of ChR variants in cultured neurons
its action spectrum was red shifted, with peaks at 590 and 610 nm We compared the properties of ReaChR with those of other ChR varifor the maximum and steady-state (plateau) responses, respectively ants in cultured neurons20. ReaChR traffics to the membrane well and(Fig. 1e,f). The channel kinetics of C1V1E122T were significantly expresses strongly in neurons (n = 22), as we observed in HEK293 cells
slower than those of VCOMET and C-VChR1, with a channel clo- (Fig. 3a). The variants C1V1E122T (n = 13) and C1V1E122T with an addisure time constant of τ1/e = 315 ± 26 ms (n = 8), although this value tional trafficking sequence, denoted C1V1E122T-TS (n = 17)11,20, trafis similar to that of the parent construct, C1V1 (τ1/e = 306 ± 10 ms, ficked to the membrane as well as ReaChR in cultured neurons (Fig. 3a,b),n = 6; Fig. 2d). The activation kinetics of C1V1E122T were also 1.5- to which is in contrast to the relatively greater trafficking that we observed
3-fold slower than ReaChR and C-VChR1 at the same light intensities for ReaChR in HEK293 cells. However, the expression levels of C1V1E122T
for 610 and 630 nm light (Fig. 2c). However, the photocurrent ampli- and C1V1E122T-TS were approximately 80–84% lower than those oftudes of C-VChR1, ReaChR and C1V1E122T showed similar functional ReaChR under identical conditions (Fig. 3a,b). We observed occasional
forms in response to incident light intensity (Supplementary Fig. 4). cells with high expression levels of C1V1E122T and C1V1E122T-TS,
With C-VChR1, C1V1E122T and ReaChR, increasing the stimula- although they occurred too infrequently to be of general utility.
In order to compare the photocurrent amplitudes of different ChR varition intensity of 610 nm light led to reduction of the steady-state(plateau) response amplitudes at higher light intensities (Fig. 2a and ants, we used a titer-matched lentivirus with a truncated human synapsin 1

C© 2013 Nature America, Inc. All rights reserved.

neither C1V1 nor C1V1E122T trafficked to theaChannel on rate (ms)Figure 2 Kinetics of C-VChR1, C1V1E122T
and ReaChR. (a) Representative responses ofa C-VChR1–expressing (left), a C1V1E122Texpressing (middle) and a ReaChR-expressing(right) HEK293 cell to 0.08, 0.19, 0.34, 0.74,
1.93, 4.09, 7.65 and 11.75 mW mm−2 of
610 nm light. (b) The responses of thesame cells as in a to 630 nm light of varying
intensities. (c) Channel onset time constantsof C-VChR1 (n = 10), C1V1E122T (n = 6) and
ReaChR (n = 10) to 610 nm (left) and 630 nm(right) light of different intensities. Data areshown as the mean ± s.e.m. (d) Channel closure
time constants of C-VChR1 (n = 11), C1V1
(n = 6), C1V1E122T (n = 8), VCOMET (n = 9)
and ReaChR (n = 11). *P < 0.05, **P < 0.01,***P < 0.001, Kruskal-Wallis test with post-hoc
Dunn’s multiple comparison tests on all pairsof variants (H = 36.76, k = 5, P < 0.0001).
Data are shown as the mean ± s.e.m.

Table 1 Comparisons of the channel kinetics and properties of C-VChR1, VCOMET, ReaChR, C1V1 and C1V1 E122T
Response spectra (nm)
Variant

Maximum

Steady state

C-VChR1

~570

~550

VCOMET~590~530

ReaChR

~590

~630

C1V1

ND

ND

C1V1E122T

~600

~610

Mean ratio of
membrane to
Mean photocurrent
Mean membrane(pA pF–1)
fluorescence (AU) cytosol fluorescence
58 ± 11(n = 29)
ND
218 ± 29(n = 21)87 ± 17(n = 26)72 ± 11(n = 16)0.98 ± 0.07
(n = 29)
1.10 ± 0.07
(n = 26)a1.12 ± 0.07
(n = 21)0.70 ± 0.06
(n = 26)
0.58 ± 0.06
(n = 16)6.9 ± 1.1
(n = 13)38.9 ± 7.8(n = 13)33.5 ± 3.6(n = 9)13.0 ± 3.0(n = 10)4.4 ± 0.6
(n = 10)Channel on rate,τ1/e (ms), 610 nm
at 7.6 mW mm–2

Channel on rate,τ1/e (ms), 630 nm
at 7.6 mW mm–2

19.4 ± 0.8(n = 11)ND

49.4 ± 2.0(n = 10)ND

20.7 ± 0.6(n = 11)ND

68.1 ± 4.2(n = 10)ND

41.5 ± 4.6(n = 7)115.8 ± 11.1
(n = 6)

Channel off rate,τ1/e (ms)84.9 ± 3.9(n = 11)100.4 ± 6.6(n = 9)137.2 ± 7.1(n = 11)306.3 ± 10.3
(n = 6)315.4 ± 26.0
(n = 8)

Electrophysiological characterizations were made under voltage-clamp recordings in HEK293 cells in which the membrane potential could be accurately clamped at −60 mV.
Plasma membrane and intracellular fluorescence were measured in HEK293 cells transiently expressing ChR fused to Citrine imaged with a confocal laser-scanning microscope.
ND, not determined; AU, arbitrary units.
aThe value of VCOMET was acquired in a separate experiment with different pixel-dwelling time settings.

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ReaChR: 470 nm
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Maximum
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Vmem (mV)

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400

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c

R -TS
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-TS

***
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600

E1
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C1V1

Plasma membrane
fluorescence (AU)

b

E122T

Plasma membrane/
intracellular fluorescenceC
C 1V
1V 1 E
121aVmem (mV)

Figure 3 Characterization and comparisonof different ChR variants in primary cultured
hippocampal neurons. (a) Representative
confocal images of neurons expressing
C1V1E122T-TS-Citrine (C1V1E122T-TS) or
ReaChR-Citrine (ReaChR). Scale bar, 20 µm.
(b) Quantification of plasma membrane
fluorescence (left) and the ratio of plasma
membrane to cytosolic fluorescence (right)of C1V1E122T-Citrine (n = 13), C1V1E122TTS-Citrine (n = 17) and ReaChR-Citrine(n = 22). (c) Photocurrent amplitudes ofprimary cultured neurons expressing
hChR2H134R (n = 16), oChIEF (n = 17),
C1V1E122T-TS (n = 14) or ReaChR (n = 16) as
measured with voltage-clamping recordings.
The hChR2H134R- and oChIEF-expressing
neurons were stimulated with 10 mW mm−2of 470 nm light, and the C1V1E122T-TS–
expressing and ReaChR-expressing neurons
were stimulated with 10 mW mm−2 light at
590 nm. The data in b and c are shown as
the mean ± s.e.m. **P < 0.01, ***P < 0.001,
Kruskal-Wallis test with post-hoc Dunn’s
multiple comparison tests on all pairs ofvariants. H = 37.66, k = 3, P < 0.0001 (b, left);
H = 1.09, k = 3, P = 0.58 (b, right); H = 18.32,
k = 4, P = 0.0004 (c). (d) Representative
recordings of neurons expressing different ChRvariants to 1 s of 10 mW mm −2 of LED lightof the indicated wavelengths under currentclamp recordings. Depolarization of membranepotential (Vmem) is indicated with upward
inflections of the traces. (e) Quantification of
the amounts of light-induced depolarizationin neurons expressing the different variants tolight of increasing intensities. (f) Quantificationof the action potential latencies from the onsetof the light pulse to increasing intensities oflight. The lighter colored traces in e and f are
the responses of individual cells, and the darker
colored traces are the mean ± s.e.m.

Vmem (mV)© 2013 Nature America, Inc. All rights reserved.

t e c h n ic a l r e p o r t s

1

10

100
–2

Light intensity (mW mm )

30
20
10
0

Light intensity (mW mm–2)

promoter (hSyn) to express enhanced yellow fluorescent protein–tagged human codon–optimized ChR2H134R (hChR2H134R-eYFP),oChIEF-Citrine, C1V1E122T-TS-Citrine and ReaChR-Citrine in cultured neurons. We selected cells for recording on the basis of theirmorphology under bright-field visualization. We did not use fluorescence signal–based selection or the selective α-CamKIIα promoter20
to avoid bias in the selection process. In all cases, ChRs were activated by 10 mW mm−2 of light at the respective maximum response
wavelengths. We recorded the photocurrents under voltage clamp.
We observed that currents from ReaChR-Citrine–expressing cells(219 ± 50 pA, n = 16) were greater than those from hChR2H134Rexpressing (37 ± 21 pA, n = 16) and C1V1E122T-TS–expressing (23 ±11 pA, n = 14) neurons but were non-significantly greater than thosefrom oChIEF-expressing neurons (75 ± 31 pA, n = 17) (Fig. 3c).
None of the ReaChR-expressing cells tested were unresponsive tolight, whereas many hChR2H134R-expressing (n = 9) and C1V1E122TTS–expressing (n = 5) neurons had no detectable response to light.
To test the utility of ReaChR to induce suprathreshold depolarization in neurons, we recorded cells under a current clamp without
blockers of voltage-gated channels. We injected current throughthe patch pipette to maintain the membrane potentials of all cells at−65 mV; we did not correct junction potentials. In ReaChR-expressing
neurons, we were able to achieve suprathreshold depolarization

with blue (470 nm), red-orange (617 nm) and red light (627 nm) in
response to 1s light pulses (Fig. 3d). The amount of depolarizationand the spike-delayed time were dependent on wavelength, light intensity and expression level, in addition to the membrane properties of
the neurons (cell type, membrane resistance and capacitance). Cells
expressing ReaChR retained normal morphological appearances andphysiological membrane properties (Supplementary Fig. 5), suggesting minimal toxic effects with expression. With 617 nm light,
we were able to achieve 25–45 mV depolarization (mean, 35 mV)in the expressing cells (Fig. 3e) and trigger action potentials with a
7–40 ms delay time (mean, 15 ms; Fig. 3f) when stimulated at a highlight intensity (n = 14). With 627 nm light, we were able to achieve
24–44 mV depolarization (mean, 34 mV; Fig. 3e) and spike delaysof 7–35 ms (mean, 17 ms; Fig. 3f) (n = 14). Blue light at 470 nm wasalso effective in achieving suprathreshold depolarization of ReaChRexpressing cells, with depolarization of 30–40 mV (mean, 34 mV; Fig. 3e)and a spike delay of 4–19 ms (mean, 9 ms; Fig. 3f) (n = 8). In comparison, the maximum depolarization achieved in neurons expressing
hChR2H134R was 22–32 mV (mean, 26 mV; Fig. 3e), and the spike delay
ranged from 7 to 25 ms (mean, 11 ms) (Fig. 3f) (n = 8). In oChIEFexpressing neurons, the amount of depolarization was 8–38 mV(mean, 26 mV; Fig. 3e), and the spike delay ranged from 1.6 to 7 ms
(mean, 8 ms; Fig. 3f) when stimulated with 470 nm light (n = 5).

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b
50
0
–50

c
100

Pulses with extra
spikes (%)

Vmem (mV)

ReaChR: 627 nm

Light pulses evoking
spiking (%)

a

50
0

1

2.5

5

10

25

50

30
20
10
0

1

0
–50

100

Pulses with extra
spikes (%)

Vmem (mV)

50

Light pulses evoking
spiking (%)

Light intensity (mW mm )ReaChR: 617 nm

50
0

1

2.5

5

10

25

50

Vmem (mV)oChIEF: 470 nm

d

50
0
–50
0.5 s
617 and 627 nm,–2
5 mW mm , 5 ms

40

0Pulses with extra
spikes (%)
1 2.5 5 10 25–2Light intensity (mW mm )

100
50
0

1 2.5 5 10
–2Light intensity (mW mm )ReaChR627 nmReaChR617 nm

30
20
10
0
1

e

50

40
30

5

10
15
Pulse number

617 and 627 nm,–2
10 mW mm , 1 ms

50

20
10
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1

2.5

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50

30
20
10
0

1

2.5

5

10

25

30
20
10
0

1

2.5

5

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–2
Light intensity (mW mm )30

0.25 ms
0.5 ms
1 ms
2 ms
5 ms
10 ms
20 ms

20
10
0

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2.5

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10

–2
Light intensity (mW mm )–2
470 nm, 5 mW mm , 5 ms

hChR2H134R
oChIEF
ReaChR

30
20
10
0

20

1

5

10
15
Pulse number

470 nm, 10 mW mm–2, 1 ms
ReaChR627 nmReaChR617 nm25–2
Light intensity (mW mm )Pulses with extra
spikes (%)–50

1 2.5 5 10 25–2Light intensity (mW mm )

100

10

–2
Light intensity (mW mm )Pulses with extra
spikes (%)

00

Spike delay (ms)50

50

Spike delay (ms)Vmem (mV)hChR2H134R: 470 nm

Light pulses evoking
spiking (%)–50

Light pulses evoking
spiking (%)

0

Light pulses evoking
spiking (%)

Vmem (mV)

50

100

5

30

Light intensity (mW mm–2)
ReaChR: 470 nm

2.5–2Light intensity (mW mm )–2

Spike delay (ms)Figure 4 The responses of neurons expressing
the different ChR variants to a 10 Hz pulsedlight stimulation train. (a) Example recordingsof neurons expressing the indicated ChRvariants to 10 Hz of light stimulation at
10 mW mm−2 of 1 ms duration. Two ten-pulse
trains 250 ms apart were used to simulate twobursting episodes. Currents were injected tosustain the resting membrane potential at−65 mV. (b) The percentage of pulses resulting
in action potentials of varying light intensities
and pulse durations recorded from neurons
expressing the different variants. (c) Percentageof pulses resulting in extra action potentials ofvarying light intensities and pulse durations of
the different variants. For 627 nm stimulationof ReaChR in b and c, n = 5–12 for each of theconditions. For 617 nm stimulation of ReaChR
in b and c, n = 3–11. For 470 nm stimulationof ReaChR in b and c, n = 4–8. For stimulationof hChR2H134R in b and c, n = 7–8. For the
stimulation of oChIEF in b and c, n = 5–7(see also Supplementary Data Set 1). The datain b and c are shown as the mean ± s.e.m.
(d,e) Summaries of the mean latencies ands.d. of the light-triggered action potentialsof each pulse in ReaChR-, hChR2 H134R- andoChIEF-expressing neurons to the indicatedwavelengths, intensities and durations. Pulsesthat did not trigger action potentials were
not included in the analysis. For 627 nm
stimulation of ReaChR in d and e, 7 and8 cells were tested, respectively. Each data
point in d and e is the mean of 2–6 and 3–6
values, respectively. For 617 nm stimulation of
ReaChR in d and e, 8 and 9 cells were tested,
respectively. Each data point in d and e is themean of 2–6 and 1–6 values, respectively. For
470 nm stimulation of ReaChR in d and e,
8 cells were tested, and each data point is themean of 2–8 values. For the stimulation ofhChR2H134R in d and e, 8 cells were tested,and each data point is the mean of 2–8 values.
For the stimulation of oChIEF in d and e, 6 cells
were tested, and each data point is the meanof 6 values (see also Supplementary Data
Set 1). The data in d and e are shown as
the mean ± s.d.

Spike delay (ms)npg

© 2013 Nature America, Inc. All rights reserved.

t e c h n ic a l r e p o r t s

30

20

hChR2H134R
oChIEF
ReaChR

Pulsed illumination at 10 Hz was an effec20
20
tive trigger for spiking in ReaChR-expressing
1010
neurons at 470, 617 and 627 nm (Fig. 4a).
00Light pulses of weak intensity and short dura1
5
10
15
20
1
5
10
15
20
Pulse number
Pulse number
tion often lead to loss of temporal fidelity
from insufficient depolarization (Fig. 4b).
Light pulses of too high an intensity lead to extra action potentials andWith regard to the fidelity of spike generation in neurons with ChR
depolarization block as a result of insufficient repolarization between variants other than ReaChR, we observed lower firing reliabilities
light pulses, which were the main reasons for the loss in temporal fidel- with hChR2H134R-expressing cells in response to 470 nm light. This
ity that we observed (Fig. 4c). In addition to stimulation intensity and variant introduced a high amount of channel desensitization that led
pulse duration, cell membrane properties and the expression level of to subthreshold depolarization with light pulses toward the end of a
ReaChR also affect the ability to trigger action potentials in response pulse train (Fig. 4a). As the overall amount of depolarization that weto pulsed light. Thus, one specific stimulation protocol that achieved observed with hChR2H134R was lower, extra spiking was rare. Cells
complete fidelity in one ReaChR-expressing cell, for example, 0.5 ms expressing oChIEF had the highest temporal precision, as measuredof 5 mW mm−2 of 617 nm light or 1 ms of 10 mW mm−2 of 627 nm by the percentage of pulses achieving suprathreshold depolarization,light, could fail to trigger action potentials in another cell with differ- the shortest spike delay and a variability in spike latency (Fig. 4b–e),
ent membrane properties and expression levels. We observed this same and this higher fidelity was sustained at higher stimulation frequencies (Supplementary Fig. 6). Yet even with oChIEF, we observed
phenomenon with stimulation at 5 Hz (Supplementary Fig. 6).
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t e c h n ic a l r e p o r t sabcFigure 5 In vivo expression and utilization of
L1
ReaChR for cortical control. (a) Schematic ofAGm
617 nmL2/3
vM1 stimulation and recording. ReaChR was
L4
expressed in vM1 and visualized by Citrine
vM1
AGl
L5
fluorescence (green). vM1 was exposed for* *L6electrophysiology, and ReaChR-expressing
100
ReaChR-Citrine
neurons were activated with 617 nm light.
expression(b) Coronal section through the medial (AGm)0Nissl ReaChR-Citrine
200
and lateral (AGl) agranular vM1 of an infected
5 Hz
10 Hz
20 Hz
30 Hz
mouse showing ReaChR expression (green).
Neurons were counterlabeled with a fluorescentVmarker (NeuroTrace; magenta). Scale bar,
500 µm. (c) ReaChR-expressing neurons in
vM1. Scale bars, 10 µm. (d) Photoactivated1
spikes in a ReaChR-expressing neuron recorded
6
in vivo during anesthesia (recording depth,
6410 µm). Single 2 ms pulses of 617 nm
light (orange bar) evoked one or more spikes(indicated by asterisks; n = 12 pulses at
02 Hz). Arrows indicate low-amplitude artifacts
0
2.5 0
1.2
0
0.7 0
0.5
Time (s)Time (s)Time (s)Time (s)associated with the light switching on andoff. Vertical scale bar, 100 µV; horizontal
scale bar, 2 ms. (e) Spike interval histogram
2 Hz
2 Hz
5 ms pulse
5 ms pulse
and waveforms (inset) of the same unit
6
1.0
1.0
1.0
demonstrating the unit as a single neuron.
Vertical scale bar, 100 µV; horizontal scale4bar, 0.5 ms. (f) A ReaChR-expressing neuron
0.5
0.5
0.5
activated with 2 ms pulses of 617 nm light2
at 5, 10, 20 and 30 Hz (12 pulses). Top,0000voltage trace during a train of 12 pulses
1 2
5 10 20
1 2
5 10 20
1 2
5 10 20 30
1 2
5 10 2030(vertical scale bar, 100 µV). Middle, rasters of
Stimulus duration (ms)
Stimulus duration (ms)
Stimulus rate (Hz)Stimulus rate (Hz)spikes during six trains. Bottom, peristimulus
time histogram of spikes across all trains.
***(g,h) Spikes per pulse (normalized to the20
20
470–655 nm
maximum number of spikes evoked by the
wavelengths
light pulses of the indicated duration; g) andprobability of one or more evoked spikes (h)vM1***across a population of ReaChR-expressing
neurons (n = 8) as a function of pulse duration(2–20 ms; pulse rate, 2 Hz). (i,j) Number of
spikes per pulse (normalized to the maximum
00
as in g; i) and the latency to the first spike (j)Veh 470 617 655
0
2
4
6
Time
Wavelength (nm)Time(s)
in neurons as a function of stimulus rate
(1–30 Hz; pulse duration, 5 ms). (k) Schematicof in vivo activation of vM1 with ReaChR (green) through intact skin and bone of awake mice. Vibrissae movements were measured with high-speed
video. (l) Traces of vibrissae movements in response to single 100 ms pulses (orange arrows and bar) of 617 nm light emitted by an LED placed
10 mm above the skin. Increasing values denote vibrissae protraction. Vertical scale bar, 40°; horizontal scale bar, 1 s. (m) Absolute movement
amplitudes evoked by 100 ms pulses of 470, 617 and 655 nm light through intact skin in ReaChR-expressing mice (n = 3 mice, ten stimulus
repetitions per condition per mouse). Additionally, three mice injected with viral vehicle solution (mock control) were stimulated through the skinwith 617 nm light (black). (n) Boxplots of movements during the first second after vM1 photoactivation through the intact skull of mock-transduced(veh, black; n = 3 mice; 617 nm illumination) and ReaChR-expressing mice (n = 3 mice; 470–655 nm wavelengths). Vertical lines indicate the data
range, boxes indicate the 25th to 75th percentile ranges, and the central lines mark the median. ***P < 0.001, one-sided Kolmogorov-Smirnov test.
The light intensity used in a–n was 100 mW.

e

Spikesper bind

Spikes per bin

f

npg

m

n

Average movement
amplitude (°)

lMovement amplitude (°)

kVibrissa angle

Latency to first spike (ms)jNormalized responsei

Probability of spikehNormalized response© 2013 Nature America, Inc. All rights reserved.

gExcitation of ReaChR-expressing neurons in vivo
As red light can penetrate mammalian tissues in vivo with lessattenuation compared to blue or green light12, we used ReaChR tostimulate deep brain structures in vivo. We targeted two areas forin vivo stimulation: vM1, which is involved in the control and execution of vibrissa motion21, and the facial motor nucleus of the seventh
cranial nerve, whose motoneurons innervate the muscles that are
responsible for vibrissa movements. We incorporated ReaChR-Citrine

into a recombinant adeno-associated virus (rAAV) with a hSyn promoter and injected it into either vM1 or the facial motor nucleus ofindividual mice.
We confirmed ReaChR expression in vM1 3 weeks after injection. We head fixed the mice and monitored vibrissae movementswith high-speed video either during light anesthesia with 1.0–1.5%(vol/vol) isoflurane or while the mice were awake (Fig. 5). For electrophysiological recordings, we removed the bone over vM1, mapped
the zone of infection with epifluorescence imaging of the corticalsurface and positioned a 617 nm LED 10 mm above the surface of thebrain (Fig. 5a,b). We used short pulses of light, 1–20 ms in duration,to activate ReaChR-expressing neurons (Fig. 5c) and evoke spikes, as
recorded extracellularly (Fig. 5d–f). ReaChR-expressing vM1 neurons

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extra action potentials after strong depolarization in cells with highexpression. The spike latency and variability were similar between
ReaChR and hChR2H134R, with a higher variability in the responses
to stimulation pulses present later in the pulse train.

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t e c h n ic a l r e p o r t sabcFigure 6 In vivo expression and utilization of
Nissl
ReaChR-Citrine
Overlap
ReaChR for brainstem activation. (a) Horizontal
R
40×L
section through the facial motor nucleus(FN, indicated by the white outline) showing
FN
ReaChR-expressing neurons and the associatedFN
processes (green). Cells were labeled with a
470–655 nm
orwavelengths
fluorescent marker (NeuroTrace; magenta).
(b) Confocal images of ReaChR-expressing
motoneurons (arrows). Scale bars (a,b),0� (nm)
100 µm. R, rostral; L, lateral. (c) Schematic
20
470 nm470
of an awake mouse expressing ReaChR in the
617
627
facial motor nucleus photoactivated by LEDs
–20
655
placed at the opening of the external auditory
No light
Light/protract
No light
Light/retract0
canal. Vibrissae movements were recorded with
617 nmhigh-speed video. (d) Vibrissae movements–40
617 nm–10
470 nm
470 nmevoked by stimulating the facial motor nucleus
0
50
100
0
50
100
617 nmin a ReaChR-expressing mouse. Left, video
Light intensity (mW)
Light intensity (mW)frames (top) showing vibrissae in the reference
protracted position (no light) and at the peak
5 Hz, 3 ms pulse
retraction during photoactivation (light/retract)hChR2H134R
ReaChR
5
60*
and traces of movements (bottom) in response30
4
to 470 and 617 nm light. The black trace40
3indicates the movement of contralateral C2
20vibrissa. Vertical scale bar, 100 ms light pulse
220
10(100 mW light output); horizontal scale bars,
6
1
10° and 1 s. Right, movement amplitude as0000a function of light output power. (e) Vibrissa
0
20
40
60
0
2.5
movements evoked by stimulating the facial| Movement amplitude
Time (s)Wavelength (nm)(°, 617 nm) |motor nucleus in a separate ReaChR-expressing
mouse. Left, video frames (top) showing
vibrissae in the reference retracted position (no light) and at peak protraction during stimulation (light/protract) and traces of movements (bottom) in
response to 470 and 617 nm light. Right, movement amplitude as a function of light output power. Vertical scale bar, 100 ms light pulses (100 mW
light output); horizontal scale bar, 10° and 1 s. (f) Population data of the absolute movement amplitudes evoked by 470 and 617 nm through-ear
illumination (100 ms pulses at 1 Hz; n = 12 mice). (g) Comparison of the movement amplitudes evoked with light between 470 and 655 nm in
ReaChR-expressing (left; n = 12 mice) and hChR2H134R-expressing (right; n = 3 mice) mice (100 mW light output). Movement amplitudes at the same
wavelengths were larger in ReaChR- compared to hChR2 H134R-expressing mice (P < 0.001, Kolmogorov-Smirnov test). (h) In vivo recording of a single
unit in the facial motor nucleus region (based on stereotaxic coordinates) during photoactivation with 617 nm light (100 mW light output). Top left,
voltage trace aligned to a 3 ms light pulse (orange bar; n = 12 pulses). Small artifacts are associated with the light pulses switching on and off (arrows).
A single spike was evoked after each pulse (asterisk) with low temporal jitter and short latency (4 ms), suggesting that the unit expressed ReaChR and
was directly activated. Vertical scale bar, 100 µV; horizontal scale bar, 2 ms. Bottom left, overlapped spikes from the same unit demonstrating this as asingle neuron. The unit was not spontaneously active and fired a single spike in response to the light pulse. Vertical scale bar, 100 µV; horizontal scalebar, 0.5 ms. Top right, voltage trace recorded during a single train of 12 light pulses (vertical scale bar, 100 µV). Middle right, rasters of spikes during
six trains. Bottom right, peristimulus time histogram of spikes across all trains. The data in d,e,f and g are shown as the mean ± s.e.m.

e

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47
530
590
611
7
62
657
5

47
530
590
611
627
657
5

were reliably photoactivated at short latencies and with low temporal
jitter (Fig. 5d). The evoked activity of a representative cortical single
unit is shown in Figure 5d–f. This unit, which probably expressed
ReaChR, fired one or more spikes in response to 2 ms pulses withsubmillisecond jitter and a short, 2.4 ms spike latency. The unit was
reliably activated with trains of light pulses that ranged from 5 to
30 Hz. Increasing the rate of optical activation to greater than 20 Hz
resulted in a larger number of extra spikes per pulse (Fig. 5f). We
observed a monotonic increase in the number of evoked spikes
and in the spiking probability as a function of stimulus duration(n = 8 single units; Fig. 5g,h). The spiking probability was above
0.95 when the stimulus duration was 5 ms or longer (Fig. 5h). Whenthe stimulus rate exceeded 10 Hz, the population response increased(P = 0.002, one-sided Kolmogorov-Smirnov test; Fig. 5i) and thelatency to the first spike decreased (P = 0.01, one-sided KolmogorovSmirnov test; Fig. 5j); these effects probably result from the slow
closing kinetics of ReaChR.
Consistent with in vivo neural activation of ReaChR-expressing
neurons, we found that vibrissae movements could be elicited by
LED illumination in awake mice (Fig. 5k–n). Removal of skinand bone was not required to evoke these movements, and placing
the stimulating LEDs 10 mm above the fur line was sufficient in all

Spikes per bing| Movement amplitude(°) || Movement amplitude(°, 470 nm) |© 2013 Nature America, Inc. All rights reserved.

fMovement amplitude (°)

Movement amplitude (°)

dcases (Fig. 5k). Movements were elicited with both blue (470 nm)
and red (617 and 655 nm) illumination. Evoked movements werecharacteristic of those observed with electrical stimulation of vM1,
showing both a rapid component22,23 and a sustained period, albeit
with unpredictable duration, of rhythmic whisking that outlasted thestimulus24 (Fig. 5l,m).
Our in vivo cortical experiment demonstrated stronger evoked
movement responses to 617 nm as compared to 470 nm light(P < 0.0001, one-sided Kolmogorov-Smirnov test; Fig. 5m,n),which is consistent with the larger responses to orange-red light that
we observed in cultured HEK293 cells (Fig. 1f and Supplementary
Fig. 7) and the greater attenuation of blue compared to red light inmammalian tissue12. We confirmed that these movements were causedby photoactivation of ReaChR by comparison with movements measured in a cohort of mock-transduced mice injected with a viral vehicle(Fig. 5m,n). Because we were able to evoke movements with 470 nm
light in ReaChR-expressing mice, we tested whether movement could
be evoked non-invasively with a standard blue light–activated ChRvariant. We thus expressed hChR2H134R-eYFP in vM1 with an identical rAAV vector and viral titer. Vibrissa movements could be evokedin mice expressing hChR2H134R in vM1 with 470 nm light illumination(n = 3), but these movements were more infrequent, notably smaller
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t e c h n ic a l r e p o r t s
The variability in whisking between individual mice in response
to illumination of the facial motor nucleus was great (Fig. 6f). Thiswas probably caused by variations in the exact locations of ReaChRexpressing motoneurons within the facial motor nucleus, which is~1 mm in width, and/or high expression levels in individual motoneurons that resulted in very low spiking thresholds. In principle, thisvariability could also be caused by direct stimulation of the facial
motor nerve. We confirmed that motoneuron axons were labeled with
ReaChR-Citrine and that vibrissa movements could also be evokedby direct illumination of the peripheral motor nerve through the skinof the lower cheek. These movements, however, were smaller and of
shorter duration than those evoked through the ear (Supplementary
Fig. 7a). In addition, movements were not evoked when stimulating through the ear contralateral to the side of ReaChR expression(617 nm, 100 mW light output), which shows that the lateralizationof optogenetically evoked brainstem activity can be controlled withthrough-skull stimulation (Supplementary Fig. 7b).

and shorter lasting compared to the movements evoked with 617 nm
light in ReaChR-expressing mice (Supplementary Fig. 7c–f).
The durations and amplitudes of the movements evoked by
vM1 stimulation in ReaChR-expressing mice were unpredictable(Fig. 5l), mirroring the results obtained with electrical stimulationin awake mice24 but nonetheless complicating comparisons of different stimulation parameters. As a more stringent test of the sensitivity of ReaChR to different wavelengths in vivo, we targeted ReaChR
to the mystacial motoneurons in the facial motor nucleus of thebrainstem that directly control vibrissa movements (Fig. 6a,b).
It has been shown previously that in deeply anaesthetized mice,direct electrical stimulation of these neurons can reliably drive
vibrissa movements, producing a relatively noise-free and controlled
behavioral output25. In mice, the facial motor nucleus is locatedat a depth of up to 6 mm in the ventral part of the brainstem. We
delivered light at 470, 530, 591, 617, 627 and 655 nm wavelengths in a
non-invasive manner by placing an LED at the opening of the external auditory canal, thus illuminating the brainstem at a distance of
8–10 mm from the midline through intact tissue and bone (Fig. 6c).
The external ear canal provides a convenient anchor point for noninvasive LED placement, bypasses fur and provides an opportunity
to limit photoactivation to one side of the brainstem. We typically
flashed the LEDs for periods of 100 ms at 1 Hz with a 1–100 mW
light output; we found no visual indications of any heat-related damage to the outer ear tissue. Activation of ReaChR-expressing neurons
elicited highly reproducible and temporally precise vibrissae movements, which is consistent with the direct activation of motoneurons(Fig. 6d,e and Supplementary Video 1). Although a topographicorganization of the facial muscle representation within the facial
motor nucleus has been documented, the exact distribution of all the
motoneurons innervating muscles that are involved in vibrissa control
is not known26. Both protraction and retraction of the vibrissae are
actively controlled by multiple extrinsic and intrinsic muscles 22,27.
We found no consistent pattern between the intrafacial motor nucleus
locations of infected motoneurons and the evoked movement trajectories, and in several mice, both net protraction and retraction could
be elicited by adjusting the light intensity appropriately (Fig. 6d,e).
As an example, Figure 6d shows evoked movements in a mouse inwhich light stimulation led to the retraction of all vibrissae independently of light intensity (10–100 mW light output, 100 ms pulses;
Supplementary Video 2). Evoked retractions were three times
larger when ReaChR was activated at 617 nm as compared to 470 nm(40° compared to 13°, respectively, at maximum amplitude). Similarly,
light stimulation of a different mouse (Fig. 6e) produced sixfold larger
movements at 617 nm compared to 470 nm (19° compared to 3°,
respectively, at maximum amplitude). We observed this pattern ofstronger activation at 617 nm compared to 470 nm in all ReaChRexpressing mice (Fig. 6f).
Vibrissa movements in ReaChR-expressing mice could be evoked
across a broad range of wavelengths, which is consistent with ourin vitro results. The largest movements were evoked at 617 nm, followed by 627 nm and 470 nm. Smaller vibrissa movements werealso evoked with 530, 591 and 655 nm illumination (Fig. 6g). We
confirmed that these movements resulted from photoactivation of
ReaChR and not LED-related heating of neural tissue or visually
evoked responses by the fact that we did not observe any movement ina cohort of mice expressing the blue light–activated hChR2H134R channel in the facial motor nucleus (n = 15; Fig. 6g and Supplementary
Fig. 7g–i) and by recording single units in the brainstem of ReaChRexpressing mice that reliably responded with short latencies andsubmillisecond temporal jitter to light stimulation (Fig. 6h).

DISCUSSION
The optimal wavelength range for optical imaging into mammaliantissue is near infrared (600–1,300 nm), where light scattering decreases
with increasing wavelength and absorption by enodogenous chromophores is reduced, yet absorption by water is still negligible. This paves
the way for deeper penetration of light into tissue with reduced attenuation12. Optogenetic tools to manipulate neuronal activity should ideally be excited by near-infrared light. Current development of ChRs has
produced many new variants that are maximally activated by blue andgreen light, such as ChR2H134R, ChETA, TC, SFOD156A, ChD, oChEF,
oChIEF, CatCh and ChRGR7,8,10,17,18,28,29. Many of these variants have
improved properties regarding kinetics, expression and amounts ofdesensitization compared with native ChR2. However, there has been
little progress in the development of red-shifted ChRs.
In this study, we engineered two red-shifted ChR variants, VCOMET
and ReaChR, that had strong membrane expression in mammaliancells. The ReaChR variant responded strongly to red light, with a secondary steady-state spectral peak at 630 nm in addition to a primarysteady-state spectral peak at ~540 nm. The mechanism for this shift
involves the L171I mutation in VCOMET. Past work attributed thisposition to the red shift of the response spectrum of VChR1 (Leu126)
relative to ChR2 (Ile131)14, which implies that this L171I modification should lead to a blue shift in the response spectrum. However,this idea is based on the charge distribution of all-trans retinal in
the binding pocket of bacteriorhodopsin in the dark state. In bacteriorhodopsin, some transient intermediate photocycle states haveabsorption spectra above 600 nm, whereas the initial activation of theprotein has a λmax value of ~570 nm30. It seems that the main effectof the L171I mutation in ReaChR is to extend the lifetime of the redshifted transient states and reduce the desensitization of the transientstate, leading to a greater photocurrent to red light. In support of thishypothesis, we found differential spectral peaks with the transient andsteady-state responses of C-VChR1 and VCOMET, with the transientstates having λmax values of ~570–590 nm and the steady-state havinga λmax value of ~530 nm (Fig. 1f and Supplementary Fig. 2b).
The initially described red-shifted ChR, VChR1, does not express
well in mammalian cells and traffics poorly to the membrane, limiting
its utility for in vivo applications14,15. The recently published variant C1V1 and its derivatives have been reported to have improved
expression, membrane trafficking and kinetic properties compared to
VChR1 (ref. 11). However, in our tests, C1V1 and its variants were still
limited in their membrane trafficking and expression compared to
VCOMET and ReaChR, in addition to having slower channel kinetics

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t e c h n ic a l r e p o r t s(Figs. 1 and 2). The most red-shifted C1V1 derivative, C1V1E122T, hasa spectral peak at ~600 nm and slower channel kinetics and limited
expression compared with ReaChR (Figs. 1–3). The E122T mutation variant also has a reduced photocurrent, as has been previously
reported11, that may result from the position of this residue within
the putative channel pore of ChR, as predicted from the crystal structure of ChEF31. Thus, the reduction of C1V1E122T photocurrents andslow kinetics negate the spectral advantage that the E122T mutation
provides. In contrast, ReaChR is strongly expressed, consistently traffics to the membrane and can be used to reliably trigger temporally
precise spiking.
Although ReaChR has an improved spectral response to light atwavelengths greater than 600 nm, it still suffers slow kinetics in its
channel closure rate compared to variants such as ChR2, ChIEF, ChD
and ChETA7,8,10,17,18,28,29. In the blue light–activated ChR variants,
single point mutations that improve the channel kinetics also reducethe channel’s light sensitivity7,15. The other known ChR mutationthat increased the channel kinetics, E123T of ChR2, E162T of C1V1
and E163T of VCOMET, does so at the expense of reduced lightsensitivity and reduced photocurrents17. In the context of ReaChR,
this E-to-t mutation increases the channel kinetics (off rate <30 ms)
and surpasses C1V1E162T in terms of kinetics11 but blue shifts the
spectral peak to 550 nm (Supplementary Fig. 8) and increases thedesensitization of the channel. We did not find incorporation of thismutation useful in the current development of ReaChR. Important
future goals in developing red-shifted ChR should include improving
light sensitivities and faster kinetics simultaneously and reducing theactivation of these variants by light below 500 nm to allow for the
independent manipulation of two populations of neurons with two
different wavelengths of light.
We were able to exploit the spectral advantages of ReaChR toachieve efficient activation of expressing neurons through fur,skin and intact bone of adult mice with red-orange (617 nm), red(627 nm) and even far-red (655 nm) light (Figs. 5 and 6). This enables
new in vivo applications of transcranial and deep-brain stimulation
with optogenetics. Transcranial stimulation is essential for many
chronic studies, as cranial windows can lead to activated microglia
and astrocytes as part of an inflammatory response32 that in turn
alters neuronal physiology33 and plasticity34, as well as pial vasculature35,36. Alternatives to our approach for non-invasive transcranial
stimulation include clinically approved treatments for several neurological disorders and stroke, such as electroconvulsive therapy, repetitive transcranial magnetic stimulation and transcranial direct-current
stimulation. These techniques do not, however, have the spatial andcellular specificity that can be achieved through optogenetics. Thus,
optogenetic approaches using red-shifted ChRs, such as ReaChR, havethe potential to improve the efficiency of transcranial stimulation totreat neurological disorders.
In the present study, we introduced the ChR ReaChR throughinjections of an engineered virus directly into the region of interest.
In future work, it may be possible to label specific populations ofneurons by retrograde transport of ReaChR from a known target37,38.
For example, pools of motoneurons in the brainstem or the spinal
could be labeled by injection into specific muscles rather than into
motor nuclei themselves. Such an approach would substantially reducethe invasiveness of an optogenetic strategy for future therapeuticuse. Further, one could label opposing muscle groups with short- or
long-wavelength ChRs to permit differential optical control of opposing muscle groups. The weak absorption of short wavelengths by
ReaChR will not compromise this strategy if the anatomically deeper
motor pools are labeled with ReaChR. ReaChR may also facilitate
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VOLUME 16 | NUMBER 10 | OCTOBER 2013neurological treatment and neuroprosthetic control through transcranial and possibly transvertebral stimulation.
Methods
Methods and any associated references are available in the online
version of the paper.
Accession codes. Nucleotide sequences for VCOMET and ReaChR
have been deposited in the NCBI GenBank nucleotide database underaccession codes KF448070 and KF448069, respectively.
Note: Any Supplementary Information and Source Data files are available in the
online version of the paper.
Acknowledgments
J.Y.L. was funded by the Foundation of Research, Science and Technology
New Zealand, and P.M.K. was supported by a long-term fellowship from the
Human Frontier Science Program (HFSP). The project was supported by grants
to R.Y.T. from the US National Institutes of Health (NS027177) and the Howard
Hughes Medical Institute and grants to D.K. from the US National Institutesof Health (DA029706, OD006831 and NS058668). We thank P. Tsai for suggesting
the name ReaChR. We thank K. Deisseroth (Stanford University) for thehChR2H134R-eYFP construct, K. Svoboda (Howard Hughes Medical Institute
Janelia Farm Research Campus) for the CAG promoter vector, E. Boyden(Massachusetts Institute of Technology) for the lentiviral vector, L. Tian
(Howard Hughes Medical Institute Janelia Farm Research Campus) for the
AAV2 vector and D. Trono (École Polytechnique Fédérale De Lausane) forthe psPAX2 and pMD2.G lentivirus packaging vectors. AAV2-ReaChRCitrine and pLenti-ReaChR-Citrine constructs can be requested fromhttp://tsienlab.ucsd.edu/Samples.htm.
AUTHOR CONTRIBUTIONS
J.Y.L. designed and developed ReaChR and conducted and analyzed theexperiments in HEK293 and neuron cultures. P.M.K. and A.M. conducted
and analyzed the in vivo experiments. D.K. and R.Y.T. contributed to the design
and analysis of the experiments. All authors contributed to the writing anddiscussions of the manuscripts.
COMPETING FINANCIAL INTERESTS
The authors declare no competing financial interests.
Reprints and permissions information is available online at http://www.nature.com/
reprints/index.html.

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npg© 2013 Nature America, Inc. All rights reserved.

ONLINE METHODS

Molecular cloning and transgene expression. ChR chimeras and point mutants
were generated by overlapping PCR with Phusion PCR mix (New England
Biolabs, Ipswich, MA, USA). Genes coding mammalian codon-optimized VChR1,
VChR2 and ChIEF were synthesized separately according the published peptide
sequence (GenScript, Piscataway, NJ). The gene encoding hChR2H134R-eYFP wasa generous gift from K. Deisseroth (Stanford University). The gene and peptide
sequences of ReaChR and C1V1E122T are shown in Supplementary Figures 9
and 10. Standard digestion and ligation techniques were used to insert the
mutant into the expression vector. For experiments with HEK293 cells, the ChRvariants were expressed with the pcDNA3.1 vector under the cytomegalovirus (CMV) promoter and fused to the YFP variant Citrine19 with an in-frame
XhoI restriction site (LeuGlu). Cells were transfected with Fugene HD (Roche,
Basel, Switzerland). In the experiments measuring membrane expression ofhChR2, ChIEF, VChR1, C-VChR1 and VCOMET in primary cultured neurons,
ChR-Citrine fusions (with an in-frame ClaI restriction site) were expressed
under the CAG promoter with a WPRE (woodchuck hepatitis virus posttranscriptional regulatory element) sequence inserted after the stop codon of the
ChR-Citrine coding sequence (plasmid courtesy of K. Svoboda, Janelia Farm
Research Campus). In the experiments measuring membrane expression of
C1V1E122T, C1V1E122T-TS and ReaChR, ChR-Citrine fusions (with an in-frame
XhoI restriction site) were expressed under the hSyn promoter with a WPRE
sequence inserted after the stop codon of the ChR-Citrine coding sequence inan AAV2 vector (plasmid courtesy of L. Tian, Howard Hughes Medical Institute
Janelia Farm Research Campus). The resulting constructs (at the same DNA
concentration) were electroporated into the neurons before plating (Lonza,
Walkersville, MD). For the stimulation of cultured primary hippocampal neurons
with red light, ReaChR-Citrine was introduced with recombinant lentivirus.
Lentivirus and rAAV production. The genes encoding hChR2H134R-eYFP,C1V1E122T-TS-Citrine, oChIEF-Citrine and ReaChR-Citrine were subcloned
into a generation-two lentiviral construct with the hSyn promoter. The lentivirus
was made according to the protocols at http://vectorcore.salk.edu/protocols.php
with minor modifications. In brief, 293A cells (Life Technologies, Carlsbad, CA)
were grown to 85% confluency, and transfer vectors containing ChR–fluorescentprotein, psPAX2 and pMD2.G (gifts from D. Trono, École Polytechnique Fédérale
De Lausane) were transfected with calcium phosphate (Clontech, Mountainview,CA). Virus particles were harvested from serum-free medium and concentrated
with a 20% sucrose cushion with ultracentrifugation. The titer of the lentivirus was estimated with the Lentivirus Rapid Quantitation Kit (Cell Biolabs Inc.
San Diego, CA) in parallel just before each infection. The lentiviral vector was agift from E. Boyden (Massachusetts Institute of Technology). rAAV with serotype
8 containing hChR2E134R-eYFP and ReaChR-Citrine was produced and purified
according to the protocols at http://vectorcore.salk.edu/protocols.php by transfecting an AAV2 inverted terminal repeat (ITR) vector (gift from L. Tian, Howard
Hughes Medical Institute Janelia Farm Research Campus) containing ReaChRCitrine and the helper plasmids XX6-80 and XR8 (National Vector Biorepository)
into 293A cells. rAAV2/8 (recombinant AAV serotype 8 packaged with AAV2
ITR) were released from the cells by freeze thawing and purified with iodixanol
gradient purification. The virus was further concentrated using an Amicon Ultra
centrifugal filter (Millipore, Billerica, MA) with a 50 kDa cutoff. The rAAV titerwas measured by the Salk Vectorcore service with quantitative PCR and wasestimated to be 3 × 1013 GC ml−1.
Measurement of relative efficiencies of ChR membrane expression. Relative
levels of plasma membrane expression of ChR-Citrine fusions in HEK293 andcultured cortical neurons were measured by imaging on a Zeiss Live 5 Confocal
microscope with Zen software (Thornwood, NY). Transfections and measurements of expression were performed with the same concentrations of DNA electroporated into the neurons. The transfected cells were imaged with the samesetting for comparison. The measurements of expression were performed on
all cells with detectable visible fluorescence and normal cell morphology nondiscriminatively in the culture dish to ensure fair comparisons, typically startingfrom one end of the dish and moving to the other. Membrane expressions were
measured by taking the mean fluorescence intensities of the membrane and thecytosol of a single in-focus imaging plane with ImageJ software. In the experiments
in which ChR photocurrents were normalized to the membrane fluorescence,

doi:10.1038/nn.3502

images were acquired with an electron multiplying charge-coupled device(EMCCD) camera (Photometric, Tucson, AZ) at a 512 × 512 pixel resolution with
Slidebook (Intelligent Imaging Innovations, Inc., Denver, CO) in epifluorescencemode before electrophysiological recordings.
Cell culture, electrophysiological recordings and stimulation of cultured cells.
Characterization of spectral responses, reversal potentials, kinetics and membrane trafficking of C-VChR1, C1V1, C1V1E122T, VCOMET, ReaChR, CatCh,
oChIEF and oChEF were done with whole-cell patch clamping on 293A cells 2 dafter transfection. HEK293 cells, which have a smaller size, high membrane resistance and minimal expression of voltage-gated ion channels, were used for thesecharacterizations to reduce the known voltage-clamping errors in neurons39. All
recordings were performed with an extracellular solution containing 118 mM
NaCl, 3 mM KCl, 2 mM CaCl2, 1 mM MgCl2, 10 mM 4-(2-hydroxyethyl)-1piperazineethanesulfonic acid (HEPES), 20 mM glucose (pH 7.35, 310 mOsm)
and an intracellular solution containing 110 mM Cs-methanesulfonate, 30 mM
tetraethylammonium chloride, 10 mM ethylene glycol tetraacetic acid (EGTA),
10 mM HEPES, 1 mM CaCl2, 1 mM MgCl2, 2 mM Mg-ATP and 0.15 mM
Na3-GTP (pH 7.25, 285 mOsm), except for the reversal-potential measurements,
for which the intracellular solution contained 125 mM K-gluconate, 10 mM
K4–1,2-bis-(o-aminophenoxy)-ethane-N,N,N′,N′-tetraacetic acid (BAPTA),
5 mM NaCl, 1 mM CaCl2, 10 mM HEPES, 2 mM MgATP and 0.3 mM Tris-GTP(pH 7.25, 285 mOsm). Series resistance compensation (at 70–75%) was used in
the kinetics and reversal-potential measurements in HEK293 cells. HEK293 cellswith low membrane resistance (<200 MΩ) were often discarded from analysis
and testing because of the inaccuracy of voltage clamping in these conditions.
These cells are typically found in clusters. All chemicals were acquired from
Sigma-Aldrich (St. Louis, MO). Electrophysiological characterization of ChR inneurons were performed on in vitro day 14–25 neurons extracted from postnatal
day 2 neonatal Sprague-Dawley rat pups (both sexes were used, and the neurons
were pooled together for the culture) after at least 9 d of infection with lentivirus. For the measurement of photocurrent amplitudes in neurons, the recordings were performed with Cs-methanesulfonate–based intracellular solution toblock the potassium channel, and 1 µM tetrodotoxin and 100 µM Cd2+ were
included in the extracellular solution to block voltage-gated sodium and calcium
channels, respectively. Also included in the extracellular solution were 10 µM
NBQX (6-nitro-2,3-dioxo-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide),
10 µM bicuculline and 20 µM AP5(d(–)-2-amino-5-phosphonovaleric acid) toblock fast synaptic transmission (Tocris, Ellisville, MO). To ensure the accuracyof the voltage clamping in neurons, light illumination was limited to a circulararea of 150 µm diameter around the soma to reduce space-clamp error, andseries resistance was compensated at 65%. Four-hundred-seventy nanometer
light was used to activate hChR2H134R and oChIEF for photocurrent measurements, and 590 nm light was used for C1V1E122T-TS and ReaChR. Although theexperimenters were not blinded to groups, the cells tested were selected on thebasis of a healthy appearance under bright-field illumination without visualization of fluorescence to ensure unbiased selection. All cells tested were includedin the analysis regardless of detectable responses to light. For testing the effectiveness of light in evoking action potentials, the recordings were performed
with a K-gluconate–based intracellular solution in the presence of extracellular
10 µM NBQX, 10 µM bicuculline and 20 µM AP5. Recordings were performedin current-clamp mode with the current injected to sustain a −65 mV membrane potential at rest. In pulsed stimulation experiments, cells that did not reachsuprathreshold depolarization with 20 ms of 50 mW mm−2 light pulses were
excluded from the analysis. For experiments of neurons with 10 Hz stimulation
under the current clamp, ReaChR-Citrine– and oChIEF-Citrine–expressing cells
were selected on the basis of bright-field morphology without visualization withfluorescence. High membrane eYFP fluorescence was used to select hChR2H134R
cells for recordings, as most cells with medium to low levels of fluorescence did
not reach the threshold when stimulated with light. Recordings were performed
with the Axopatch 200B patch clamp amplifier (Molecular Devices, Union City,CA) and acquired through Digidata 1320 (Molecular Devices) to a personal computer (Dell, Austin, TX) running pClamp 9.2 or pClamp 10 software (Molecular
Devices). Analyses were conducted with AxographX (Sydney, New South Wales,
Australia). Junction potentials were not corrected.
Most light stimulation was provided by a monochromator xenon lightsource (Polychrome IV, TILL Photonic, Victor, NY) with 15 nm half width.

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npg© 2013 Nature America, Inc. All rights reserved.

The shuttering and intensity of the light were controlled with a custom-fitted
25 mm mechanical shutter (Vincent Associates, Rochester, NY) and a neutral
density wheel (Thorlab, Newton, NJ). For the spectral response measurements
and experiments in which the light intensity was not described, cells were
stimulated with ~5.1 × 1016 photon mm−2 s−1 across the light spectra. The photon flux of the monochromator at each wavelength was measured with a power
meter and integrating sphere (Newport Corporation, Irvine, CA) placed on theobjective, and the photon flux was corrected with the neutral density wheel togive the same flux. The response spectra of the ChRs were measured with a
1 s light pulse from 650 to 410 nm of the same photon flux at 20 nm intervals,
with the maximum response taken as the maximal photocurrent obtained within
the 1 s pulse at the described wavelength, and the steady-state response wasmeasured between 0.95–1.00 s after the onset of the stimulation light pulse. For
most experiments, 410 nm light was delivered 20 s after the initial stimulation
to recondition the protein before the delivery of the next testing pulse 20 s later.
Stimulation of neurons under the current clamp was conducted with 470 nm(SR-05-B0040), 617 nm (SR-05-H2070) or 627 nm (SR-05-D2050) LED illumination (Luxeonstar, Brantford, Ontario, Canada). The LEDs were connected to
a computer-controlled current source (Mightex, Pleasanton, CA) coupled to aquartz fiber into the microscope.
Expression and stimulation of ChR-expressing neurons in vivo. Recombinant
AAV2/8-hSyn-ReaChR-Citrine or AAV2/8-hSyn-hChR2H134R-eYFP virus
was injected stereotaxically into the vibrissa motor cortex (vM1) or the facial
motor nucleus in the brainstem of C57BL/6 female mice using a nanoliter injector (Nanoject II, Drummond, Broomall, PA) under isoflurane anesthesia (2%(vol/vol)). The injection coordinates for vM1 were 1 mm posterior, 1 mm
lateral and 0.8 mm ventral, and the coordinates for the facial motor nucleus
were 4.8–5.6 mm posterior, 1.2–1.4 mm medial and 5.3–6.0 mm ventral to thebregma. The skin was retracted to expose the injection coordinates, and a single
0.3 mm diameter hole was drilled for each injection site. Suspension of virus was
injected in ten 50 nl aliquots every 5 min (total volume, 500 µl) in vM1 and in
five 12 µl aliquots (total volume, 60 µl) every 5 min in the facial motor nucleus.
The injection hole was filled with sterile saline and topped with a thin layerof antibiotic ointment after the injection pipette was withdrawn. The skin was
sutured back in place, and the mouse was left to recover for the viral incubation
period. After a waiting period of 4 weeks, the mice were prepared for in vivo
experiments. The injections of virus were done on 3-month-old mice, and thetests were performed 3–6 weeks later. All mice were housed on a normal 12 h
light, 12 h dark cycle in groups of between 3 and 5 mice per cage, and all mice
were tested during the light cycle.
One day before the experiments, a single 10 mm incision was made perpendicular to the midline and caudal to lambda, the skull was exposed, and a titanium
alloy head bar was attached to the skull using cyanoacrylate gel and a layer ofdental cement (C&B-Metabond, Parkell Inc., Edgewood, NY) during isoflurane
anesthesia. The skin rostral to the lambda was not damaged, and the skull under it
was neither exposed nor covered by any amount of cement, except for during theelectrophysiological recordings in vM1, for which a new craniotomy was opened

nature NEUROSCIENCE

where the virus had been injected previously. Over the next several daysmice
were head fixed either when awake or during isoflurane anesthesia (0.5–2%),
as indicated. ReaChR was activated in vivo by LEDs with wavelengths of 470 nm(LXML-PB01-0030), 530 nm (LXML-PM01-0100), 591 nm (LXM2-PL01-0000),
617 nm (LXM2-PH01-0070), 627 nm (LXM2-PD01-0050) and 655 nm (LXM3PD01-0260, Luxeonstar, Brantford, Ontario, Canada) connected to a computercontrolled current source (Mightex, Pleasanton, CA).
Single units in vM1 and the facial motor nucleus were recorded extracellularly
with 9–12 MΩ tungsten electrodes (UEWLCESMLN1G, FHC Inc., Bowdoin,ME), buffered, preamplified (Alpha Omega Co., Alpharetta, GA) and acquired
onto a personal computer (PCIe-6361, National Instruments, Austin, TX) using
custom-written software for Matlab (MathWorks, Natick, MA). Spikes were
sorted using the Chronux library in Matlab (http://chronux.org).
Vibrissa movements were monitored with high-speed video36 and tracked
offline using the WhiskerTracker software40 (code available at https://github.com/
pmknutsen/whiskertracker). After in vivo experiments, the mice were perfusedwith 4% paraformaldehyde, the brains were extracted, and ReaChR expression
was confirmed with epifluorescence imaging and localized histologically using afluorescent Nissl counterstain (NeuroTrace N21479, Life Technologies, Carlsbad,
CA). The bone overlying the injection sites was inspected after perfusions andwas invariably found to have regrown entirely. In most mice, the bone that had
regrown after viral injections appeared thickened. Only mice with ChR expression in the correct regions identified with postmortem histochemical analysis
were included in the analysis of spiking and vibrissae movement. Although theexperimenter was not blinded to group status, the measurement was automated,so blinding status would not affect the outcome of the experiment. All animal
procedures, including the extraction of primary neurons, were approved by the
UCSD Institutional Animal Care and Use Committee.
Statistical analyses. Comparisons of the properties of ChR variants in culture
were done by nonparametric Kruskal-Wallis test with post-hoc Dunn’s multiple
comparison tests between all possible pairs. Only the P values for the KruskalWallis tests are shown. The statistical analyses were done with Graphpad Prism
5.0 (San Diego, CA). The comparisons in vivo were conducted with nonparametric one-sided Kolmogorov-Smirnov tests in Matlab. All values are presented as
the mean ± s.e.m. All data in the graphs are presented as the mean ± s.e.m., withthe exception of the 10 Hz stimulation experiments and spike latency analysis,
in which the s.d. is shown to illustrate the variability. No statistical methods wereused to predetermine sample sizes, but our sample sizes were similar to thosereported in previous publications7,20. Most analyses in cultured cells were summarized from multiple transfection or transduction experiments. The full resultsof the statistical analyses are available in Supplementary Data Set 1.
39. Armstrong, C.M. & Gilly, W.F. Access resistance and space clamp problems
associated with whole-cell patch clamping. Methods Enzymol. 207, 100–122(1992).
40. Knutsen, P.M., Derdikman, D. & Ahissar, E. Tracking whisker and head movements
in unrestrained behaving rodents. J. Neurophysiol. 93, 2294–2301 (2005).

doi:10.1038/nn.3502

Supplementary Information

ReaChR: A red-shifted variant of channelrhodopsin enables deep transcranial optogenetic
excitation
John Y. Lin, Per Magne Knutsen, Arnaud Muller, David Kleinfeld and Roger Y. Tsien

	
  

1	
  

Supplementary Figure 1. Comparison of membrane trafficking and expression levelof channelrhodopsin variants in primary cultured cortical neurons and HEK293
cells. (a) Representative fluorescent images of ChR2-Citrine, ChIEF-Citrine, VChR1Citrine, C-VChR1-Citrine and VCOMET-Citrine expressed in primary cortical cultured
neurons. The ChR2 and ChIEF coding sequences are not mammalian codon-optimized.
(b) Quantification of the mean plasma membrane fluorescence (left) and plasma

	
  

2	
  

membrane / cytosol fluorescence ratio (right) of the different variants in primary cultured
cortical neurons. (c) Identical analysis of the different variants in HEK293 cells. *indicates 0.05 level of significance, ** indicates 0.01 level of significance and ***indicates 0.001 level of significance. Statistical tests were conducted with Kruskal-Wallis
test with post-hoc Dunn’s multiple comparison tests between all possible pairs. For (b), H= 30.58, k = 5, P < 0.0001 for the left panel and H = 63.90, k = 5, P < 0.0001 for the rightpanel. For (c), H = 53.94, k = 7, P < 0.0001 for the left panel and H = 70.78, k = 7, P <0.0001 for the right panel. In (b), only significant differences compared to ChIEF andVCOMET from Dunn’s tests were indicated. In (c), only significant differencescompared to oChIEF and VCOMET from Dunn’s tests were indicated on the graphs.
Graphs are shown as mean ± S.E.M.

	
  

3	
  

Supplementary Figure 2. Properties of VCOMET. (a) Comparison of mean
photocurrent amplitudes of mammalian codon-optimized ChEF (oChEF), C-VChR1 andVCOMET without (left) and with (right) adjustment to membrane fluorescence recorded
in HEK293 cells. (b) Representative electrophysiological traces of VCOMET to lightstimulation of different wavelength (left) and the response spectrum (right). (c)Representative electrophysiological traces of VCOMET in response to 570 nm light at
different holding potentials in voltage-clamp (left) and the I-V relationship of mammaliancodon-optimized ChIEF (oChIEF), CatCh and VCOMET (right). Photocurrent
amplitudes for VCOMET, C-VChR1, oChEF, oChIEF, ReaChR, C1V1 andC1V1(E122T) were compared with Kruskal-Wallis test followed by Dunn’s multiple
comparison tests for all possible pairs (H = 48.02, k = 7, P < 0.0001). Photocurrent
amplitudes normalized to membrane fluorescence for oChEF, C-VChR1 and VCOMET
were compared with Kruskal-Wallis test (H = 0.9482, k = 3, P = 0.6225). Graphs areshown as mean ± S.E.M. ** indicates 0.01 level of significance and *** indicates 0.001

	
  

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level of significance. For right panel of (a), the n for oChEF, C-VChR1 and VCOMET
are 12, 8 and 10, respectively.

	
  

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Supplementary Figure 3. The recovery of VCOMET, C-VChR1 and ReaChR after
desensitization / inactivation. (a) With 2 repetitive stimulations 20 seconds apart, thedesensitized transient component of C-VChR1 and VCOMET failed to recovercompletely in the dark without re-activation with 410 nm light. (b) The recovery of thedesensitized transient peak response with various second pulse delay, both C-VChR1 andVCOMET failed to achieve 100% recovery after 25 seconds. (c) The responses of

	
  

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ReaChR to 750 ms light pulses 30 s apart at the indicated wavelength. With 570 and 610
nm stimulation but not with 630 nm, there were desensitized components that did notrecovery fully. (d) Summary graph of the experiment shown in (c). Unpaired Student’s ttests (2-tailed) were used to compare the recovery of photo-responses of C-VChR1 and
ReaChR at 570, 610 and 630 nm. For 570 nm stimulation, t(11) = 4.24 and P = 0.0014,
for 610 nm stimulation, t(11) = 2.381, P = 0.0364 and for 630 nm stimulation, t(10) =2.068, P = 0.0655. Graph in (d) is shown as mean ± S.E.M.

	
  

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Supplementary Figure 4. The light-intensity-photocurrent relationships of CVChR1, C1V1(E122T) and ReaChR. (a) The summary of light intensity-photocurrent
amplitude relationships of C-VChR1 (left), C1V1(E122T) (middle) and ReaChR (right)
to 610 nm light. (b) The summary of light intensity-photocurrent relationships of CVChR1 (left), C1V1(E122T) (middle) and ReaChR (right) to 630 nm light. n = 10 for CVChR1, n = 6 for C1V1(E122T) and n = 6 for ReaChR. Graphs are shown as mean ±S.E.M.

	
  

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Supplementary Figure 5. The membrane properties of ReaChR-expressing primarycultured hippocampal neurons compared to hChR2(H134R) and oChIEFexpressing neurons. The mean resting membrane potential (a) is not significantly
different between the three groups. The mean cell capacitance (b) of the ReaChRexpressing neuron is significantly greater than hChR2(H134R)-expressing neurons,
indicating the expressing cells are bigger in size. The mean membrane resistance (c) of
ReaChR-expressing neurons are lower than hChR2(H134R)-expressing neurons,consistent with greater cell size as measured with capacitance. The hChR2(H134R)expressing cells are chosen based on the fluorescence of the expression, whereas
ReaChR-expressing neurons are chosen based on healthy morphology under bright fieldvisualization. The cells expressing a high level of hChR2(H134R) typically had smallersize, whereas the larger cells only expressed a low level of hChR2(H134R). Statisticaltests were conducted with Kruskal-Wallis test with post-hoc Dunn’s multiple comparison
tests between all possible pairs. For (a), H = 3.539, k = 3, P = 0.1704. For (b), H = 6.823,
k = 3, P = 0.033. For (c), H = 11.47, k = 3, P = 0.0032. * indicates 0.05 level ofsignificance. Graphs are shown as mean ± S.E.M.

	
  

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Supplementary Figure 6. The fidelity of ReaChR, hChR2(H134R) and oChIEFexpressing neurons to different frequencies of light stimulation. (a) The response of
ReaChR-expressing cultured neurons to 627 nm light at 5 Hz (n = 2 - 9). An example ofthe electrophysiological recording of ReaChR-expressing neuron to 10 mW/mm2 627 nm
light stimulation of 10 ms pulse duration at 5 Hz (left). The graphs summarize thepercentages of light pulses resulting in successful action potentials (middle) and thepercentages of pulses resulting in extra action potential (right). (b) The response of

	
  

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ReaChR-expressing cultured neurons to 617 nm light at 5 Hz (n = 2 - 6) as in (a). The
electrophysiological recording shows the response of a ReaChR-expressing neuron to 10
mW/mm2 617 nm light stimulation at 10 ms pulse duration (left) (c) Examples ofoChIEF-expressing cultured neurons to 10, 25 and 50 Hz of light pulse stimulation. The
stimulation light was 470 nm at 10 mW/mm2 with 1 ms pulse duration for all threefrequencies. (d) The percentage of light pulses resulting in light-triggered action
potentials in neurons expressing hChR2(H134R)(n = 6) (top) and oChIEF (n = 6)(bottom) to 25 Hz blue light stimulation. (e) The percentage of light pulses resulting inlight-triggered action potentials in neurons expressing hChR2(H134R)(n = 7) (top) andoChIEF (n = 5) (bottom) to 50 Hz blue light stimulation. No extra spikes were detected inany of the conditions tested. Graphs are shown as mean ± S.E.M.

	
  

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Supplementary Figure 7. Peripheral nerve activation in vivo and comparison of
ReaChR and hChR2(H134R) expressing mice. (a) Comparison of through-ear (orange)and direct stimulation of the peripheral facial motor nerve (cranial VII; black) in an
isoflurane anesthetized mouse. (b) Photo-activation of ReaChR expressing neurons in FN
by stimulating through the ipsi- (orange) or contra-lateral (black) ear relative to the sideof ReaChR expression in an isoflurane anesthetized mouse. Individual light pulses areindicated by bars (617 nm, 100 mW light output). Asterisk (*) indicates movements
	
  

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correlated with breathing. (c) Schematic of through-skull photo-activation ofhChR2(H134R) expressing neurons in vM1 of the awake, head-fixed mouse. Whisker
movements were monitored with high-speed video. (d) Coronal section through themedial (AGm) and lateral (AGl) agranular motor cortex (vM1) of an rAAV infectedmouse shows hChR2(H134R)-EYFP (green) expression. Neurons were counterstainedwith a fluorescent Nissl-substance marker (NeuroTrace; magenta). Scale bar: 500 µm. (e)Traces of evoked whisker movements in response to single, 100 ms pulses (blue arrows
and bar) of 470 nm light emitted by a LED placed 10 mm above the skin overlying vM1
cortex of an hChR2(H134R) expressing mouse. Increasing values denote protraction of
the vibrissae. Scale bars: 40 deg and 1 s. (f) Average absolute movement amplitudes
evoked by 100 ms pulses of 470 nm (blue) or 617 nm (orange) light through the intact
skin overlying vM1 in hChR2(H134R) (n = 3 mice) or ReaChR (n = 3 mice) expressing
mice, respectively (10 stimulus repetitions per condition/mouse). (g) Schematic of
hChR2(H134R)-EYFP expressing motoneurons in the facial nucleus (FN) of awake miceilluminated through the ear by placing LEDs in the opening of the external auditory canal.
Vibrissae movements were recorded with high-speed video. (h) Horizontal section
through FN showing hChR2(H134R)-EYFP expressing neurons and associated processes(mostly motoneurons axons traversing FN and surrounding regions; green) and cellbodies counter-labelled with a fluorescent Nissl marker (NeuroTrace; magenta). (i)Example of absence of evoked whisker movements when stimulating a mouse expressing
hChR2(H134R) in FN motoneurons. Top: Video frames show the whiskers in thereference retracted position (No-light) and at 100 ms following photo-activation (Light).
Bottom: Traces of whisker position during attempted photo-activation with 470 nm light(blue).

	
  

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Supplementary Figure 8. The photocurrent responses of ReaChR + E163T. (a) The
representative recordings of ReaChR + E163T to different wavelengths of light of thesame intensity. (b) The response spectrum of ReaChR + E163T.

	
  

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Supplementary Figure 9. The nucleotide and amino acid sequence of ReaChR
ChIEF/ChR1 sequence
VChR1 sequence
VChR2 sequence
Kozak sequence
Leu 171 Ile: CTG -> ATT
1 M V S R R P W L L A L A L A V A L A A G 20
-3 ACC ATGGTGAGCAGAAGACCCTGGCTGCTGGCCCTGGCCCTGGCCGTGGCCCTGGCCGCCGGC 60
21 S A G A S T G S D A T V P V A T Q D G P 40
61 AGCGCCGGCGCCAGCACCGGCAGCGACGCCACCGTGCCCGTGGCCACCCAGGACGGCCCC 120
41 D Y V F H R A H E R M L F Q T S Y T L E 60
121 GACTACGTGTTCCACAGAGCCCACGAGAGAATGCTGTTCCAGACCAGCTACACCCTGGAG 180
61 N N G S V I C I P N N G Q C F C L A W L 80
181 AACAACGGCAGCGTGATCTGCATCCCCAACAACGGCCAGTGCTTCTGCCTGGCCTGGCTG 240
81 K S N G T N A E K L A A N I L Q W V V F 100
241 AAGAGTAACGGCACCAACGCCGAGAAGCTGGCCGCCAACATCCTGCAGTGGGTGGTGTTT 300
101 A L S V A C L G W Y A Y Q A W R A T C G 120
301 GCGCTGAGCGTGGCGTGCCTGGGCTGGTATGCGTATCAGGCGTGGCGCGCGACCTGCGGC 360
121 W E E V Y V A L I E M M K S I I E A F H 140
361 TGGGAAGAAGTGTATGTGGCGCTGATTGAAATGATGAAAAGCATTATTGAAGCGTTTCAT 420
141 E F D S P A T L W L S S G N G V V W M R 160
421 GAATTTGATAGCCCGGCGACCCTGTGGCTGAGCAGCGGCAACGGCGTGGTGTGGATGCGC 480
161 Y G E W L L T C P V I L I H L S N L T G 180
481 TATGGCGAATGGCTGCTGACCTGCCCCGTGATTCTGATTcatCTGAGCAACCTGACCGGC 540
181 L K D D Y S K R T M G L L V S D V G C I 200
541 CTGAAAGATGATTATAGCAAACGCACCATGGGCCTGCTGGTGAGCGACGTGGGCTGCATT 600
201 V W G A T S A M C T G W T K I L F F L I 220
601 GTGTGGGGCGCGACCAGCGCGATGTGCACCGGCTGGACCAAAATTCTGTTTTTTCTGATT 660
221 S L S Y G M Y T Y F H A A K V Y I E A F 240
661 AGCCTGAGCTATGGCATGTATACCTATTTTCATGCGGCCAAAGTGTATATTGAAGCGTTT 720
241 H T V P K G L C R Q L V R A M A W L F F 260
721 CATACCGTGCCGAAAGGCCTGTGCAGACAGCTGGTGAGAGCCATGGCCTGGCTGTTCTTC 780
261 V S W G M F P V L F L L G P E G F G H I 280
781 GTGAGCTGGGGCATGTTCCCCGTGCTGTTCCTGCTGGGCCCCGAGGGCTTCGGCCATATT 840
281 S P Y G S A I G H S I L D L I A K N M W 300
841 AGCCCGTATGGCAGCGCGATTGGCCATAGCATTCTGGATCTGATTGCGAAGAACATGTGG 900
301 G V L G N Y L R V K I H E H I L L Y G D 320
901 GGCGTGCTGGGCAACTATCTGCGCGTGAAAATTCATGAACATATTCTGCTGTATGGCGAT 960
321 I R K K Q K I T I A G Q E M E V E T L V 340
961 ATTCGCAAAAAACAGAAAATTACCATTGCGGGCCAGGAAATGGAAGTGGAAACCCTGGTG 1020
341 A E E E D K Y E S S 350
1021 GCGGAAGAAGAAGATAAGTACGAGAGCAGC 1050•

The ChIEF/ChR1, VChR1 and VChR2 sequences are mammalian-codon
optimized.

	
  

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Supplementary Figure 10. The nucleotide and amino acid sequence of C1V1(E122T)
ChIEF/ChR1 sequence
VChR1 sequence
Kozak sequence
Glu 123 Thr
1 M V S R R P W L L A L A L A V A L A A G 20
-3 ACC ATGGTGAGCAGAAGACCCTGGCTGCTGGCCCTGGCCCTGGCCGTGGCCCTGGCCGCCGGC 60
21 S A G A S T G S D A T V P V A T Q D G P 40
61 AGCGCCGGCGCCAGCACCGGCAGCGACGCCACCGTGCCCGTGGCCACCCAGGACGGCCCC 120
41 D Y V F H R A H E R M L F Q T S Y T L E 60
121 GACTACGTGTTCCACAGAGCCCACGAGAGAATGCTGTTCCAGACCAGCTACACCCTGGAG 180
61 N N G S V I C I P N N G Q C F C L A W L 80
181 AACAACGGCAGCGTGATCTGCATCCCCAACAACGGCCAGTGCTTCTGCCTGGCCTGGCTG 240
81 K S N G T N A E K L A A N I L Q W I T F 100
241 AAGAGTAACGGCACCAACGCCGAGAAGCTGGCCGCCAACATCCTGCAGTGGATCACCTTC 300
101 A L S A L C L M F Y G Y Q T W K S T C G 120
301 GCCCTGAGCGCCCTGTGCCTGATGTTCTACGGCTACCAGACCTGGAAGAGTACCTGCGGC 360
121 W E T I Y V A T I E M I K F I I E Y F H 140
361 TGGGAGaccATCTACGTGGCCACCATCGAGATGATCAAGTTCATCATAGAGTACTTCCAC 420
141 E F D E P A V I Y S S N G N K T V W L R 160
421 GAGTTCGACGAGCCCGCCGTGATCTACAGCAGCAACGGCAACAAGACCGTGTGGCTGAGA 480
161 Y A E W L L T C P V L L I H L S N L T G 180
481 TACGCCGAGTGGCTGCTGACCTGCCCCGTGCTGCTGATTCATCTGAGCAACCTGACCGGC 540
181 L K D D Y S K R T M G L L V S D V G C I 200
541 CTGAAAGATGATTATAGCAAACGCACCATGGGCCTGCTGGTGAGCGACGTGGGCTGCATT 600
201 V W G A T S A M C T G W T K I L F F L I 220
601 GTGTGGGGCGCGACCAGCGCGATGTGCACCGGCTGGACCAAAATTCTGTTTTTTCTGATT 660
221 S L S Y G M Y T Y F H A A K V Y I E A F 240
661 AGCCTGAGCTATGGCATGTATACCTATTTTCATGCGGCCAAAGTGTATATTGAAGCGTTT 720
241 H T V P K G I C R E L V R V M A W T F F 260
721 CATACCGTGCCGAAAGGCATTTGCCGCGAACTGGTGCGCGTGATGGCGTGGACCTTTTTT 780
261 V A W G M F P V L F L L G T E G F G H I 280
781 GTGGCGTGGGGCATGTTTCCGGTGCTGTTTCTGCTGGGCACCGAAGGCTTTGGCCATATT 840
281 S P Y G S A I G H S I L D L I A K N M W 300
841 AGCCCGTATGGCAGCGCGATTGGCCATAGCATTCTGGATCTGATTGCGAAGAACATGTGG 900
301 G V L G N Y L R V K I H E H I L L Y G D 320
901 GGCGTGCTGGGCAACTATCTGCGCGTGAAAATTCATGAACATATTCTGCTGTATGGCGAT 960
321 I R K K Q K I T I A G Q E M E V E T L V 340
961 ATTCGCAAAAAACAGAAAATTACCATTGCGGGCCAGGAAATGGAAGTGGAAACCCTGGTG 1020
341 A E E E D K Y E S S 350
1021 GCGGAAGAAGAAGATAAGTACGAGAGCAGC 1050

* Both ChIEF/ChR1 and VChR1 sequences are mammalian-codon optimized

	
  

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