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Series GSE98632 Query DataSets for GSE98632
Status Public on Feb 12, 2018
Title A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus
Organism Mus musculus
Experiment type Other
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary ABSTRACT
The binding of the transcriptional regulator CTCF to the genome has been implicated in the formation of topologically associated domains (TADs). However, the general mechanisms of folding the genome into TADs are not fully understood. Here, we tested the effects of deleting a CTCF-rich locus on TAD boundary formation. Using genome-wide chromosome conformation capture (Hi-C), we focus on one TAD boundary on chromosome X harboring ~15 CTCF binding sites, and located at the long non-coding RNA (lncRNA) locus Firre. Specifically, this TAD boundary is invariant across evolution, tissues, and temporal dynamics of X-chromosome inactivation. We demonstrate that neither the deletion of this locus, nor the ectopic insertion of Firre cDNA or its ectopic expression are sufficient to alter TADs in a sex-, or allele-specific manner. In contrast, Firre’s deletion disrupts the chromatin super-loop formation of the inactive X-chromosome. Collectively, our findings suggest that apart from CTCF binding, additional mechanisms may play roles in establishing TAD boundary formation.

This SuperSeries is composed of the SubSeries listed below.
 
Overall design Refer to individual Series.
 
Contributor(s) Barutcu AR, Maass PG, Lewandowski JP, Weiner CL, Rinn JL
Citation(s) 29654311
Submission date May 08, 2017
Last update date May 15, 2019
Contact name Rasim Barutcu
Organization name ScitoVation
Street address 6 Davis Drive
City Durham
State/province NC
ZIP/Postal code 27709
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (68)
GSM2602196 Female_MEF_WT_HiC_Biological_Rep1_Technical_Rep1
GSM2602197 Female_MEF_WT_HiC_Biological_Rep1_Technical_Rep2
GSM2602198 Female_MEF_WT_HiC_Biological_Rep2_Technical_Rep1
This SuperSeries is composed of the following SubSeries:
GSE104367 A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus [HiC_MEF]
GSE104427 A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus [RNA-Seq, HiC_C2C12, ChIP-Seq]
GSE104814 A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus [HiC_mESC]
Relations
BioProject PRJNA385778

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