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Series GSE135180 Query DataSets for GSE135180
Status Public on Oct 15, 2020
Title Dynamic cohesin is required for lineage specific distal gene regulation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary The cohesin complex plays essential roles in sister chromatin cohesin, chromosome organization and gene expression. The role it plays in the regulation of genes is incompletely understood. Here, we report that the cohesin release factor WAPL in mouse embryonic stem cells is crucial for maintaining a pool of dynamically bound cohesin to regions in the genome that are associated with lineage specific genes. These regions are enriched for active enhancer marks and transcription factor binding sites. Stabilization of cohesin, which leads to a loss of dynamic cohesin from these regions does not affect transcription factor binding or active enhancer marks, but does result in changes in promoter-enhancer interactions and downregulation of genes. Acute cohesin depletion can phenocopy the effect of WAPL depletion, showing that cohesin plays a crucial role in maintaining expression of lineage specific genes. The binding of dynamic cohesin to chromatin is dependent on the pluripotency transcription factor OCT4, but not NANOG. Finally, sites of dynamic cohesin binding sites are also found in differentiated cells, suggesting that they represent a general regulatory principle. We propose that the binding of dynamic cohesin to regulatory sites creates a favorable spatial environment in which promoters and enhancers can communicate to ensure proper gene expression.
 
Overall design Acute depletion of WAPL, RAD21, SOX2, OCT4 and NANOG using degron techniques, followed by multiple molecular readouts using different sequencing techniques
 
Contributor(s) Liu N, de Wit E
Citation(s) 33318687
Submission date Jul 31, 2019
Last update date Nov 11, 2022
Contact name Ning Qing Liu
E-mail(s) n.liu@erasmusmc.nl
Organization name Erasmus University Medical Center Rotterdam
Department Hematology
Street address Wytemaweg 80
City Rotterdam
ZIP/Postal code 3015 CN
Country Netherlands
 
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
GPL21626 NextSeq 550 (Mus musculus)
Samples (128)
GSM3992897 1_Wapl-C6_0h_antiWapl
GSM3992898 2_Wapl-C6_24h_antiWapl
GSM3992899 3_Wapl-C6_0h_antiCtcf
Relations
BioProject PRJNA557678
SRA SRP216929

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
GSE135180_107-112_WaplC6_TTseq_htseqcounts_normalized_2019-08.txt.gz 489.8 Kb (ftp)(http) TXT
GSE135180_107-112_WaplC6_TTseq_htseqcounts_unnormalized_2019-08.txt.gz 582.4 Kb (ftp)(http) TXT
GSE135180_119-130_Viewpoint_4C_samples_2020-08.txt.gz 122 b (ftp)(http) TXT
GSE135180_45-46-103-104_WaplC6_ESC_NPC_RNA_htseqcounts_normalized_2019-08.txt.gz 388.9 Kb (ftp)(http) TXT
GSE135180_45-46-103-104_WaplC6_ESC_NPC_RNA_htseqcounts_unnormalized_2019-08.txt.gz 293.0 Kb (ftp)(http) TXT
GSE135180_45-58_WaplC6_Parental_RNA_htseqcounts_unnormalized_2019-07-26.txt.gz 641.7 Kb (ftp)(http) TXT
GSE135180_45-58_WaplC6_Parental_RNA_normalized_ratio_2019-07-26.txt.gz 840.3 Kb (ftp)(http) TXT
GSE135180_59-64_Rad21AID_RNA_htseqcounts_unnormalized_2019-07-26.txt.gz 368.9 Kb (ftp)(http) TXT
GSE135180_59-64_Rad21AID_RNA_normalized_ratio_2019-07-26.txt.gz 324.0 Kb (ftp)(http) TXT
GSE135180_65-66_WaplC6_hiC_10000_abs.bed.gz 1.5 Mb (ftp)(http) BED
GSE135180_65-66_WaplC6_hiC_20000_abs.bed.gz 829.4 Kb (ftp)(http) BED
GSE135180_65-66_WaplC6_hiC_40000_abs.bed.gz 409.9 Kb (ftp)(http) BED
GSE135180_67-90_Viewpoint_4C_samples_2019-07-26.txt.gz 163 b (ftp)(http) TXT
GSE135180_93-102_WaplC20_RNA_htseqcounts_normalized_2019-08.txt.gz 567.5 Kb (ftp)(http) TXT
GSE135180_93-102_WaplC20_RNA_htseqcounts_unnormalized_2019-08.txt.gz 469.8 Kb (ftp)(http) TXT
GSE135180_RAW.tar 8.4 Gb (http)(custom) TAR (of BW, TXT)
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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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