EMBO/SourceData huggingface dataset:
Figure legend: "Promoter activity of CDKN1A (E) and MDM2 (F) were quantified in Smyd2 knockdown cells before (basal, grey) and 3 h (red), 6 h (blue) and 9 h (orange) after DNA damage (10 Gy IR). Left panel: The percentage of cells with active TSS, subdivided into populations with strong (&gt; 75% of TSS, solid colors) and weak (&lt;75% of TSS, shaded colors) activity, is shown as stacked bar graphs, the mean fraction of active promoters is indicated above each bar. Right panel: Distributions of calculated transcription rates at active TSS are presented for each time point as probability density estimates (PDF, see Data Visualization section). We measured a higher fraction of active promoters upon damage compared to A549 wild type cells (Fig 3), while transcription rates remained unchanged."
NCBI gene IDs:
"CDKN1A: 1026
MDM2: 4193
Smyd2: 56950"
Figure legend: "The p53-K382 methylase Set8 was down-regulated in a clonal stable A549 cell line expressing a corresponding shRNA. Transcript levels were measured in wild type and knockdown cells by qRT-PCR. Mean levels and standard deviation from technical triplicates are indicated."
NCBI gene IDs:
"Set8: 387893"
Figure legend: "Promoter activity of CDKN1A (E) and MDM2 (F) were quantified in Set8 knock-down cells before (basal, grey) and 3 h (red), 6 h (blue) and 9 h (orange) after DNA damage (10 Gy IR). Left panel: The percentage of cells with active TSS, subdivided into populations with strong (&gt; 75% of TSS, solid colors) and weak (&lt;75% of TSS, shaded colors) activity, is shown as stacked bar graphs, the mean fraction of active promoters is indicated above each bar. Right panel: Distributions of calculated transcription rates at active TSS are presented for each time point as probability density estimates (PDF, see Data Visualization section). We measured a higher fraction of active promoters upon damage compared to A549 wild type cells (Figure 3), while transcription rates remained unchanged."
NCBI gene IDs:
"CDKN1A: 1026
Set8: 387893
MDM2: 4193"
Figure legend: "E. RT-qPCR of Axin2 in bEnd.3 cells treated with NDP (200 ng/ml), isotype control or F4L5.13 (1200 ng/ml) and transfected with control, Tspan12 or Fzd4 siRNAs. Data are presented as mean ± SD, n=3 technical replicates. Data is representative of two independent experiments. F. Time course of phosphorylated Disheveled-3 (p-DVL3) and ßcatenin protein levels in bEnd.3 cells treated with 30nM of F4L5.13 or NDP. Histogram represents the ratio of the DVL3 phosphorylation levels over total DVL3 protein and ßcatenin levels over ß-Tubulin measured by densitometry of independent experiments. Data are presented as mean ± SEM, n=4-6 (*p&lt;0.05 as compared with NT). Significance was calculated by one-way ANOVA with Bonferroni's multiple comparisons test (*p&lt;0.05 as compared with NT). "
NCBI gene IDs:
"Axin2: 12006
Fzd4: 14366
Tspan12: 269831"
Figure legend: "E. F4L5.13 rescues barrier function defects in Tspan12-/- mice as shown by an increased expression of the tight junction component CLDN5 and decreased expression of the EC fenestration component PLVAP. IB4-Alexa647 was used to stain ECs. Scale bars: 100 µm."
NCBI gene IDs:
"Tspan12: 269831"
Figure legend: "D. Flat-mounted retinas of adult Tspan12-/- mice injected systemically with sulfo-NHS-biotin show that F4L5.13 partially restored BRB function. PECAM was used to stain endothelial cells. Images are representative of 4 retinas per group. Scale bar: 500 µm."
NCBI gene IDs:
"Tspan12: 269831"
Figure legend: "E. Maximum intensity projection of adult Tspan12-/- retinas after mice were injected with F4L5.13 or isotype control. Endothelial cells were stained with IB4-Alexa 647. Images are representative of 4 retinas per group. Scale bar: 100 µm."
NCBI gene IDs:
"Tspan12: 269831"
Figure legend: "D)  HEK293  cells were genetically engineered to knockout RIG-I, MDA5, or both, and subsequently subjected to retroviral  transduction to stably express FLAG-LGP2 or an empty vector (EV). Correct gene editing and intact type I IFN responsiveness was validated by  SDS-PAGE and immunoblotting  using the indicated antibodies (n=2). *, non-specific band."
NCBI gene IDs:
"FLAG: 
RIG-I: 23586
LGP2: 79132
MDA5: 64135"
Figure legend: "E) Cells generated in (D) were transfected with siCtrl or siADAR1. The  type I IFN  response and ADAR1 knockdown efficiency was monitored 78h post-transfection as in (B). Data are means ± s.d. from a representative of four biological replicate experiments."
NCBI gene IDs:
"ADAR1: 103"
Figure legend: "F) Cells generated in (D) were transfected with siCtrl (siC) or siADAR1 (siA). Protein lysates were prepared 78h post-transfection, followed by SDS-PAGE and immunoblotting using the indicated antibodies (n=2)."
NCBI gene IDs:
"ADAR1: 103"
Figure legend: "G)  HEK293 WT cells and FLAG-LGP2-expressing HEK293 cells were transfected with siCtrl or siADAR1  and subsequently plated on coverslips for immunofluorescence. Cells were fixed, permeabilized and stained  72h post-transfection with anti-FLAG (red) and anti-IRF3 (green) antibodies. Nuclei  were  stained with DAPI (blue). Scale bar is 50 μm. Total nuclei  (&gt;450 nuclei  per experimental condition) and  IRF3-positive nuclei  were counted using semi-automated software analysis and plotted as percentage IRF3-positive nuclei of total nuclei per field of view (a representative of three biological replicate experiments is quantified). The boxplot indicates the interquartile range as a box, the median as a central line, and the whiskers extend from the minimum to the maximum value. Statistical analyses were performed using unpaired two-tailed Mann-Whitney U tests. ns, not significant; ****, p&lt;0.0001."
NCBI gene IDs:
"FLAG: 
ADAR1: 103
LGP2: 79132"
Figure legend: "A) HEK293  cells were genetically engineered to knockout ADAR1 using CRISPR/Cas9. Cells were treated for 24h with recombinant type I IFN to upregulate  ADAR1 p150 and  ISG60 to confirm correct gene editing and type I IFN  responsiveness, respectively. Protein lysates were analyzed by SDS-PAGE  followed by  immunoblotting  using the indicated antibodies (n=3)."
NCBI gene IDs:
"CRISPR: 
ADAR1: 103
Cas9: 69900935"
Figure legend: "B) ADAR1-knockout HEK293 cells (clone 1) were co-transfected with an empty vector (EV) or a FLAG-LGP2-encoding vector (LGP2) combined with a vector encoding GFP-tagged ADAR1 p110 or p150. Cells were harvested 72h post-transfection and the type I IFN  response was monitored by RT-qPCR analysis of  IFN-β  and IFIT1 expression, normalized to ACTB. Data are means ± s.d. from a representative of four biological replicate experiments."
NCBI gene IDs:
"FLAG: 
GFP: 
ACTB: 60
ADAR1: 103
ADAR1 p110: 103
LGP2: 79132
IFIT1: 3434
IFN-β: 3456"
Figure legend: "C) ADAR1-knockout cells (clone 1) were transfected as in (B). Protein lysates were analyzed by SDS-PAGE followed by  immunoblotting  using the indicated antibodies (n=4)."
NCBI gene IDs:
"ADAR1: 103"
Figure legend: "A) ADAR1-knockout HEK293 cells (clone 1) were modified with a  lentiviral-based inducible system to express FLAG-LGP2 WT or a FLAG-LGP2 RNA binding mutant (K138E/R490E/K634E, denoted as \"KRK mutant\") in a  doxycycline-regulated manner. Cells were treated 72h with  doxycycline  (dox). Protein lysates were analyzed by SDS-PAGE  and  immunoblotting  using the indicated antibodies (n=3). iEV = inducible empty vector; iLGP2  = inducible LGP2."
NCBI gene IDs:
"FLAG: 
ADAR1: 103
LGP2: 79132"
Figure legend: "E) MDA5-knockout HEK293 cells, were transfected with an ADAR1-targeting siRNA (siADAR1) or a control siRNA (siCtrl) and 8h later with an empty vector (EV) or a vector encoding the indicated WT, truncation, or point mutant(s) of MDA5. Cells were harvested 72h post-siRNA transfection and the type I IFN  response was monitored by RT-qPCR analysis of IFIT1  and ISG15  transcript  expression, normalized to ACTB. Data are means ± s.d. from a representative of two biological replicate experiments."
NCBI gene IDs:
"ACTB: 60
ADAR1: 103
MDA5: 64135
IFIT1: 3434
ISG15: 9636"
Figure legend: "B) HEK293  WT or ADAR1-knockout cells (clone 1) were transiently transfected with an empty vector (EV) or a vector encoding the indicated WT, truncation, or point mutant(s) of  LGP2. Cells were harvested 72h post-transfection and the  type I IFN response was monitored by RT-qPCR analysis of IFN-β and IFIT1 transcript expression, normalized to  ACTB. Data are means ± s.d. from a representative of three biological replicate experiments."
NCBI gene IDs:
"ACTB: 60
ADAR1: 103
LGP2: 79132
IFIT1: 3434
IFN-β: 3456"
Figure legend: "A) Kaplan-Meier plots showing overall survival  of ADARlow and ADARhigh patients stratified by DHX58 levels in bladder cancer (BLCA; n=407), breast cancer (BRCA; n=1099) and sarcoma (SARC; n=263) TCGA datasets. Median cut-offs were used for patient  stratification and logrank test P values are shown."
NCBI gene IDs:
"ADAR: 103
DHX58: 79132"
Figure legend: "B) CAL27 cells transduced with doxycycline-inducible shRNAs targeting  ADAR1 or GFP (negative control) were treated with doxycycline  and transfected with two independent siRNAs targeting LGP2  (siLGP2 #1 or #2) or a control siRNA (siCtrl). To determine  cell confluency at 120h post-transfection, cells were fixed, stained  with Crystal Violet, and imaged. Images of a representative experiment are shown (n=3). C) Crystal Violet was extracted from stained cells (B) and the dye intensity was quantified using a colorimetric assay (OD590). OD590 values of doxycycline-treated cells were normalized to the OD­590 values of untreated cells. Quantification of data from three independent experiments is shown as mean ± s.d.. Statistical analysis was performed using ordinary two-way ANOVA with Tukey's post hoc test. ns, not significant; *, p&lt;0.05; **, p&lt;0.01; ****, p&lt;0.0001."
NCBI gene IDs:
"GFP: 
ADAR1: 103
LGP2: 79132"
Figure legend: "A) HT29  cells were treated with or without 300 nM  5-AZA-CdR  for 2 days and subsequently washed and transfected with the indicated siRNAs. Cells were harvested 72h post-transfection and the  type I IFN  response was analyzed by RT-qPCR  analysis of  IFN-β, IFIT1, and  ISG15 transcript  expression, normalized to  ACTB. B) LIM1215 cells were treated with or without 300 nM 5-AZA-CdR for 2 days and subsequently washed and transfected with the indicated siRNAs. Cells were harvested 72h post-transfection and the type I IFN response was analyzed as in (A). C) LIM1215 cells were treated with 250 nM palbociclib or a DMSO  control for 7 days. Three days after treatment initiation, cells were transfected with the indicated siRNAs and cultured for an additional 72h. The type I IFN  response was monitored as in (A). Data information: Data from three biological independent experiments are shown with mean ± s.d.. Statistical analysis was performed using ordinary two-way ANOVA with Tukey's post hoc test. ns, not significant; *, p&lt;0.05; **, p&lt;0.01; ***, p&lt;0.001; ****, p&lt;0.0001. "
NCBI gene IDs:
"ACTB: 60
IFIT1: 3434
IFN-β: 3456
ISG15: 9636"
Figure legend: "Cells expressing a nearly functional FtsZ-mVenus fluorescent fusion as their sole copy of ftsZ were monitored after transition into carbon starvation. Two low motile MG1655 strains, one (wild-type) containing clpX and one without (ΔclpX), were grown in M9 glucose to steady-state. At time zero, M9 media without glucose was flushed through device. Cells rapidly ceased elongation as measured by phase contrast imaging at 2 minute intervals. Fluorescent images were taken every hour throughout to measure both total Ftsz-mVenus per cell and localization patterns Thin individual lines show the total fluorescent per cell in a single lineage (wild-type in solid blue, n = 154. ΔclpX in dotted red, n = 144). Thick solid lines are the time average across individual lineages for each subset (wild-type in blue, ΔclpX in red). After starvation, cells containing clpX degrade FtsZ faster than cells which do not. Fluorescent signals are normalized to the average value for their respective subset at time 0 Distributions of cellular fluorescence for each subset at times corresponding to the top panel. Cellular fluorescence varies widely as total FtsZ per cell is a function of cell size; a typical size distribution is shown at left. FtsZ concentration is roughly constant at steady-stat Student\"s t-test P value shown for when distributions differ with significance level α = 0.01. Representative images from cells in a single lineage with and without clpX. Wild-type strains may contain the characteristic FtsZ ring at midcell after shift down but it dissipates after several hours. ΔclpX strains display an abnormal FtsZ localization pattern even in steady-state. After shift down, the FtsZ may disassemble and reform along the cell body in distinct puncta. Image timing corresponds to the abscissa in the top"
NCBI gene IDs:
"clpX: 945083"
Figure legend: "Genetically induced titration of PdhR in a pdhR mutant reintroduced lag commensurate with expression level for a given TI feedrate (f = 0.38 mmol/g/h). Induction level corresponds to the amount of doxycycline (max - 50 ng/uL, half - 10 ng/uL, and zero 0 ng/uL) added at the onset of starvation. The TI feedrate is abbreviated as f (units: mmol glucose/g dry cell weight/hour). Wild-type lag (from Figure 2A empirical fit) is indicated by the dotted grey line. Lag time reduced with synthesis levels of titrated FtsZ in the wild-type strain at f = 0.31-0.32 mmol/g/h. Lag time increased with titrated synthesis of ClpX in wild-type cells at f = 0.43-0.45 mmol/g/h"
NCBI gene IDs:
"ClpX: 945083
FtsZ: 944786
PdhR: 944827
pdhR: 944827"
Figure legend: "B Induction of NF-κB targets in Jurkat T cells in response to 20 ng/ml TNF treatment for 1, 2, and 4 hours as measured by RT-qPCR. Target values were normalized to GAPDH and are reported as fold change relative to basal expression. Data are presented as mean ± standard deviation (SD) of 3 biological replicates."
NCBI gene IDs:
"GAPDH: 2597
NF-κB: 4792"
Figure legend: "D Maximum intensity projections of smFISH fluorescence microscopy z-stacks of basal Jurkat T cells stained for the indicated genes. Nfkbia, Tnfaip3, Tnf, and  Il6 were labeled with Quasar 670, and Il8  and Csf2 were labeled with  fluorescein. All images were filtered as described in Materials and Methods. Brightness and contrast were enhanced for visualization. Scale bars: 10 μm."
NCBI gene IDs:
"Csf2: 1437
Il8: 3579
Il6: 3569
Nfkbia: 4792
Tnf: 7124
Tnfaip3: 7128"
Figure legend: "A Maximum  intensity projections of  smFISH fluorescence microscopy z-stacks of Jurkat T cells  stained for the indicated genes after 1-hour (Nfkbia, Tnfaip3, Tnf,  Il8) or 4-hour (Il6, Csf2) treatment with 20 ng/mL TNF. Nfkbia, Tnfaip3, Tnf, and Il6 were labeled with Quasar 670, and Il8  and Csf2 were labeled with fluorescein. All images were filtered as described in Materials and Methods. Brightness and contrast were enhanced for visualization. Scale bars: 10 μm. B Bar graphs of mean of smFISH distributions before and after TNF treatment for the indicated genes. Cells were combined from three replicates (Nfkbia 1h; Tnfaip3 1h; Tnf  1h, 2h; and  Il6 2h, 4h) two replicates (Nfkbia 2h) or one replicate (Tnfaip3 2h; Il8 1h, 2h; Csf2 2h, 4h). Basal data are same as in Fig. 1E. Error bars indicate bootstrapped 95% CIs for the samples in (C). Significant differences indicated by non-overlapping CIs. C "
NCBI gene IDs:
"Csf2: 1437
Il8: 3579
Il6: 3569
Nfkbia: 4792
Tnf: 7124
Tnfaip3: 7128"
Figure legend: "B-C Burst size  (B) and burst frequency (C) parameter fits from the two-state model in the basal state and after treatment with 20 ng/mL  TNF for 1, 2 or 4 hours. Error bars indicate bootstrapped 95% CIs. Significant differences indicated by non-overlapping CIs. The fit for Nfkbia (1h TNF) was unstable and thus is not reported"
NCBI gene IDs:
"Nfkbia: 4792"
Figure legend: "C Bar graphs of mean mRNA level for basal condition, 1h TNF, 1h TNF + 4h pretreatment with 300nM A-485, and 1h TNF+62.5nM JQ1 cotreatment measured by smFISH for  Tnfaip3 (left) and Tnf (right). Cells were combined from two replicates (Tnfaip3 A-485, JQ1; Tnf A-485) or one replicate (Tnf JQ1). Error bars indicated bootstrapped 95% CIs. Samples with non-overlapping CIs are significant. D Change in enrichment of total and Serine-5-phosphorylated RNAPII  after 20ng/mL TNF treatment for 1 hour with 62.5nM  JQ1 measured by  ChIP-qPCR and shown as % input (non-IP control) normalized to the uninhibited control for each gene. Data are presented as mean for two biological replicates. E "
NCBI gene IDs:
"Tnf: 7124
Tnfaip3: 7128"
Figure legend: "a-c, Expression of CD45RO and CCR7 (a), CD45RO and CD27 (b), CD27 and CD28 (c) on peripheral blood CD8 T cells of three participants [P1 (heterozygous mutation), P2 (homozygous mutation) and P3 (heterozygous) for the c.192G&gt;C mutation in the DJ-1 gene]. d-g, Expression of CD57 (d), PD-1 (e), EOMES (f) and T-bet (g) on peripheral blood CD8 T cells of three participants. The enlarged number in the corresponding gate represents the corresponding percentage out of the parent population. h"
NCBI gene IDs:
"DJ-1: 11315"
Figure legend: "b-c, Percentages of CD44low CD62Lhigh (Tn) (b) and CD44high CD62Llow (Tem) (c) cells among total CD8 T cells of spleen and pLNs from young and 45-wk-old Dj-1 KO and WT littermates (young KO, n=5; young WT, n=5; 45-wk-old KO, n=8; 45-wk-old WT, n=6; for 45-wk-old mice, data pooled from 2 independent experiments)."
NCBI gene IDs:
"Dj-1: 57320"
Figure legend: "e, Percentages of Ki-67+ cells among total CD8 T cells. f, Percentage of Ki-67+ cells among splenic CD8 Tn, Tem and Tcm in 45-wk-old Dj-1 KO and age- and sex-matched WT mice. g"
NCBI gene IDs:
"Dj-1: 57320"
Figure legend: "b, Percentages of KLRG1+ CD8 T cells derived from 45-wk-old Dj-1 KO and WT BM cells within young Dj-1 KO (n=4) or WT recipients (n=5). c, Percentages of KLRG1+ among CD8 Tem derived from 45-wk-old Dj-1 KO and WT BM cells within young Dj-1 KO or WT recipients. d d, Percentages of PD-1+ population among CD8 T cells derived from 45-wk-old Dj-1 KO and WT BM cells within young Dj-1 KO (n=4) or WT recipients (n=5)."
NCBI gene IDs:
"Dj-1: 57320"
Figure legend: "(A) Transcription at GAL3 is visualized by addition of PP7 loops at the 5' of GAL3 in budding yeast. Example trace of the quantified fluorescence intensity of the transcription site. Traces are binarized to determine on (active) and off (inactive) times."
NCBI gene IDs:
"GAL3: 851572"
Figure legend: "(B) Histogram of GAL3 on time (burst duration) for cells with wt and mutated UAS, respectively, reveals shorter on times for mutated UAS. Errors indicate SE of 3 experiments, n = 324 cells UASwt, n = 250 cells UASmut. (C) Histogram of GAL3 off times. Errors indicate SE of 3 experiments. "
NCBI gene IDs:
"GAL3: 851572"
Figure legend: "(G) Example traces of quantified fluorescence intensity at the transcription site for 5'PP7 and 3'MS2 at GAL3."
NCBI gene IDs:
"GAL3: 851572"
Figure legend: "(I) Distribution of number of nascent RNAs at the transcription site determined by smFISH. The distribution of UASwt does not fit a Poisson distribution (grey line), supporting that GAL3 is not constitutively transcribed, but is transcribed in bursts. Example image in shown, yellow arrows indicate TSs. Scale bars: 5 μm. n = 11,839 cells. (J) for cells with UASmut. The distribution of UASmut fits a Poisson distribution, indicating that GAL3-UASmut is transcribed with random initiation of individual polymerases, similar to constitutive genes. n = 10,616 cells."
NCBI gene IDs:
"GAL3: 851572"
Figure legend: "(A) Competitive binding experiments were performed to determine relative affinity of Gal4 to UASwt (green) and UASmut (blue) motifs. Gal4 occupancy on UASwt Cy3/Cy5 DNA was determined by measuring protein induced fluorescence enhancement (PIFE) on 51 bp oligos containing either Gal4 UASwt or UASmut site 1 bp away from Cy3 fluorophore)."
NCBI gene IDs:
"Gal4: 855828"
Figure legend: "(C) Comparison between relative affinities of Gal4 UASwt versus UASmut in naked or nucleosomal DNA shows 4.3 ± 1.1x difference in KD from naked DNA and 6.8 ± 1.7x from nucleosomal DNA. n = 3. Error bars indicate SD."
NCBI gene IDs:
"Gal4: 855828"
Figure legend: "(D) Experimental setup for smFRET experiments to measure Gal4 binding at nucleosomal DNA. Gal4 binds to site 8 bp into nucleosome. A FRET pair in the entry/exit region provides readout on binding events (one fluorophore on DNA, one on histone). In the absence of Gal4, nucleosomes are in the high FRET state. A Gal4 binding event traps nucleosome in low FRET state."
NCBI gene IDs:
"Gal4: 855828"
Figure legend: "(E) Gal4 affinity to nucleosomes containing UASwt or UASmut sequences gives S1/2 of 7.2 ± 0.8 nM and 48.9 ± 10.8 nM, respectively. n = 3. Error bars indicate SD."
NCBI gene IDs:
"Gal4: 855828"
Figure legend: "(F) Example smFRET traces showing Gal4 binding to UASwt in nucleosomal DNA at two different Gal4 concentrations. States are determined using HMM fit. (G) Same as F but for UASmut. "
NCBI gene IDs:
"Gal4: 855828"
Figure legend: "(H) Binding-rates of Gal4 are concentration dependent, but are similar for UASwt and UASmut: kon UASwt = 0.011 ± 0.002 s-1 nM-1, kon UASmut = 0.009 ± 0.001 s-1 nM-1. n = 2 for all, except n = 4 for UASwt 10 nM Gal4 and n = 3 for UASwt 20 nM Gal4. Error bars indicate SD."
NCBI gene IDs:
"Gal4: 855828"
Figure legend: "(I) The dissociation-rate of Gal4 at UASwt is ~5-fold slower compared to the UASmut: koff UASwt = 0.20 ± 0.01 s-1, koff UASmut = 0.92 ± 0.05 s-1. n = 2 for all, except n = 4 for UASwt 10 nM Gal4 and n = 3 for UASwt 20 nM Gal4. Error bars indicate SD."
NCBI gene IDs:
"Gal4: 855828"
Figure legend: "(J) Histogram of Gal4 dwell time to nucleosomal DNA containing UASwt and UASmut sequences. n = 11 for UASwt, n = 8 for UASmut. Error bars indicate SE."
NCBI gene IDs:
"Gal4: 855828"
Figure legend: "(K) Scatter plot showing the average number of nascent RNA at TS (from smFISH) vs affinity of Gal4 to different UAS sequences in nucleosomal DNA (from in vitro measurements). In vivo transcription levels correlate with in vitro affinity of Gal4, but transcription saturates above wildtype sequence. UAS sequences are shown in the box. For mean number of nascent RNA from smFISH, n = 2 for UASconsensus, UAS-2C, UAS-8T and n = 8 for UASwt, UASmut and errors indicate SEM. For in vitro affinity measurements, n = 3 and errors indicate SD."
NCBI gene IDs:
"Gal4: 855828"
Figure legend: "Profiles of nucleosome midpoint positions by MNase-seq experiments. Samples were digested with the indicated MNase concentrations in both raffinose (raf) and galactose (gal) containing media. Midpoints of nucleosomes are smoothed by 31 bp. In galactose the stable nucleosomes move away from the Gal4UAS, creating space for an additional fragile nucleosome (indicated by arrow)."
NCBI gene IDs:
"Gal4: 855828"
Figure legend: "(A) Simultaneous imaging of Gal4 binding kinetics in vivo using single-molecule tracking and RNA imaging of the GAL10 target gene. Gal4 is tagged with a HALO-tag, which covalently binds to the dye JF646. Transcription of the target gene GAL10 is visualized by PP7-loops."
NCBI gene IDs:
"HALO: 
GAL10: 852307
Gal4: 855828"
Figure legend: "(B) Example image of a cell, showing the GAL10 TS (arrow, left panel), single molecules of Gal4 (arrows, middle panel) and an overlay (right panel). Scale bar: 2 μm."
NCBI gene IDs:
"GAL10: 852307
Gal4: 855828"
Figure legend: "(C) Example kymograph of a cell. Upper panel (PP7-GAL10) shows the position of the TS over time. Middle panel (Gal4-HALO) show tracks of Gal4. Data is in white, colored lines show analyzed tracks. Lower panel shows overlay, showing colocalization of some the Gal4 tracks to the GAL10 TS. Scale bar: 1 μm."
NCBI gene IDs:
"HALO: 
GAL10: 852307
Gal4: 855828"
Figure legend: "(D) Survival probability of the duration of Gal4 tracks (after displacement thresholding) at 200 ms interval from cells grown in raffinose (n = 258 tracks in 30 cells) or galactose (n = 346 tracks in 25 cells). Lines show bi-exponential fit, indicating 2 Gal4 populations. Inset shows data in semi-logarithmic plot. (E) Residence time of the fast and slow component of the fits from (D). The slow component changes between conditions. Error bars indicate 95% CI. "
NCBI gene IDs:
"Gal4: 855828"