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| Status |
Public on Feb 23, 2023 |
| Title |
Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Chromatin features are widely used for genome-scale mapping of enhancers. However, discriminating active enhancers from other cis-regulatory elements, predicting enhancer strength, and identifying their target genes remains challenging. Here we establish histone H2B N-terminus multisite lysine acetylation (H2BNTac) as a genuine signature of active enhancers. H2BNTac prominently marks candidate active enhancers and a subset of promoters and discriminates them from ubiquitously active promoters. Two mechanisms afford the distinct H2BNTac specificity. (1) Unlike H3K27ac, H2BNTac is specifically catalyzed by CBP/p300. (2) H2A-H2B, but not H3-H4, are rapidly exchanged through transcription-induced nucleosome remodeling. H2BNTac-positive candidate enhancers show a high validation rate in orthogonal enhancer activity assays, and a vast majority of endogenously active enhancers are marked by H2BNTac and H3K27ac. Notably, H2BNTac intensity predicts enhancer strength and outperforms the current state-of-the-art models in predicting CBP/p300 target genes. These findings have broad implications for generating fine-grained enhancer maps and modeling CBP/p300-dependent gene regulation.
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| Overall design |
H2BNTac ChIP-seq before and after A-485 treatment in mES cell grown in 2i. As a reference, H3K9ac, H3K4me3, H3K27ac, H3K27me3, Med1 ChIP-seq are included. H2BK20ac and H3K27ac ChIP-seq in K562 cell are included.
H3K27ac and H2BK20ac ChIP seq were performed in mouse ESC and human K562 cell lines.
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| Contributor(s) |
Narita T, Higashijima Y, Choudhary C |
| Citation(s) |
37024579 |
| |
| Submission date |
Oct 21, 2021 |
| Last update date |
May 25, 2023 |
| Contact name |
Chunarum Choudhary |
| E-mail(s) |
chuna.choudhary@cpr.ku.dk
|
| Organization name |
University of Copenhagen
|
| Department |
Novo Nordisk Foundation Center for Protein Research
|
| Lab |
Choudhary Group
|
| Street address |
Blegdamsvej 3B
|
| City |
Copenhagen N |
| State/province |
--- Select a state --- |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (41)
|
| GSM5645994 |
H2BK5ac (CST12799) ChIP in ESC rep2 |
| GSM5645995 |
H2BK5ac (CST12799) ChIP in ESC rep3 |
| GSM5645996 |
H2BK5ac (CST12799) ChIP in ESC rep4 |
| GSM5645997 |
H2BK5ac (CST12799) ChIP in ESC after A-485 5min treatment, rep1 |
| GSM5645998 |
H2BK5ac (CST12799) ChIP in ESC after A-485 5min treatment, rep2 |
| GSM5645999 |
H2BK5ac (CST 12799) ChIP in ESC after A-485 15min treatment, rep1 |
| GSM5646000 |
H2BK5ac (CST12799) ChIP in ESC after A-485 15min treatment, rep2 |
| GSM5646001 |
H2BK5ac (ab40866) ChIP in ESC rep1 |
| GSM5646002 |
H2BK5ac (ab40866) ChIP in ESC after A-485 5min treatment, rep1 |
| GSM5646003 |
H2BK5ac (ab40866) ChIP in ESC after A-485 15min treatment, rep1 |
| GSM5646004 |
H2BK12ac (ab40883) ChIP in ESC rep1 |
| GSM5646005 |
H2BK12ac (ab40883) ChIP in ESC rep2 |
| GSM5646006 |
H2BK12ac(ab40883) ChIP in ESC after A-485 5min treatment, rep1 |
| GSM5646007 |
H2BK12ac(ab40883) ChIP in ESC after A-485 15min treatment, rep1 |
| GSM5646008 |
H2BK12ac(ab40883) ChIP in ESC after A-485 15min treatment, rep2 |
| GSM5646009 |
H2BK16ac (ab177427) ChIP in ESC rep1 |
| GSM5646010 |
H2BK16ac (ab177427) ChIP in ESC rep2 |
| GSM5646011 |
H2BK16ac (ab177427) ChIP in ESC after A-485 5min treatment rep1 |
| GSM5646012 |
H2BK16ac (ab177427) ChIP in ESC after A-485 15min treatment rep1 |
| GSM5646013 |
H2BK16ac (ab177427) ChIP in ESC after A-485 15min treatment rep2 |
| GSM5646014 |
H2BK20ac (ab177430) ChIP in ESC rep1 |
| GSM5646015 |
H2BK20ac (ab177430) ChIP in ESC rep2 |
| GSM5646016 |
H2BK20ac (CST34156) ChIP in ESC rep1 |
| GSM5646017 |
H2BK20ac (ab177430) ChIP in ESC after A-485 5min treatment rep1 |
| GSM5646018 |
H2BK20ac (ab177430) ChIP in ESC after A-485 15min treatment rep1 |
| GSM5646019 |
H2BK20ac (ab177430) ChIP in ESC after A-485 15min treatment rep2 |
| GSM5646020 |
H2BK20ac (CST34156) ChIP in ESC after A-485 15min treatment rep1 |
| GSM5646021 |
H3K4me3 ChIP in ESC rep1 |
| GSM5646022 |
H3K27ac (ab4729) ChIP in ESC rep1 |
| GSM5646023 |
H3K27me3 ChIP in ESC rep1 |
| GSM5646024 |
H3K9ac ChIP in ESC rep1 |
| GSM5866899 |
H3K27ac ChIP in K562 cell line rep1 |
| GSM5866900 |
H2BK20ac ChIP in K562 cell line rep1 |
| GSM5866901 |
H2BK20ac ChIP in K562 cell line rep2 |
| GSM5866902 |
Input of K562 |
| GSM6372101 |
H2BK20ac (CST34156) ChIP in ESC |
| GSM6372102 |
H2BK20ac (CST34156) ChIP in ESC after NVP2 120min treatment rep1 |
| GSM6372103 |
H2BK11ac ChIP in ESC rep1 |
|
| Relations |
| BioProject |
PRJNA773732 |
| SRA |
SRP342694 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE186349_ESC_A485_10uM_TC15_H2BK12ac.ab40883_CC8.CC15.n2.smooth.bw |
794.2 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_A485_10uM_TC15_H2BK16ac.ab177427_CC8.CC15.n2.smooth.bw |
787.7 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_A485_10uM_TC15_H2BK20ac.CST34156_CC15.n2.smooth.bw |
721.2 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_A485_10uM_TC15_H2BK20ac.ab177430_CC8.CC15.n2.smooth.bw |
772.3 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_A485_10uM_TC15_H2BK5ac.CST12799_CC1.n2.smooth.bw |
824.5 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_A485_10uM_TC15_H2BK5ac.ab40886_CC8.n2.smooth.bw |
701.8 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_A485_10uM_TC5_H2BK12ac.ab40883_CC8.n2.smooth.bw |
743.3 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_A485_10uM_TC5_H2BK16ac.ab177427_CC8.n2.smooth.bw |
712.9 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_A485_10uM_TC5_H2BK20ac.ab177430_CC8.n2.smooth.bw |
713.9 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_A485_10uM_TC5_H2BK5ac.CST12799_CC1.n2.smooth.bw |
827.0 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_A485_10uM_TC5_H2BK5ac.ab40886_CC8.n2.smooth.bw |
682.2 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_H2BK11ac.RM456_CC20.n2.smooth.bw |
739.3 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_H2BK11ac.RM456_CC20_peak.bed.gz |
78.4 Kb |
(ftp)(http) |
BED |
| GSE186349_ESC_Ctrl_TC0_H2BK12ac.ab40883_CC8.CC15.n2.smooth.bw |
790.0 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_H2BK12ac.ab40883_CC8.CC15_peak.bed.gz |
89.1 Kb |
(ftp)(http) |
BED |
| GSE186349_ESC_Ctrl_TC0_H2BK16ac.ab177427_CC8.CC15.n2.smooth.bw |
765.4 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_H2BK16ac.ab177427_CC8.CC15_peak.bed.gz |
195.1 Kb |
(ftp)(http) |
BED |
| GSE186349_ESC_Ctrl_TC0_H2BK20ac.CST34156_CC15.n2.smooth.bw |
674.8 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_H2BK20ac.CST34156_CC27.n2.smooth.bw |
746.3 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_H2BK20ac.ab177430.CST34156_CC8.CC15_peak.bed.gz |
199.4 Kb |
(ftp)(http) |
BED |
| GSE186349_ESC_Ctrl_TC0_H2BK20ac.ab177430_CC8.CC15.n2.smooth.bw |
764.2 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_H2BK5ac.CST12799_CC1.CC11.CC15.n2.smooth.bw |
854.1 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_H2BK5ac.CST12799_CC1.CC11.CC15_peak.bed.gz |
98.3 Kb |
(ftp)(http) |
BED |
| GSE186349_ESC_Ctrl_TC0_H2BK5ac.ab40886_CC8.n2.smooth.bw |
660.3 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_H2BK5ac.ab40886_CC8_peak.bed.gz |
242.4 Kb |
(ftp)(http) |
BED |
| GSE186349_ESC_Ctrl_TC0_H3K27ac.ab4729_CC1.CC11.n2.smooth.bw |
808.0 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_H3K27ac.ab4729_CC1.CC11_peak.bed.gz |
232.3 Kb |
(ftp)(http) |
BED |
| GSE186349_ESC_Ctrl_TC0_H3K27me3_CC8.n2.smooth.bw |
706.3 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_H3K27me3_CC8_peak.bed.gz |
267.0 Kb |
(ftp)(http) |
BED |
| GSE186349_ESC_Ctrl_TC0_H3K4me3_CC10.n2.smooth.bw |
640.1 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_H3K4me3_CC10_peak.bed.gz |
197.3 Kb |
(ftp)(http) |
BED |
| GSE186349_ESC_Ctrl_TC0_H3K9ac_CC14.n2.smooth.bw |
735.4 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_H3K9ac_CC14_peak.bed.gz |
238.6 Kb |
(ftp)(http) |
BED |
| GSE186349_ESC_Ctrl_TC0_Med1_dfix_CC10.CC12.n2.smooth.bw |
736.3 Mb |
(ftp)(http) |
BW |
| GSE186349_ESC_Ctrl_TC0_Med1_dfix_Spike.HEK293_CC10.CC12_peak.bed.gz |
254.2 Kb |
(ftp)(http) |
BED |
| GSE186349_ESC_NVP2_100nM_TC120_H2BK20ac.CST34156_CC27.n2.smooth.bw |
748.7 Mb |
(ftp)(http) |
BW |
| GSE186349_K562_Ctrl_TC0_H2BK20ac.ab177430.CST34156_CC16.CC20.n2.smooth.bw |
752.6 Mb |
(ftp)(http) |
BW |
| GSE186349_K562_Ctrl_TC0_H2BK20ac.ab177430.CST34156_CC16.CC20_peak.bed.gz |
198.5 Kb |
(ftp)(http) |
BED |
| GSE186349_K562_Ctrl_TC0_H3K27ac.ab4729_CC10.n2.smooth.bw |
625.4 Mb |
(ftp)(http) |
BW |
| GSE186349_K562_Ctrl_TC0_H3K27ac_CC10_peak.bed.gz |
193.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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