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Series GSE133292

Query DataSets for GSE133292

Status

Public on Dec 31, 2019

Title

The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence

Organism

Experiment type

Other
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing

Summary

Heterochromatin remodeling is critical for various cell processes. In particular, the “loss of heterochromatin” phenotype in cellular senescence engages with the progress of aging and age-related disorders. Although biological processes of senescent cells including senescence-associated heterochromatin foci (SAHF) formation, chromosome compaction and entry into senescence have been closely associated with high-order chromatin structure. the relationship between the high-order chromatin organization and the loss of heterochromatin phenotype during senescence has not been fully understood. By using senescent and late senescent fibroblasts induced by DNA damage harboring the “loss of heterochromatin” phenotype, we observed progressive 3D reorganization of heterochromatin during senescence. Facultative and constitutive heterochromatin marked by H3K27me3 and H3K9me3, respectively, showed different alterations. Facultative heterochromatin tends to switch from the repressive B-compartment to the active A-compartment, whereas constitutive heterochromatin shows no significant changes at the compartment level but enhanced interactions between themselves. Interestingly, both types show increased chromatin accessibility and gene expression leakage during senescence. Furthermore, increased chromatin accessibility in potential CTCF binding sites accompanies by the establishment of novel loops in constitutive heterochromatin. Finally, we also observed aberrant expression of repetitive elements, including LTR (long terminal repeat) and satellite classes. Overall, facultative and constitutive heterochromatin show multiscale but distinct alterations in the 3D map, meanwhile they also share the same features of increased chromatin accessibility and gene expression leakage. This study provides an epigenomic map of heterochromatin reorganization during senescence.

Overall design

We build five cell states including growing, quiescence, senescence, deep senescence with human diploid BJ fibroblasts and carried out Hi-C, ATAC-seq,RNA-seq and ChIP-seq.

Contributor(s)

Citation(s)

Submission date

Jun 25, 2019

Last update date

Jun 28, 2021

Contact name

Xianglin Zhang

E-mail(s)

xl-zhang15@mails.tsinghua.edu.cn

Phone

15101669184

Organization name

Tsinghua University

Street address

Haidian District

City

Beijing

State/province

Beijing

ZIP/Postal code

100084

Country

China

Platforms (3)

GPL16791	Illumina HiSeq 2500 (Homo sapiens)
GPL20795	HiSeq X Ten (Homo sapiens)
GPL24676	Illumina NovaSeq 6000 (Homo sapiens)

Samples (46)

More...

GSM3905152	Foreskin fibroblasts, Hi-C growing rep1
GSM3905153	Foreskin fibroblasts, Hi-C growing rep2
GSM3905154	Foreskin fibroblasts, Hi-C quiescence rep1

GSM3905155	Foreskin fibroblasts, Hi-C quiescence rep2
GSM3905156	Foreskin fibroblasts, Hi-C senescence rep1
GSM3905157	Foreskin fibroblasts, Hi-C senescence rep2
GSM3905158	Foreskin fibroblasts, Hi-C deep senescence rep1
GSM3905159	Foreskin fibroblasts, Hi-C deep senescence rep2
GSM3905160	Foreskin fibroblasts, Hi-C reversal of senescence rep1
GSM3905161	Foreskin fibroblasts, Hi-C reversal of senescence rep2
GSM3905162	Foreskin fibroblasts, RNA-seq growing rep1
GSM3905163	Foreskin fibroblasts, RNA-seq growing rep2
GSM3905164	Foreskin fibroblasts, RNA-seq quiescence rep1
GSM3905165	Foreskin fibroblasts, RNA-seq quiescence rep2
GSM3905166	Foreskin fibroblasts, RNA-seq senescence rep1
GSM3905167	Foreskin fibroblasts, RNA-seq senescence rep2
GSM3905168	Foreskin fibroblasts, RNA-seq deep senescence rep1
GSM3905169	Foreskin fibroblasts, RNA-seq deep senescence rep2
GSM3905170	Foreskin fibroblasts, RNA-seq reversal of senescence rep1
GSM3905171	Foreskin fibroblasts, RNA-seq reversal of senescence rep2
GSM4295137	Foreskin fibroblasts, ATAC-seq growing rep1
GSM4295138	Foreskin fibroblasts, ATAC-seq growing rep2
GSM4295139	Foreskin fibroblasts, ATAC-seq quiescence rep1
GSM4295140	Foreskin fibroblasts, ATAC-seq quiescence rep2
GSM4295141	Foreskin fibroblasts, ATAC-seq senescence rep1
GSM4295142	Foreskin fibroblasts, ATAC-seq senescence rep2
GSM4295143	Foreskin fibroblasts, ATAC-seq deep senescence rep1
GSM4295144	Foreskin fibroblasts, ATAC-seq deep senescence rep2
GSM4295145	Foreskin fibroblasts, ATAC-seq reversal of senescence rep1
GSM4295146	Foreskin fibroblasts, ATAC-seq reversal of senescence rep2
GSM4981040	growing cells - H3K9me3_rep1
GSM4981041	growing cells - H3K9me3_rep2
GSM4981042	quiescent cells - H3K9me3_rep1
GSM4981043	quiescent cells - H3K9me3_rep2
GSM4981044	senescent cells - H3K9me3_rep1
GSM4981045	senescent cells - H3K9me3_rep2
GSM4981046	deep senescent cells - H3K9me3_rep1
GSM4981047	deep senescent cells - H3K9me3_rep2
GSM4981048	growing cells - H3K27me3_rep1
GSM4981049	growing cells - H3K27me3_rep2
GSM4981050	quiescent cells - H3K27me3_rep1
GSM4981051	quiescent cells - H3K27me3_rep2
GSM4981052	senescent cells - H3K27me3_rep1
GSM4981053	senescent cells - H3K27me3_rep2
GSM4981054	deep senescent cells - H3K27me3_rep1
GSM4981055	deep senescent cells - H3K27me3_rep2

Relations

BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE133292_DS_cat.fithic.txt.gz	124.8 Mb	(ftp)(http)	TXT
GSE133292_DS_cat_1Mb.iced_contact_map.txt.gz	24.6 Mb	(ftp)(http)	TXT
GSE133292_DS_cat_40kb.iced_contact_map.txt.gz	556.6 Mb	(ftp)(http)	TXT
GSE133292_G_cat.fithic.txt.gz	137.7 Mb	(ftp)(http)	TXT
GSE133292_G_cat_1Mb.iced_contact_map.txt.gz	24.6 Mb	(ftp)(http)	TXT
GSE133292_G_cat_40kb.iced_contact_map.txt.gz	521.5 Mb	(ftp)(http)	TXT
GSE133292_Q_cat.fithic.txt.gz	136.2 Mb	(ftp)(http)	TXT
GSE133292_Q_cat_1Mb.iced_contact_map.txt.gz	24.7 Mb	(ftp)(http)	TXT
GSE133292_Q_cat_40kb.iced_contact_map.txt.gz	602.2 Mb	(ftp)(http)	TXT
GSE133292_RAW.tar	7.4 Gb	(http)(custom)	TAR (of BW, NARROWPEAK, TXT)
GSE133292_RS_cat.fithic.txt.gz	136.8 Mb	(ftp)(http)	TXT
GSE133292_RS_cat_1Mb.iced_contact_map.txt.gz	24.5 Mb	(ftp)(http)	TXT
GSE133292_RS_cat_40kb.iced_contact_map.txt.gz	470.5 Mb	(ftp)(http)	TXT
GSE133292_S_cat.fithic.txt.gz	130.4 Mb	(ftp)(http)	TXT
GSE133292_S_cat_1Mb.iced_contact_map.txt.gz	24.5 Mb	(ftp)(http)	TXT
GSE133292_S_cat_40kb.iced_contact_map.txt.gz	505.9 Mb	(ftp)(http)	TXT
GSE133292_five_conditions.Counts.txt.gz	594.6 Kb	(ftp)(http)	TXT
GSE133292_five_condtions.FPKM.txt.gz	2.4 Mb	(ftp)(http)	TXT
GSE133292_genomic_intervals.1Mb.bed.gz	17.2 Kb	(ftp)(http)	BED
GSE133292_genomic_intervals.20kb.bed.gz	938.2 Kb	(ftp)(http)	BED
GSE133292_genomic_intervals.40kb.bed.gz	464.7 Kb	(ftp)(http)	BED
SRA Run Selector
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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