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Series GSE134620 Query DataSets for GSE134620
Status Public on Jun 24, 2020
Title TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [H3K27ac ChIP]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Within mammalian nuclear space, chromosomes are hierarchically folded into active (A) and inactive (B) compartments composed of topologically associating domains (TADs). Genomic regions interact with nuclear lamina, termed lamina-associated domains (LADs), associated with transcriptional repression. However, the molecular mechanisms underlying these 3D chromatin architectures remain undeciphered. Here, we demonstrate the role of a potential tumor suppressor, TOP1 Binding Arginine/Serine Rich Protein (TOPORS), in genome organization. Topors knockdown in mouse hepatocytes results in cell proliferation and migration promotion, as well as arrest in the S phase of the cell cycle. RNA-seq analysis shows that 373 genes are up-regulated, some of which are associated with nuclear structure, and 316 genes exhibit down-regulated, many related to metabolic process. Chromatin accessibility is inclined to alter in the intergenic regions, including enhancers. Chromatin-lamina interactions decrease globally, and the coverage of LADs reduces from 53.31% to 46.52%. Furthermore, Topors knockdown leads to significantly increasing interactions between A and B compartments in cis and in trans. Correspondingly, strength of TAD boundaries located at A/B borders is weakened. Collectively, our data reveal that TOPORS functions as a regulator in chromosome folding, providing novel insights into the architectural role of tumor suppressors in higher-order genome organization.
 
Overall design H3K27ac ChIP-seq data in Control and Topors knockdown cells.
 
Citation(s) 32113985
Submission date Jul 22, 2019
Last update date Sep 25, 2020
Contact name Bo Wen
E-mail(s) bowen75@fudan.edu.cn
Organization name Fudan University
Street address 130 Dongan Rd.
City ShangHai
ZIP/Postal code 200032
Country China
 
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (4)
GSM4276200 Control_1_H3K27ac
GSM4276201 Control_2_H3K27ac
GSM4276202 Topors_1_H3K27ac
This SubSeries is part of SuperSeries:
GSE134624 TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes
Relations
BioProject PRJNA555879
SRA SRP215891

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
GSE134620_RAW.tar 1.1 Gb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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