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Series GSE123651 Query DataSets for GSE123651
Status Public on Apr 05, 2022
Title CTCF Functions as an Insulator for Somatic Genes and a Structural Regulator for Pluripotent Genes during Reprogramming [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
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 Analysis of CTCF binding sites in reprogramming cells with OSKM plus control, OSKM plus Ctcf overexpression, OSKM with Ctcf overexpression plus Smarca5 knockdown on day 10. Analysis of CTCF binding sites in wild type (WT) and Smarca5 knockout mESCs, sorted reprogramming intermediate cells in the TetOn lentivirus OSKM reprogramming system with both control shRNA and Ctcf knockdown. Analysis of SMARCA5 binding sites in mESCs.
 
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
E-mail(s) song_yawei@gibh.ac.cn
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 (59)
GSM3508689 D10_control_CTCF [ChIP-seq]
GSM3508690 D10_oeCTCF_CTCF [ChIP-seq]
GSM3508691 D10_oeCTCF_shSmarca5_CTCF [ChIP-seq]
This SubSeries is part of SuperSeries:
GSE123670 CTCF Functions as an Insulator for Somatic Genes and a Structural Regulator for Pluripotent Genes during Reprogramming
Relations
BioProject PRJNA509453
SRA SRP173292

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
GSE123651_Mm_ctcf_D0_shCtcf.bed.gz 271.8 Kb (ftp)(http) BED
GSE123651_Mm_ctcf_D0_shCtrl.bed.gz 330.4 Kb (ftp)(http) BED
GSE123651_Mm_ctcf_D10_ctrl.bed.gz 494.0 Kb (ftp)(http) BED
GSE123651_Mm_ctcf_D10_oeCtcf.bed.gz 590.6 Kb (ftp)(http) BED
GSE123651_Mm_esc_smarca5.bed.gz 528.6 Kb (ftp)(http) BED
GSE123651_RAW.tar 3.0 Gb (http)(custom) TAR (of BED, BW)
GSE123651_stage1_shCtcf.bed.gz 511.6 Kb (ftp)(http) BED
GSE123651_stage1_shLuc.bed.gz 593.5 Kb (ftp)(http) BED
GSE123651_stage2_shCtcf.bed.gz 500.5 Kb (ftp)(http) BED
GSE123651_stage2_shLuc.bed.gz 572.4 Kb (ftp)(http) BED
GSE123651_stage3_shCtcf.bed.gz 504.3 Kb (ftp)(http) BED
GSE123651_stage3_shLuc.bed.gz 584.7 Kb (ftp)(http) BED
GSE123651_stage4_shCtcf.bed.gz 405.7 Kb (ftp)(http) BED
GSE123651_stage4_shLuc.bed.gz 596.8 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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