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Series GSE123653 Query DataSets for GSE123653
Status Public on Apr 05, 2022
Title CTCF Functions as an Insulator for Somatic Genes and a Structural Regulator for Pluripotent Genes during Reprogramming [BL-Hi-C]
Organism Mus musculus
Experiment type Other
Summary CCCTC binding factor (CTCF) has been implicated in mediating chromatin insulation and long-distance interactions between enhancer and promoter. In this study, to study the roles of CTCF in somatic cell reprogramming, we performed RNA-seq, Hi-C, ChIP-seq and ATAC-seq at the specific stage of reprogramming. Through bioinformatics analysis, our data indicated that CTCF promotes enhancer-promoter interactions and chromatin accessibility to regulate the expression of key pluripotency genes; meanwhile, it serves as an insulator to suppress the expression of key somatic genes. Smarca5 loss inhibits CTCF-promoted reprogramming by reversing CTCF insulator activity on MEF-specific genes and leading to incorrect nucleosome positioning adjacent to CTCF binding sites. These findings reveal the dual functions of CTCF as both a structural regulator and insulator in conjunction with a key chromatin remodeler to drive cellular reprogramming towards pluripotency.
Overall design Examination of chromatin interactions in mouse embryonic fibroblast (MEF) and OSKM reprogrammed cells on day 10. Examination of chromatin interactions in reprogramming cells with OSKM plus control, OSKM plus Ctcf overexpression and OSKM with Ctcf overexpression plus Smarca5 knockdown, reprogramming cells with OSKM plus control or Ctcf shRNA on day 10. Examination of chromatin interactions in sorted reprogramming intermediate cells in the TetOn lentivirus OSKM reprogramming system with both control shRNA and Ctcf knockdown by BL-Hi-C deep sequencing.
Contributor(s) Hutchins AP, Liang Z, Hu G, Song Y
Citation(s) 35385732
Submission date Dec 11, 2018
Last update date Jul 05, 2022
Contact name ya wei song
Phone 13288824450
Organization name Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences
Department South China Institute for Stem Cell Biology and Regenerative Medicine
Street address 190 Kai Yuan Avenue, Science Park
City Guangzhou
State/province Guangdong
ZIP/Postal code 510530
Country China
Platforms (2)
GPL21273 HiSeq X Ten (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (40)
GSM3508805 OG2MEF_rep1 [BL-Hi-C]
GSM3508806 OG2MEF_rep2 [BL-Hi-C]
GSM3508807 OSKM_D10_rep1 [BL-Hi-C]
This SubSeries is part of SuperSeries:
GSE123670 CTCF Functions as an Insulator for Somatic Genes and a Structural Regulator for Pluripotent Genes during Reprogramming
BioProject PRJNA509470
SRA SRP173305

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Supplementary file Size Download File type/resource
GSE123653_RAW.tar 66.0 Gb (http)(custom) TAR (of HIC)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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