The corrected Figure S1J is shown below. The text changes are as follows, with additions in bold and deletions in bracketed italics:

Transcription

1 Correction H3K4me3 readth Is Linked to Cell Identity and Transcriptional Consistency érénice A. enayoun, Elizabeth A. Pollina, Duygu Ucar, Salah Mahmoudi, Kalpana Karra, Edith D. Wong, Keerthana Devarajan, Aaron C. Daugherty, Anshul. Kundaje, Elena Mancini, enjamin C. Hitz, Rakhi Gupta, Thomas A. Rando, Julie C. aker, Michael P. Snyder, J. Michael Cherry, and Anne runet* *Correspondence: (Cell 158, , July 31, 214) Our paper reported that broad H3K4me3 domains in a given cell type are associated with genes that are important for the identity/function of that cell type and that they are associated with increased transcriptional consistency, but not increased expression. It has come to our attention that we made a programming error in the code used to generate Figure S1J. When the code is corrected, the top 5% broadest H3K4me3 domains display a statistically significant increased expression compared to the rest of the distribution (see corrected Figure S1J below). In addition, if one uses the rank-based Spearman correlation instead of the Pearson correlation we had used, H3K4me3 breadth exhibits a positive correlation with gene expression. Thus, the correct conclusion is that broad H3K4me3 domains are, on average, more expressed than non-broad H3K4me3 domains. This error does not affect our conclusions that H3K4me3 breadth is associated with cell identity and transcriptional consistency. However, we acknowledge that the increased transcriptional consistency of genes marked by broad H3K4me3 domains could be due to their increased average expression, as normalized transcriptional variability and average expression have been observed to be anti-correlated. The corrected Figure S1J is shown below. The text changes are as follows, with additions in bold and deletions in bracketed italics: Summary: Indeed, genes marked by the broadest H3K4me3 domains exhibit enhanced transcriptional consistency and [rather than] increased transcriptional levels. Page 674, second paragraph of Results: H3K4me3 breadth quantiles did not linearly correlate with mrna levels (Figures 1D and 1E, Pearson correlation). However, H3K4me3 breadth showed positive rank correlation with mrna levels (R , Spearman correlation). In addition, the top 5% broadest H3K4me3 domains were more highly expressed on average compared to the rest of the distribution (Figure S1J) [even when comparing the most extreme example to the rest of the distribution (Figure S1J)]. Thus, broad H3K4me3 domains are present in many cell types across taxa but cannot be explained as simple readouts of promoter complexity [or high expression levels]. Figure 1 title: readth Is an Evolutionarily Conserved Feature [that Is Not Predictive of Expression Levels] After we identified this programming error, we had the entire manuscript and lines of code independently scrutinized. This process identified the following inadvertent errors that do not affect our conclusions but that we would like to correct. In Figures 1E and S6A, there was an incorrect attribution of datasets (C2C12 myotubes for myoblasts and H1 hesc population for single cells). The corrected Figures 1E and S6A are shown below. The conclusions are not changed. In Figures 7D, 7E, 7G, and S7L, the statistical analyses were done using two different tests (one-sided one-sample and one-sided two-sample Wilcoxon tests), but only one set of p values was reported in the original panels, and the corresponding statistical tests were not appropriately described. Results from both tests are shown in updated Figures 7D, 7E, 7G, and S7L. Upper p values (7D, 7G), black lines (7E, S7L): one-sided two-sample Wilcoxon tests for increased variability between genes with maintained versus changed H3K4me3 breath. Lower p values (7D, 7G), gray lines (7E, S7L): one-sided one-sample Wilcoxon tests for increased variability between genes with changed H3K4me3 breadth versus the expectation of no change in variability. The overall conclusions are not changed. Cell 163, , November 19, 215 ª215 Elsevier Inc. 1281

2 We sincerely regret these errors and apologize for any inconvenience they may have caused. We would also like to thank Wei Li and Kaifu Chen from the aylor College of Medicine for alerting us to the discrepancy between the Pearson and Spearman correlation results and for helping us to identify the error in Figure S1J. A Distribution of H3K4me3 ChIP-seq peaks in Distribution of H3K4me3 ChIP-seq peaks in C2C12 myotubes Number of ChIP-seq peaks (Density of distribution) chr kb chr11 63,755, 63,76, 63,765, 86 chr9 11,25, 11,255, 2 OTU1 1,635, 1,64, 1,645, ZIC2 KLF H3K4me3 breadth (kb) C H3K4me3 signal around transcription start sites Number of ChIP-seq peaks (Density of distribution) chr17 34,255, H3K4me3 breadth (kb) Metazoans Metaphytes Fungi Mammals Human Mouse D. melanogaster C. elegans A. thaliana S. cerevisiae HeLa-S3 C2C12 myotubes S2 cells Embryos Leaves Cells chr7 1 1 kb chr7 134,515, 134,525, 1 Zfp747 74,51, 74,52, Mef2a 34,265, rd2 H3K4me3 domain breadth -5kb +5kb -5kb +5kb -5kb +5kb -5kb +5kb -5kb +5kb -5kb +5kb -5kb +5kb -5kb +5kb D H3K4me3 breadth and mrna levels () mrna levels (FPKM) % broad H3K4me3 domains Cell population R ~ Single cells 1-7 R ~ E H3K4me3 breadth and mrna levels (C2C12 myoblasts) mrna levels (FPKM) % broad H3K4me3 domains Cell population Single cells R ~ R ~ Figure 1. H3K4me3 readth Is an Evolutionarily Conserved Feature 1282 Cell 163, , November 19, 215 ª215 Elsevier Inc.

3 A C D E F G H Figure 7. Experimental Perturbation of H3K4me3 readth Results in Changes to Transcriptional Consistency Cell 163, , November 19, 215 ª215 Elsevier Inc. 1283

4 chr16 1M 5M M 5M M M M 5M M M 1M 5M M M A Skewness of breadth distribution H. sapiens (99) Skewed distribution.4 Symmetric distribution M. musculus (74) E MACS2 HOMER QuEST CCAT Liver one marrow Myotubes HOMER.947 QuEST C Read density and breadth () 95th percentile Read density per bp of MACS peak (tag per bp) H3K4me3 breadth quantile Spearman rank correlation of H3K4me3 breadth CCAT SICER chr17 chr15 chr18 5M M chr19 5M M M 5M D Read density per bp of MACS peak (tag per bp) chr2 M 5M M Read density and breadth (C2C12 myotubes) 95th percentile M 5M chr21 chr M chrx 5M H3K4me3 breadth quantile F Genomic localization in 1M 15M chry 5M chr1 1M 15M 2M M 5M chr2 Top 5% broadest H3K4me3 domains 1M 15M 2M M 5M 1M chr3 15M M 5M 1M 15M 5M 1M 15M chr4 chr all pairs correlated with p < 2.2E-38 chr14 1M 5M M 1M 15M M 5M 1M chr6 chr13 5M 1M 5M M 15M chr12 M 1M 5M M 1M 5M 1M 5M M 1M 5M chr8 chr11 chr7 G H3K4me3 breadth and gene length H -95% broad H3K4me3 domains I Associated gene length (kb) H3K4me3 breadth and TSS usage from PolII-ChIP Number of PolII peaks % broad H3K4me3 domains A GM HeLa-S HepG2 1 C2C12 myotubes K S2 cells Number of TSSs J H3K4me3 breadth and TSS usage from RNA-seq 5 ends -95% broad H3K4me3 domains H3K4me3 breadth and mrna levels Median normalized mrna levels (A.U.) H9 hescs A GM % broad H3K4me3 domains H9 hescs A549 GM HeLa-S3 1 chr1 3 6 chr9 HepG K562 1 C. el Embryos S2 cells E E E E-1 1.6E E-7 4.2E E E E-1 6.4E-7 1.2E-12 HeLa-S3 HepG2 K562 C2C12 C. el Embryos S2 cells NPCs Figure S1. road H3K4me3 Stretches Are Present in Different Cell Types and Organisms but Are Independent of Signal Intensity, Promoter Architecture, Gene Length, and Genomic Location, Related to Figure Cell 163, , November 19, 215 ª215 Elsevier Inc.

5 A Scaled log1(p value) for low transcriptional variability H3K4me3 breadth and transcriptional variability (single cells) LNCaP MCF 7 HCT 116 C2C12 myoblasts MEFs H3K4me3 domain breadth quantile (%) Intensity quantile (%) Transcriptional variability (cell populations, continued from Fig. 6C) -95% broad H3K4me3 domains C Transcriptional variability (cell populations) Scaled and normalized expression variance between replicates(a.u.) E-97 HUVECs 2.E E E E E E 51 MEFs C2C12 Myoblasts C2C12 Myotubes CH12 Kc167 A. thaliana leaves Scaled and normalized expression variance between replicates(a.u.) E 9 8.9E 23-95% broad H3K4me3 domains after exclusion of bivalent/poised genes Top 5% broadest H3K4me3 domains after exclusion of bivalent/poised genes D Transcriptional variability (cell populations) E H3K4me3 breadth and transcriptional consistency (cell populations, nascent RNA) Nornalized mean scaled variance of genes in sample set (A.U.) Signal-matched H3K4me3 promoters (N=1, samples) 1.1E 49 9.E 126 Scaled log1(p value) for low transcriptional variability IMR C.elegans embryos H3K4me3 domain breadth quantile (%) Intensity quantile (%) Figure S6. H3K4me3 readth Is Associated with Increased Transcriptional Consistency, Related to Figure 6 Cell 163, , November 19, 215 ª215 Elsevier Inc. 1285

6 A C D E F G H I J K L Figure S7. Effect of H3K4me3 Regulators on H3K4me3 readth and Transcriptional Consistency, Related to Figure Cell 163, , November 19, 215 ª215 Elsevier Inc.