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Series GSE125595 Query DataSets for GSE125595
Status Public on Sep 12, 2019
Title RNA interactions are essential for proper CTCF function
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The function of the CCCTC-binding factor (CTCF) in the organization of the genome has become an important area of investigation, but the mechanisms by which CTCF dynamically contributes to genome organization are not clear. We previously discovered that CTCF binds to large numbers of endogenous RNAs, promoting its self-association. In this regard, we now report two independent features that disrupt CTCF association with chromatin: inhibition of transcription and disruption of CTCF-RNA interactions through mutations of two of its 11 zinc fingers which are not required for CTCF binding to its cognate DNA site: zinc finger-1 (ZF1) or -10 (ZF10). These mutations alter gene expression profiles as CTCF mutants lose their ability to form chromatin loops and thus, the ability to insulate chromatin domains as well as mediate CTCF long-range genomic interactions. Our results point to the importance of CTCF-mediated RNA interactions as a structural component of genome organization.
Overall design In this experiment with characterized mESC under transcriptional inhibition or Rnase digestion using Chip-Seq and 5C experiments. As well as rescue cell lines where endogenous CTCF was depleted and a mutant CTCF was expressed using ChIP-Seq, RNA-Seq, scRNA-Seq and Hi-C
Contributor(s) Saldaña-Meyer R, Reinberg D
Citation(s) 31522988
Submission date Jan 24, 2019
Last update date Oct 04, 2019
Contact name Ricardo Saldana-Meyer
Organization name NYUMC - HHMI
Department Biochemistry and Molecular Pharmacology
Lab 211
Street address 522 First Avenue
City New York
State/province NY
ZIP/Postal code 10016
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (24)
GSM3577965 CTCF_ChIP_Seq_Transcriptional_Inhibition, DMSO
GSM3577966 CTCF_ChIP_Seq_Transcriptional_Inhibition, 1h
GSM3577967 CTCF_ChIP_Seq_Transcriptional_Inhibition, 4h
BioProject PRJNA517076
SRA SRP182063

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
GSE125595_All_Rescues.cloupe.gz 301.9 Mb (ftp)(http) CLOUPE
GSE125595_RAW.tar 4.2 Gb (http)(custom) TAR (of BW, HIC, 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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