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Series GSE134623 Query DataSets for GSE134623
Status Public on Jun 24, 2020
Title TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [RNA-seq]
Organism Mus musculus
Experiment type Expression 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 RNA-seq data in Ctrl and Topors KD AML12 cells.
Citation(s) 32113985
Submission date Jul 22, 2019
Last update date Sep 25, 2020
Contact name Bo Wen
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)
GSM3959437 RNA-seq_shCtrl-1
GSM3959438 RNA-seq_shCtrl-2
GSM3959439 RNA-seq_shTopors-1
This SubSeries is part of SuperSeries:
GSE134624 TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes
BioProject PRJNA555874
SRA SRP215874

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE134623_Genes_tpm_table.txt.gz 773.7 Kb (ftp)(http) TXT
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Processed data are available on Series record

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