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Series GSE104367 Query DataSets for GSE104367
Status Public on Feb 12, 2018
Title A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus [HiC_MEF]
Organism Mus musculus
Experiment type Other
Summary 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, Firreā€™s deletion disrupts the chromatin super-loop formation of the inactive X-chromosome. Collectively, our findings suggest that apart from CTCF binding, additional mechanisms can play roles in establishing TAD boundary formation.

 
Overall design Allele-specific and traditional Hi-C in Firre lncRNA loss and gain of function mouse embryonic fibroblasts
 
Contributor(s) Barutcu AR, Maass PG, Lewandowski JP, Weiner CL, Rinn JL
Citation(s) 29654311
Submission date Sep 28, 2017
Last update date May 15, 2019
Contact name Rasim Barutcu
Organization name University of Toronto
Department Donnelly Centre
Street address 160 College Street, Room 1030
City Toronto
State/province ON
ZIP/Postal code M5S 3E1
Country Canada
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (37)
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 SubSeries is part of SuperSeries:
GSE98632 A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus
Relations
BioProject PRJNA412458
SRA SRP119332

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
GSE104367_Combined_femaleKO_40000_iced.matrix.gz 829.4 Mb (ftp)(http) MATRIX
GSE104367_Combined_femaleWT_40000_iced.matrix.gz 1.4 Gb (ftp)(http) MATRIX
GSE104367_Female_BL6_CAST_KO_WT_COMBINED_40000_BL6_iced.matrix.gz 309.0 Mb (ftp)(http) MATRIX
GSE104367_Female_BL6_CAST_KO_WT_COMBINED_40000_Cast_iced.matrix.gz 273.4 Mb (ftp)(http) MATRIX
GSE104367_Male_BL6CAST_COMBINED_40000_BL6_iced.matrix.gz 134.4 Mb (ftp)(http) MATRIX
GSE104367_Male_BL6CAST_COMBINED_40000_Cast_iced.matrix.gz 121.2 Mb (ftp)(http) MATRIX
GSE104367_MinusDOX_40000_iced.matrix.gz 268.9 Mb (ftp)(http) MATRIX
GSE104367_PlusDOX_40000_iced.matrix.gz 210.1 Mb (ftp)(http) MATRIX
GSE104367_WT_male_combined_40000_iced.matrix.gz 1.5 Gb (ftp)(http) MATRIX
GSE104367_male_FirreKO_MEF_40000_iced.matrix.gz 370.5 Mb (ftp)(http) MATRIX
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Raw data are available in SRA
Processed data are available on Series record

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