|
| Status |
Public on Jul 28, 2016 |
| Title |
ZMYND8 reads the dual histone mark H3K4me1-H3K14ac to antagonize the expression of metastasis-linked genes |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
Histone acetylation, including acetylated H3K14 (H3K14ac), is generally linked to gene activation. Monomethylated histone H3 lysine 4 (H3K4me1), together with other gene-activating marks, denotes active genes. In contrast to usual gene-activating functions of H3K14ac and H3K4me1, we here show that the dual histone modification mark H3K4me1-H3K14ac is recognized by ZMYND8 (also called RACK7) and functions to counteract gene expression. We identified ZMYND8 as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 antagonizes the expression of metastasis-linked genes, and its knockdown increases the cellular invasiveness in vitro and in vivo. The plant homeodomain (PHD) and Bromodomain cassette in ZMYND8 mediates the combinatorial recognition of H3K4me1-H3K14ac and H3K4me0-H3K14ac by ZMYND8. These findings uncover an unexpected role for the signature H3K4me1-H3K14ac in attenuating gene expression and reveal a previously unknown metastasis-suppressive epigenetic mechanism in which ZMYND8's PHD-Bromo cassette couples H3K4me1-H3K14ac with repression of metastasis-linked genes.
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| |
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| Overall design |
i) ChIP-Seq data of ZMYND8, JARID1D, H3K4me1, H3K14ac, H3K4me3, and H3K27me3 in normal DU145 cells.
ii) ChIP-Seq data of H3K4me1 and H3K4me3 in shLuciferase-, shJARID1D-, or shZMYND8-treated DU145 cells.
iii) RNA-Seq data in shLuciferase-, shJARID1D-, or shZMYND8-treated DU145 cells.
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| |
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| Contributor(s) |
Lee MG, Li W |
| Citation(s) |
27477906 |
| Submission date |
Jun 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
JIE Lv |
| E-mail(s) |
lvjcmb@gmail.com
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Department of Computational Biology
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
|
| Samples (35)
|
|
| Relations |
| BioProject |
PRJNA324450 |
| SRA |
SRP076126 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE82260_H3K14ac.bgsub.Fnor.wig.gz |
107.9 Mb |
(ftp)(http) |
WIG |
| GSE82260_H3K27me3.bgsub.Fnor.wig.gz |
80.5 Mb |
(ftp)(http) |
WIG |
| GSE82260_H3K4me1-shControl.bgsub.Fnor.wig.gz |
112.2 Mb |
(ftp)(http) |
WIG |
| GSE82260_H3K4me1-shJARID1D.bgsub.Fnor.wig.gz |
110.2 Mb |
(ftp)(http) |
WIG |
| GSE82260_H3K4me1-shZMYND8.bgsub.Fnor.wig.gz |
116.4 Mb |
(ftp)(http) |
WIG |
| GSE82260_H3K4me1.bgsub.Fnor.wig.gz |
147.7 Mb |
(ftp)(http) |
WIG |
| GSE82260_H3K4me3-shControl.bgsub.Fnor.wig.gz |
64.6 Mb |
(ftp)(http) |
WIG |
| GSE82260_H3K4me3-shJARID1D.bgsub.Fnor.wig.gz |
62.3 Mb |
(ftp)(http) |
WIG |
| GSE82260_H3K4me3-shZMYND8.bgsub.Fnor.wig.gz |
59.9 Mb |
(ftp)(http) |
WIG |
| GSE82260_H3K4me3.bgsub.Fnor.wig.gz |
26.3 Mb |
(ftp)(http) |
WIG |
| GSE82260_Input-Control.uniq.wig.gz |
48.3 Mb |
(ftp)(http) |
WIG |
| GSE82260_Input-shJARID1D.uniq.wig.gz |
43.9 Mb |
(ftp)(http) |
WIG |
| GSE82260_Input-shZMYND8.uniq.wig.gz |
39.1 Mb |
(ftp)(http) |
WIG |
| GSE82260_JARID1D.bgsub.Fnor.wig.gz |
188.6 Mb |
(ftp)(http) |
WIG |
| GSE82260_JARID1D_input.Fnor.wig.gz |
124.3 Mb |
(ftp)(http) |
WIG |
| GSE82260_ZMYND8.bgsub.Fnor.wig.gz |
149.8 Mb |
(ftp)(http) |
WIG |
| GSE82260_ZMYND8_input.Fnor.wig.gz |
143.4 Mb |
(ftp)(http) |
WIG |
| GSE82260_genes.count_tracking.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE82260_input.Fnor.wig.gz |
78.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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