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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 Homo sapiens
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) Wang X, Xie W
Citation(s) 34140314
Submission date Jun 25, 2019
Last update date Jun 28, 2021
Contact name Xianglin Zhang
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)
GSM3905152 Foreskin fibroblasts, Hi-C growing rep1
GSM3905153 Foreskin fibroblasts, Hi-C growing rep2
GSM3905154 Foreskin fibroblasts, Hi-C quiescence rep1
BioProject PRJNA551006
SRA SRP212073

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
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