|
| Status |
Public on Mar 27, 2020 |
| Title |
DNMT1 drives 4D genome rewiring during oncogene induced senescence |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Other
Methylation profiling by high throughput sequencing
|
| Summary |
While, transcriptional and epigenetic changes associated senescence processes are well studied, the 3D chromatin changes associated with it remains elusive. In this study, we have generated genome wide chromatin interaction maps (Hi-C), epigenetic (ChIP-Seq), replication-timing and gene expression (RNA-Seq) profiles from replication induced (RS) and oncogene induced (OIS) senescent cells. As senescence associated heterochromatin foci (SAHFs) differentiates both RS and OIS nuclei, we identified the regions that constitute SAHFs and called them Senescence Associated Heterochromatin Domains (SAHDs). Further, screening of candidate factors for SAHF induction allowed us to identify DNMT1 as a novel component that induces SAHFs by stimulation of HMGA2 expression. DNMT1 depletion does not reverse the senescence process, however, instead, depleted cells transition to a 3D genome conformation akin to that of cells in replicative senescence, suggesting that acute senescence induction (OIS) involves SAHF formation in addition to the RS-dependent 3D genome rewiring.
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| |
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| Overall design |
Hi-C, RNAseq, ChIPseq, WGBS in huamn proliferative and senescent fibroblats
|
| |
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| Contributor(s) |
Sati S, Bonev B, Szabo Q, Bensadoun P, Loubiere V, Papadopoulos GL, Bantignies F, Fritsch L, Lemaitre J, Cavalli G |
| Citation(s) |
32220303 |
| |
| Submission date |
Apr 25, 2019 |
| Last update date |
Jun 10, 2020 |
| Contact name |
Satish Sati |
| E-mail(s) |
satisatish16@gmail.com
|
| Phone |
+12675863881
|
| Organization name |
University of Pennsylvania
|
| Department |
Dermatology
|
| Lab |
Thomas Leung
|
| Street address |
421 Curie Blvd, BRB 1039
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (92)
|
|
| Relations |
| BioProject |
PRJNA535444 |
| SRA |
SRP193843 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE130306_ChIP_OISD0_H3K27me3.bw |
642.4 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD0_H3K27me3_peaks.bed.gz |
106.1 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_OISD0_H3K4me3.bw |
322.1 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD0_H3K4me3_peaks.bed.gz |
751.7 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_OISD0_H3K9me3.bw |
655.9 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD0_H3K9me3_peaks.bed.gz |
35.0 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_OISD0_IN.bw |
529.1 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD10_H3K27me3_peaks.bed.gz |
132.0 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_OISD10_H3K27me3_rpm.bw |
535.2 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD10_H3K4me3_peaks.bed.gz |
558.6 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_OISD10_H3K4me3_rpm.bw |
502.2 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD10_H3K9me3_peaks.bed.gz |
65.7 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_OISD10_H3K9me3_rpm.bw |
530.6 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD10_IN_rpm.bw |
513.1 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD2_H3K27me3.bw |
681.1 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD2_H3K27me3_peaks.bed.gz |
111.7 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_OISD2_H3K4me3.bw |
410.5 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD2_H3K4me3_peaks.bed.gz |
667.9 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_OISD2_H3K9me3.bw |
374.8 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD2_H3K9me3_peaks.bed.gz |
69.6 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_OISD2_IN_rpm.bw |
378.5 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD6_H3K27me3_peaks.bed.gz |
118.9 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_OISD6_H3K27me3_rpm.bw |
593.3 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD6_H3K4me3_peaks.bed.gz |
501.6 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_OISD6_H3K4me3_rpm.bw |
492.4 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD6_H3K9me3_peaks.bed.gz |
33.1 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_OISD6_H3K9me3_rpm.bw |
644.8 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_OISD6_IN_rpm.bw |
517.5 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_RS_Proliferative_H3K27me3.bw |
533.5 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_RS_Proliferative_H3K27me3_peaks.bed.gz |
113.6 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_RS_Proliferative_H3K4me3_peaks.bed.gz |
499.1 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_RS_Proliferative_H3K4me3_rpm.bw |
523.5 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_RS_Proliferative_H3K9me3_peaks.bed.gz |
33.2 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_RS_Proliferative_H3K9me3_rpm.bw |
588.9 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_RS_Proliferative_IN.bw |
660.2 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_RS_Senescent_H3K27me3_peaks.bed.gz |
139.9 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_RS_Senescent_H3K27me3_rpm.bw |
524.1 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_RS_Senescent_H3K4me3_peaks.bed.gz |
800.0 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_RS_Senescent_H3K4me3_rpm.bw |
385.1 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_RS_Senescent_H3K9me3_peaks.bed.gz |
146.4 Kb |
(ftp)(http) |
BED |
| GSE130306_ChIP_RS_Senescent_H3K9me3_rpm.bw |
586.0 Mb |
(ftp)(http) |
BW |
| GSE130306_ChIP_RS_Senescent_IN_rpm.bw |
518.1 Mb |
(ftp)(http) |
BW |
| GSE130306_RAW.tar |
132.1 Gb |
(http)(custom) |
TAR (of TAR, TXT) |
| GSE130306_siDNMT1_CpG.bw |
79.4 Mb |
(ftp)(http) |
BW |
| GSE130306_siNT_CpG.bw |
204.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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