EMBO/SourceData huggingface dataset:
Figure 2(A) Bar graph showing qPCR quantification of SEC61B level in MCF10A MECs ligated with rBM in 2D and 3D 12h post-plating (mean ± SEM; n=3 independent biological replicates). Statistical analysis by one-way ANOVA followed by Uncorrected Fisher's LSD, **P = 0.0022.(B) MCF10A MECs expressing VSVGts045-EGFP were ligated to rBM in 2D or 3D and incubated at 40°C for 16h to trap VSVGts045-EGFP protein in the ER. Cells were shifted to 32°C for 2h to release VSVGts045-EGFP into the secretory pathway. Representative fluorescence microscopy images of MECs expressing VSVGts045-EGFP 2h post incubation at 32°C. Scale bar (whole cell), 10 μm; Scale bar (magnified), 2 μm. (C) Scatter plot of the secretory trafficking efficiency of VSVGts045-EGFP based on the fluorescence of VSVGts045 at the plasma membrane versus total fluorescence measured in cells from Panel B (mean ± SEM; 2D, n=45; 3D, n=49 cells from three independent experiments). ****P < 0.0001 (Student's t test).(D) Representative line graph showing the changes in cytosolic [Ca2+] levels of MCF10A MECs under different treatment. Fura-2-loaded MECs ligated to 2D (blue) or 3D rBM (red) were pre-incubated with EGTA to chelate extracellular Ca2+ in the bath solution, challenged with 2μM thapsigargin to induce ER Ca2+ release, and replenished with 4 mM Ca2+ in bath solution at the indicated time. F340/F380 values for each cell were quantified over the course of imaging (mean ± SD; 2D, n=7; 3D, n=7 cells from one experiment). (E) Quantification of the amplitude of the Ca2+ response induced by thapsigargin (∆F=F-F0), where F0 is the basal fluorescence before thapsigargin treatment (mean ± SEM (2D, n=20; 3D, n=21 cells from three independent experiments). ***P = 0.0007 (Student's t test).(F) Bar graph showing qPCR of the relative level of ATF3 mRNA in MCF10A MECs ligated with rBM in 2D and 3D 12h post-plating (mean ± SEM; n=3 independent biological replicates). Statistical analysis by one-way ANOVA followed by Uncorrected Fisher's LSD, **P = 0.0037.(G) Representative immunoblots of phosphorylated EIF2a (pEIF2a), total EIF2a and alpha-tubulin in cell lysate from MCF10A MECs ligated to a rBM in 2D or 3D and corresponding quantification data (mean ± SEM; n=6 independent biological replicates). Statistical analysis by Student's t test, **P = 0.0049.(H) Bar graph of qPCR data measuring the relative levels of CRACR2B mRNA in MCF10A MECs ligated with rBM in 2D and 3D 12h post-plating (mean ± SEM; n=4 independent biological replicates). *P = 0.0371 (Student's t test).(I) Representative fluorescence microscopy images of the ER-plasma membrane contact site reporter GFP-MAPPER in MCF10A MECs ligated with rBM in 2D or 3D 18h post plating. Scale bar (whole cell), 10 μm; Scale bar (magnified), 1 μm. (J) Graph of the levels of GFP-MAPPER at the plasma membrane relative total cellular GFP-MAPPER fluorescence in MCF10A MECs ligated with rBM in 2D or 3D in Panel I (mean ± SEM; 2D, n=52; 3D, n=57 cells from three independent experiments). **P = 0.0032 (Student's t test).
Figure 3(A) Representative immunofluorescence microscopy images of MCF10A MECs ligated with either a rBM in 2D or 3D for 18h and stained with antibody targeting filamin (green). F-actin was counterstained with phalloidin (red). Images show maximum intensity z-projections of xy confocal stacks (left) and middle focal plane of confocal stacks from MECs (right). Yellow arrows indicate filamin aggregates in individual MECs ligated to rBM in 2D. Yellow blunt-end lines highlight the extent of filamin distribution away from the cell edge. Scale bar, 10 μm.(B) The expression level of filamin in MCF10A MECs ligated to rBM in 2D and 3D for 18h was assessed via immunoblot and quantified relative to actin loading control (mean ± SEM; n=5 independent biological replicates). ***P = 0.0008 (Student's t test).(C) Representative fluorescence microscopy images of MCF10A MECs co-expressing the ER-plasma membrane contact site reporter GFP-MAPPER and shRNA targeting filamin (FLMN) or luciferase (Luc) ligated to rBM in 2D for 18h. Scale bar (whole cell), 10 μm; Scale bar (magnified), 2 μm.(D) Quantification of the levels of GFP-MAPPER at the plasma membrane versus total cellular fluorescence in MCF10A MECs stably expressing an shRNA targeting filamin (FLMN) or luciferase (Luc) ligated to rBM in 2D (mean ± SEM; 2D + shLuc, n=38; 2D + shFLMN , n=39 cells from three independent experiments). **P < 0.0021 (Student's t test).(E) Representative immunoblots of filamin, phosphorylated EIF2a (pEIF2a), total EIF2a and alpha-tubulin in cell lysate from MCF10A MECs that express shRNA targeting filamin (shFLMN) or luciferase (shLuc) and ligated to a rBM in 2D or 3D for 18h and corresponding quantification data (mean ± SEM; n=4 independent biological replicates). Statistical analysis by one-way ANOVA followed by Uncorrected Fisher's LSD. 2D-shLuc versus 3D-shLuc, ***P = 0.0003. 2D-shLuc versus 2D-shFLMN, ***P = 0.0004.(F) Bar graph of the relative levels of ATF3 mRNA as measured by qPCR in MCF10A MECs expressing shRNA targeting filamin (shFLMN) or luciferase (shLuc) and ligated with rBM in 2D or 3D for 18h (mean ± SEM; n=4 independent biological replicates). Statistical analysis by one-way ANOVA followed by Uncorrected Fisher's LSD. 2D-shLuc versus 3D-shLuc, ***P = 0.0005. 2D-shLuc versus 2D-shFLMN, *P = 0.0359.(G) Representative immunoblots of filamin, phosphorylated EIF2a (pEIF2a), total EIF2a and alpha-tubulin in cell lysate from MCF10A MECs ligated to rBM in 3D and treated with ethanol (mock) or doxycycline (FLMN) for 18h to induce filamin expression and corresponding quantification data (mean ± SEM; n=5 independent biological replicates). **P = 0.0018 (Student's t test).
Figure 6(A) Bar graph of qPCR data measuring the levels of SEC61B mRNA in MECs ligated with rBM in 2D and treated in the absence and presence of blebbistatin (Bleb) (mean ± SEM; n=3 independent biological replicates). **P = 0.0046 (Student's t test).(B) Change in the Helmholtz free energy of membrane protrusion assembly (∆F) as a function of cell membrane excess area (A/Ap), which is the variable conjugate to the cortical actin tension.(D) Representative time-lapse confocal microscopy images of MECs stably expressing LifeAct-RFP that were ligated to a rBM in 2D (2D) or 3D (3D). Time in seconds (s) is indicated in each inset; scale bar, 10 μm.(E) Bar graph of protrusion length measurements in MECs ligated to rBM in 2D, 3D, or in 2D treated with blebbistatin (2D + Bleb) (mean ± SEM; 2D, n= 139; 3D, n=106; 2D + Bleb, n=88 protrusions from three independent experiments). Statistical analysis by one-way ANOVA followed by Uncorrected Fisher's LSD. ****P < 0.0001. (F) Bar graph of protrusion residence time measurements in MECs ligated to rBM in 2D (2D), 3D (3D), or in 2D treated with blebbistatin (2D+ Bleb) (mean ± SEM; 2D, n= 30; 3D, n=30; 2D + Bleb, n=38 protrusions from three independent experiments). Statistical analysis by one-way ANOVA followed by Uncorrected Fisher's LSD. ****P < 0.0001.(G) 30-nm thick slice through a cellular tomogram focusing on protrusions emanating from a vitrified no-spread MECs cultured on a rBM in the absence (left, 2D) or in the presence of blebbistatin (right, 2D+ Bleb). The position of the cell body is towards the upper right-hand corner (marked with white asterisk). Scale bars, 200 nm. Note: under conditions of low cortical actin tension (blebbistatin treatment) the protrusions visualized in these MECs appeared to be highly interdigitated with sharp kinks, consistent with a compliant phenotype. By contrast, the protrusions observed in the 2D samples (higher cortical actin tension) were predominantly straight and outwardly projected, suggesting they were stiffer than the protrusions formed in the MECs with lower cortical actin tension (e.g. blebbistatin treated). (H) Quantification of membrane protrusion width in tomograms from non-spread MECs interacting with rBM treated with (2D+Bleb) and without blebbistatin (2D). n > 2000 protrusions. Statistical significance of differences between the distributions was assessed using Mann-Whitney rank tests. ****P < 0.0001.
Figure 7(C) (Top) Model of how exocyst components (including Exo70) tether vesicles during exocytosis. Representative fluorescence microscopy images of MECs stably co-expressing EGFP-Exo70 (Exo70) and the plasma membrane reporter farnesylated mCherry (PM) ligated to rBM in 2D, 3D, and treated with blebbistatin (2D+Bleb). Fluorescent images of whole cells are shown (left) and cell-edge protrusions are magnified within inset (right). Colocalization of Exo70 and membrane protrusions are highlighted with yellow arrows. Scale bar (whole cell), 5 μm; Scale bar (magnified inset), 1 μm.(D) Bar graph of the relative level of EGFP-Exo70 at the plasma membrane versus cytoplasm in MECs ligated to rBM in 2D or 3D in the absence and presence of blebbistatin (Bleb). Membrane localization of EGFP-Exo70 was quantified as a ratio of plasma membrane to cytoplasmic fluorescence (mean ± SEM; 2D, n= 59; 3D, n=60; 2D + Bleb, n=57; 3D + Bleb, n=54 cells from three independent experiments). Statistical analysis by one-way ANOVA followed by Uncorrected Fisher's LSD. ****P < 0.0001.(E) 30-nm thick slices through a cellular tomogram focusing on subplasmalemmal regions enriched with membrane-encased compartments of vitrified MECs cultured on rBM treated with (2D, right panel) or without (2D+Bleb, left panel) blebbistatin. The position of the cell body is towards the upper right-hand corners (marked with white asterisk). Scale bars, 200 nm.(F) Quantification of the number of membrane-enclosed compartments (vesicles) proximal to the plasma membrane that were classified as either 'filled' (black) or 'empty' (white), based on the absence or presence of encapsulated macromolecules. Membrane-enclosed compartments were independently classified by three cryo-EM experts using 28 tomograms per condition. The resulting standard deviation for assigning 'empty' versus 'filled' was 10.3% (n=3 independent expert classifications). Statistical significance of differences between the distributions was assessed using Mann-Whitney rank tests. ****P < 0.0001.(H) Volcano plot showing differentially associated proteins in MECs ligated to rBM in 2D treated with vehicle (DMSO; blue; log 2> 0.5; high cortical actin tension) versus blebbistatin (Bleb; red; log 2> 0.5; low cortical actin tension). Differentially expressed genes with an adjusted p-value<0.1 and log2 (fold change) > 0.5 are shown (n=2 biological replicates).(J) Representative immunofluorescence microscopy images of MECs ligated to rBM in 2D, 3D, or 2D treated with blebbistatin (2D+ Bleb) and immunostained with antibodies targeting ANXA2 or S100A14 (green). Cellular F-actin was counterstained using phalloidin (red) and actin-rich protrusions are highlighted with yellow arrows. Fluorescent images of whole cells (left) and actin-rich protrusions containing ANXA2 or S100A14 are magnified in the inset (right). The edge of the actin cortex in MECs ligated to rBM in 2D was marked with a yellow dashed line. Scale bar (whole cell), 5 μm; Scale bar (magnified insets), 1 μm.
Figure 8(A) Graph of the percent cell death measured in MCF10A MECs ligated to rBM in 2D and 3D (left) and in 2D treated with blebbistatin (2D+Bleb) 48h post-plating (right) that was quantified using calcein AM and ethidium homodimer staining (mean ± SEM; 2D, n= 3; 3D, n=3 independent experiments; 2D + DMSO, n = 5; 2D + Bleb, n=5 independent experiments). 2D versus 3D, ***P = 0.0010, 2D versus 2D + Bleb, **P = 0.0248 (Student's t test).(B) Bar graph of the percent cell death measured in MCF10A MECs stably expressing shRNAs targeting Luciferase (Luc), filamin (FLMN) or actinin (ACTN) and ligated to rBM in 2D. Cell death was assessed at 48h post-plating via calcein AM and ethidium homodimer staining (mean ± SEM; n =3 independent biological replicates). **P = 0.0034; ns= not significant (Student's t test).(C) Bar graph of the percent cell death in MCF10A MECs expressing luciferase control or filamin repeats 21-23 (FLMNIg21-Ig23) that were ligated with rBM in 2D. Cell death was assessed at 48h post-plating via calcein AM and ethidium homodimer staining (mean ± SEM; n =3 independent biological replicates). *P = 0.0489 (Student's t test).(D) Bar graph of the levels of endogenous Exo70 in MECs stably expressing shRNA against Exo70 or luciferase (Luc) (mean ± SEM; n =3 independent biological replicates). ** p = 0.0086.(E) Bar graph of the percent cell death measured in MECs expressing shRNA targeting Exo70 (shExo70) or luciferase (control) and ligated with rBM in 2D or 3D. Cell death was assessed at 48h post-plating via calcein AM and ethidium homodimer staining (mean ± SEM; n=3 independent biological replicates). Statistical analysis by one-way ANOVA followed by Uncorrected Fisher's LSD. 2D versus 3D, ***P = 0.0004. 3D + shLuc versus 3D + shExo70, **P = 0.0091.(F) Spheroids were induced to express constitutively active ROCK or left uninduced (control) and co-stained with antibodies for laminin or S100A14 (green), phalloidin (red) and DAPI (blue). Scale bar, 10 μm.(G) Representative immunoblots of phosphorylated EIF2a (pEIF2a), total EIF2a and alpha-tubulin in cell lysate from MCF10A MEC spheroids induced to express constitutively active ROCK or left uninduced (control). Corresponding quantification data are plotted at bottom (mean ± SEM; n=3 independent biological replicates). *P = 0.0442 (Student's t test).(H) Spheroids were induced to express constitutively active ROCK or left uninduced (control), treated with Paclitaxel (2nM), lysed and immunoblotted for cleaved caspase-3 and alpha-tubulin (top). In parallel, spheroids were stained with antibody and phalloidin to evaluate the levels of caspase-3 (green) and actin organization (red), respectively. Scale bar, 10 μm.(I) Bar graph of the relative mRNA levels of ER stress response genes including ATF3, STC2, PPP1R15A, and PMAIP1 in microarray analyses of TRAIL treated HMT-3522 S-1 MECs plated as monolayers on a rigid rBM (2D) or as spheroids (3D) (mean ± SEM; n=3 independent experiments). ATF3, ***P = 0.0006; STC2, *P = 0.0353; PPP1R15A, *P = 0.0254; PMAIP1, *P = 0.0127 (Student's t test).
Figure 1A-D Heat maps of the occurrence frequency of effective variants within each genotype in DENV1 (A), DENV2 (B), DENV3 (C), and DENV4 (D). Residues with the occurrence frequency <20% before 1995 were shown in the heat maps. Red square frames represent ten stable substitutions, including 171T in DENV1-I (A), 131Q, 170T, 340T, and 380V in DENV2-Asian American (B), 226K and 228E in DENV2-Asian I (B), 301S and 377I in DENV3-I (C), and 265A in DENV4-I (D). Gray boxes represent the data that were not available.E-H Growth kinetics and plaque morphology DENV2-Asian I 16681 strain (16681, U87411) (E), DENV2-Asian American DENV2/US/BID-V1164/1986 strain (BID, EU482568) (F), DENV3-I PF89/27643 strain (PF89, AY744677) (G), and DENV4-I H241 strain (H241, AY947539) (H). Vero cells were infected with each mutant at a multiplicity of infection (MOI) of 0.01, and the cell supernatant was collected at Days 1, 3, 5, 7, and 9 for the plaque assay. Data information: In (E-H), data are presented as mean ± SEM of n = 4 biological replicates.
Figure 4B The 293T cells were transfected with a pcDNA3.1 recombinant plasmid with a human DC-SIGN gene. The cells transfected by an empty pcDNA3.1 plasmid served as negative controls. Thirty-six hours after transfection, the cells were infected with DENV2 (0.01 MOI). The DENV2 viral loads were assessed at 48 h postinfection via qRT-PCR and were normalized against human GAPDH. Data information: In (B), n = 6 biological replicates. In (B, the data are presented as means ± SEM and were analyzed statistically using an unpaired t-test. The P value represents a comparison between the mutants and the 16681 WT strain. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, n.s., not significant (p > 0.05). C hu-moDCs were infected with 0.01 MOI of DENV2. The infected cells were detected at 48 h postinfection by qRT-PCR. Data information: In (C), n = 5 biological replicates. In C), the data are presented as means ± SEM and were analyzed statistically using an unpaired t-test. The P value represents a comparison between the mutants and the 16681 WT strain. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, n.s., not significant (p > 0.05). D The binding affinity between DC-SIGN and purified DENV2 virions measured by SPR. E The binding affinity between DC-SIGN (R309A/R312A) and purified DENV2 virions measured by SPR.G The binding affinity between mosGCTL-AAEL011408 and purified DENV2 virions measured by SPR.
Figure 5B The AOF prediction of the T226K substitution (left panel) and the G228E substitution (right panel) in the DENV2 Asian I genotype.C The AOF prediction of the T226K substitution (left panel) and the G228E substitution (right panel) in the DENV2 Cosmopolitan genotype.The performance of the GPR-2 in modeling the prevalence of the DENV2 Asian I genotype.E The prevalence of the DENV2 Cosmopolitan genotype predicted by the GPR-2 model (orange dashed line + squares). The orange shadow denotes the predicted prevalence range of the DENV2 Cosmopolitan genotype, with the AOF of T226K/G228E substitutions predicted by the numerical kinetics, GPR-1, and support vector machine (SVR) models serving as the GPR-2 input data.
Figure 1Schematic of single‐plane acquisition FRAP on endogenously tagged Swi6‐EGFP. Representative still images of a FRAP experiment are shown. See also Movie EV1. Green sphere: yeast nucleus containing Swi6‐EGFP; green dots: heterochromatic Swi6‐EGFP; red circle: bleached area.Normalized average intensities (black dots) of FRAP on Swi6‐EGFP heterochromatic loci (n = 31) fitted to a one‐component model (blue line). The dashed lines indicate the final relative intensity that is set to 1 and the fluorescence half‐recovery time (t 1/2).Fluorescence t 1/2 values of FRAP on Swi6‐EGFP heterochromatic loci. The box bounds the interquartile range (IQR) divided by the median, and whiskers extend to a maximum of 1.5 × IQR beyond the box.Normalized fluorescence recovery values of FRAP on Swi6‐EGFP heterochromatic loci. The box bounds the interquartile range (IQR) divided by the median, and whiskers extend to a maximum of 1.5 × IQR beyond the box.FLIP experiment showing a bleached (FRAP, red circle) and unbleached, adjacent locus (FLIP, blue circle) in the same nucleus. The graph displays average relative fluorescence of FLIP (blue), FRAP (red), and control loci (no bleach, green) in other non‐bleached cells.Schematic of a line‐scan FRAP experiment. Fluorescence intensities are measured along a line of a non‐bleached nucleus (Ctrl nucleus) and a bleached nucleus (FRAP nucleus) in Swi6‐EGFP clr4∆ cells. Red box: bleached region. Right: raw data example.Average relative intensities of a line‐scan FRAP experiment on Swi6‐EGFP in heterochromatin (blue line), euchromatin (green line), and clr4∆ (red line). The curves have a gliding average of 40.
Figure 2A, BAverage relative intensities over time and corresponding fluorescence t 1/2 values of heterochromatic Swi6 obtained from FRAP experiments performed with cells expressing NLS‐Swi6‐EGFP (blue) or NLS‐Swi6‐KR25A‐EGFP (red).C, DAverage relative intensities over time and corresponding fluorescence t 1/2 values of heterochromatic Swi6 obtained from FRAP experiments performed with wild‐type (brown) or cid14∆ (dark green) cells expressing Swi6‐EGFP.E, FAverage relative intensities over time and corresponding fluorescence t 1/2 values of heterochromatic Swi6 obtained from FRAP experiments performed with wild‐type cells expressing heterochromatic NLS‐Swi6‐EGFP (blue) or NLS‐Swi6 KR25A‐EGFP (red), or cid14∆ cells expressing NLS‐Swi6‐EGFP (green) or NLS‐Swi6‐KR25A‐EGFP (yellow).Data information: In (B), (D) and (F), the box bounds the interquartile range (IQR) divided by the median, and whiskers extend to a maximum of 1.5 × IQR beyond the box.
Figure 3Schematic of a chromosome indicating Swi6‐EGFP heterochromatic domains (green). Cnp1‐mCherry and Taz1‐mCherry (red) mark centromeres and telomeres, respectively. Representative images demonstrating Swi6‐EGFP co‐localization with centromeres (Cnp1‐mCherry) and telomeres (Taz1‐mCherry) are shown.Fluorescence t 1/2 values of centromeric or telomeric Swi6 obtained from FRAP experiments performed with cells expressing NLS‐Swi6‐EGFP.Fluorescence t 1/2 values of centromeric or telomeric Swi6 obtained from FRAP experiments performed with cells expressing the RNA‐binding mutant NLS‐Swi6‐KR25A‐EGFP.Fluorescence t 1/2 values of centromeric or telomeric Swi6 obtained from FRAP experiments performed with cells expressing Swi6‐EGFP.Fluorescence t 1/2 values of centromeric Swi6 obtained from FRAP experiments performed after release of cells expressing NLS‐Swi6‐EGFP (black dots) or the RNA‐binding mutant NLS‐Swi6‐KR25A‐EGFP (red dots) from G1/S cell cycle arrest. Each dot represents one FRAP experiment at the respective time after release from cell cycle arrest. Swi6 is dispersed in M phase due to H3S10 phosphorylation, and M phase was therefore not included in the FRAP analysis.Fluorescence t 1/2 values obtained from FRAP experiments performed on centromeric Swi6. A total of 40, 66, and 104 individual cells residing in the G1, S, and G2 phases of the cell cycle were analyzed, respectively. Representative bright‐field images of cells in G1, S, or G2 are shown. Scale bars = 2 μm.Fluorescence t 1/2 values obtained from FRAP experiments performed on centromeric Swi6 of cells expressing NLS‐Swi6‐EGFP and NLS‐Swi6‐KR25A‐EGFP that reside in the G2 of the cell cycle.Fluorescence t 1/2 values of centromeric or telomeric Swi6 obtained from FRAP experiments performed with cells expressing the RNA‐binding mutant NLS‐Swi6‐KR25A‐EGFP.
Figure 4H3K9me2 ChIP‐seq enrichment profiles for swi6+ and swi6∆ cells on centromere 1. Centromeric repeat elements (dg/dh) are indicated. Inverted repeats (IRC1) constitute heterochromatin boundaries in wild‐type cells (Cam et al, 2005). The y‐axes represent log2 ChIP‐seq enrichments in 200‐bp genomically tiled windows calculated over clr4Δ cells. Two independent biological replicates for each genotype were performed (replicates 1 and 2). Positions of genomic elements on the plus and minus strands are indicated. Blue, protein‐coding genes; white, repeats; green, long terminal repeat (LTR).H3K9me2 ChIP‐seq enrichment profiles for swi6+ and swi6∆ cells on the telomere of the right arm of chromosome 1. Two independent biological replicates for each genotype were performed (replicates 1 and 2).Differential expression of transcripts coming from centromere 1 assessed by tiling microarray gene expression analysis. Expression data for swi6+ and swi6∆ cells were taken from a previous publication (Woolcock et al, 2012).
Figure 5C-EH3K9me2 levels on heterochromatin‐adjacent genes assessed by ChIP-PCR in swi6+, swi6∆, and swi6‐L315E (CSD dimerization mutant) (C), swi6‐W104A (H3K9me2 binding mutant) (D), and epe1∆ (E) cells. Enrichments over clr4∆ are normalized to adh1+. Average fold enrichment with s.d. is shown for three (C and E) or four (D) independent experiments. P‐values were generated by the Student's t‐test (two‐tailed distribution, two‐sample, unequal variance).
Figure 6sRNA reads mapping to centromere 1 in swi6+ (green) and swi6∆ (blue) cells. The dashed red box highlights the loss of brdrRNAs at the IRC1R in the absence of Swi6. Centromeric repeat elements and the central core are indicated. Counts were normalized to the library size. Asterisks denote tRNA fragments. Note that tRNA genes flank IRC3 (Fig EV4) but not IRC1R.H3K9me2 levels on heterochromatin‐adjacent genes assessed by ChIP-PCR in swi6+, swi6∆, tas3 L479E, and tas3 L479E swi6∆ cells. Enrichments over clr4∆ are normalized to adh1+. Average fold enrichment with s.d. is shown for three independent experiments. P‐values were generated by Student's t‐test (two‐tailed distribution, two‐sample, unequal variance).