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Series GSE126635 Query DataSets for GSE126635
Status Public on Jan 07, 2020
Title The structural basis for cohesin/CTCF anchored loops [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Cohesin catalyses the folding of the genome into loops that are anchored by CTCF. The molecular mechanism of how cohesin and CTCF structure the 3D genome has remained unclear. Here we show that a segment within the CTCF N terminus interacts with the SA2-SCC1 subunits of cohesin. A 2.6 Å crystal structure of SA2-SCC1 in complex with CTCF reveals the molecular basis of the interaction. We demonstrate that this interaction is specifically required for CTCF-anchored loops and contributes to the positioning of cohesin at CTCF-binding sites. A similar motif is present in a number of established and novel cohesin ligands, including the cohesin release factor WAPL. Our data suggest that CTCF enables chromatin loop formation by protecting cohesin against loop release. These results provide fundamental insights into the molecular mechanism that enables dynamic regulation of chromatin folding by cohesin and CTCF.
Overall design RNA-Seq was performed in control and mutant CTCF (Y226A, F228A) HAP1 cells in triplicate.
Contributor(s) Haarhuis JH, Sedeño Cacciatore A, Willems L, de Wit E, Rowland BD
Citation(s) 31905366
Submission date Feb 15, 2019
Last update date Feb 21, 2020
Contact name Angela Sedeno Cacciatore
Organization name Netherlands Cancer Institute
Department Gene regulation
Lab Rowland lab
Street address Plesmanlaan 121
City Amsterdam
State/province Noord-Holland
ZIP/Postal code 1066 CX
Country Netherlands
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (6)
GSM3610139 RNA-seq_WT_rep1
GSM3610140 RNA-seq_WT_rep2
GSM3610141 RNA-seq_WT_rep3
This SubSeries is part of SuperSeries:
GSE126637 The structural basis for cohesin/CTCF anchored loops
BioProject PRJNA522781
SRA SRP186011

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

Supplementary file Size Download File type/resource
GSE126635_CTCFvsWT_DEseq2.csv.gz 983.1 Kb (ftp)(http) CSV
GSE126635_counts_WT_CTCF.Y226A.F228A.csv.gz 392.1 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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