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Series GSE178346 Query DataSets for GSE178346
Status Public on May 02, 2022
Title TCF-1 mediates 3D genome reconfiguration during T cell development (ChIP-Seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Lineage-determine transcription factors (LDTFs) can determine gene expression programs of a specific cell type, by rewiring the linear regulatory network. However, it’s not clear whether and how LDTFs can alter the 3D genome organization during development. Here, we investigated the effect of T cell factor 1 (TCF-1) on the reconfiguration of 3D genome during T cell development. Topologically associated domains (TADs) that have higher density of TCF-1 gain more intra-TAD interactions during T cell development. TCF-1 colocalized with CCCTC-binding factor (CTCF) substantially reduced the insulation and increased the local interactions, which additionally have stronger interactions with T cell development genes. We further found that a considerable number of boundaries are lost during T cell development, and that TCF-1 is enriched at the lost boundaries, including the ones near key T cell development genes. Overexpression of TCF-1 in fibroblast demonstrates that both high density of TCF-1 and TCF-1 colocalized with CTCF can optimally increase the local interactions. Correspondingly, knocking out of TCF-1 in DN3 cell line leads to decreased intra-TAD interactions and gain of insulation at some of its binding sites. Finally, we found that TCF-1 can recruit and maintain cohesin at its binding sites, which probably cause reconfiguration of the 3D genome. Taken together, our study shows that TCF-1 can change the 3D genome at both TAD level and finer scale potentially through the recruitment of cohesin.
 
Overall design Study the 3D genome reorganization mediated by TCF-1
 
Contributor(s) Wang W, Chandra A, Vahedi G
Citation(s) 35726060
Submission date Jun 16, 2021
Last update date Aug 01, 2022
Contact name Wenliang Wang
E-mail(s) bgi.wangwl@gmail.com
Organization name University of Pennsylvania
Street address 421 Curie Boulevard
City Philadelphia
State/province PENNSYLVANIA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL21626 NextSeq 550 (Mus musculus)
Samples (25)
GSM5388165 ChIP-Seq Normal NIH-3T3 cells - CTCF Rep1
GSM5388166 ChIP-Seq Normal NIH-3T3 cells - CTCF Rep2
GSM5388167 ChIP-Seq TCF1 induced NIH-3T3 cells - CTCF Rep1
This SubSeries is part of SuperSeries:
GSE178348 TCF-1 mediates 3D genome reconfiguration during T cell development
Relations
BioProject PRJNA738527
SRA SRP324445

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

Supplementary file Size Download File type/resource
GSE178346_RAW.tar 7.3 Gb (http)(custom) TAR (of BED, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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