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Series GSE123101 Query DataSets for GSE123101
Status Public on Aug 08, 2019
Title TET-catalyzed 5-carboxylcytosine promotes CTCF binding to suboptimal sequences genome-wide
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary The mechanisms supporting dynamic regulation of CTCF binding sites remain poorly understood. Here we describe the TET-catalyzed 5-methylcytosine derivative, 5-carboxylcytosine (5caC) as a factor driving new CTCF binding within genomic DNA. Through a combination of in vivo and in vitro approaches, we reveal that 5caC generally strengthens CTCF association with DNA and facilitates binding to suboptimal sequences. Dramatically, profiling of CTCF binding in a cellular model that accumulates genomic 5caC identified ∼13,000 new CTCF sites. The new sites were enriched for overlapping 5caC and were marked by an overall reduction in CTCF motif strength. As CTCF has multiple roles in gene expression, these findings have wide-reaching implications and point to induced 5caC as a potential mechanism to achieve differential CTCF binding in cells.

Overall design Characterization of CTCF binding in TDG KO condition compared to wild type, and examination of 5caC
Web link
Contributor(s) Nanan K, Sturgill D, Prigge MF, Thenoz M, Dillman AA, Mandler MD, Oberdoerffer S
Citation(s) 31404833
Submission date Nov 29, 2018
Last update date Aug 27, 2019
Contact name David Sturgill
Phone 240-760-6725
Organization name NIH
Department NCI
Street address Building 41, Rm B622
City Bethesda
State/province MARYLAND
ZIP/Postal code 20892
Country USA
Platforms (2)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
GPL21626 NextSeq 550 (Mus musculus)
Samples (20)
GSM3495173 WT_4H8_Rep1_S3
GSM3495174 WT_4H8_Rep2_S4
GSM3495175 WT_CTCF_Rep1_S1
BioProject PRJNA507546
SRA SRP171121

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
GSE123101_RAW.tar 2.7 Gb (http)(custom) TAR (of BED, BW)
GSE123101_TDG_KO_vs_WT_gene_exp_diff.txt.gz 1.5 Mb (ftp)(http) TXT
GSE123101_genes.read_group_tracking.asmatrix.txt.gz 488.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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