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Series GSE177045 Query DataSets for GSE177045
Status Public on May 12, 2022
Title Large-scale multi-omics analysis suggests an important role of intragenic cohesin in tissue-specific transcription.
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Cohesin is a protein complex that is essential for chromosome segregation. Cohesin regulates gene expression by insulation and chromatin domain formation with insulation factor CTCF. It was also reported that CTCF-independent cohesin-binding sites co-localize with transcription factors (TFs) for enhancer-promoter interaction. However, it is not a trivial task to assign whole-genome cohesin-binding regions into various functions. Also, the context-specific roles of cohesin-mediated interactions, especially on intragenic region, remains unsolved. To this end, we performed a comprehensive characterization of DNA-binding sites for cohesin and transcription factors (TFs) in MCF-7 cells with and without transcription stimulus. We integrated these epigenomic data with transcriptomic and chromatin interactions data to analyze context-specific cohesin function in genome-wide manner. As a result, we extracted a new subset of cohesin-binding sites named decreased intragenic cohesin sites (DICs), which were different from previous known functions of cohesin. DICs were negatively correlated with transcriptional regulation: a part of them were related to enhancer markers and “paused” RNA polymerase 2, while others contributed to chromatin architectures. The intron enriched DICs also showed chromatin de-compaction and special genomic bindings. Further conventional machine learning approach also captured similar DICs with distinguishable features. More importantly, DICs could be found in various tissues and cell lines, including cohesinopathy patient cells, to play a role in the disturbed transcription. These results suggested a novel function of cohesin on intragenic regions for gene transcription regulation.
 
Overall design ChIP-seq and RNA-seq in MCF-7, RPE, Fibrolast and other cell lines
 
Contributor(s) Wang J, Bando M, Shirahige K, Nakato R
Citation(s) 35680859
Submission date Jun 11, 2021
Last update date Oct 24, 2022
Contact name Jiankang Wang
E-mail(s) wangjk321@gmail.com
Organization name The University of Tokyo
Department Institute for Quantitative Biosciences
Street address 1-1-1 Yayoi, Bunkyo-ku
City Tokyo
ZIP/Postal code 113-0032
Country Japan
 
Platforms (3)
GPL16558 AB 5500 Genetic Analyzer (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (116)
GSM5373114 ChIPseq_MCF7_CBP_Ctrl
GSM5373115 ChIPseq_MCF7_CBP_E2
GSM5373116 ChIPseq_MCF7_AFF4_Ctrl
Relations
BioProject PRJNA736967
SRA SRP323742

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
GSE177045_RAW.tar 125.6 Mb (http)(custom) TAR (of BED, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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