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Series GSE39502 Query DataSets for GSE39502
Status Public on Oct 11, 2013
Title Differences in CTCF binding site sequence are associated with unique regulatory and functional trends during embryonic stem cell differentiation [ChIP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary CTCF (CCCTC-binding factor) is a highly conserved 11-zinc finger DNA binding protein with tens of thousands of binding sites genome-wide. CTCF acts as a multifunctional regulator of transcription, having been previously associated with activator, repressor, and insulator activity. These diverse regulatory functions are crucial for preimplantation development and are implicated in the regulation of numerous lineage-specific genes. Despite playing a critical role in developmental gene regulation, the mechanisms that underlie developmental changes in CTCF recruitment and function are poorly understood. Our previous work suggested that differences in CTCF’s binding site sequence may affect the regulation of CTCF recruitment, as well as CTCF’s regulatory function. To investigate these two possibilities directly during a developmental process, changes in genome-wide CTCF binding and gene expression were characterized during in vitro differentiation of mouse embryonic stem cells. CTCF binding sites were initially separated into three classes (named LowOc, MedOc, and HighOc) based on similarity to the consensus motif. The LowOc class, with lower-similarity to the consensus motif, is more likely to show changes in binding during differentiation. These more dynamically bound sites are enriched for motifs that confer a lower in vitro affinity for CTCF, suggesting a mechanism where sites with low-binding affinity are more amenable to developmental control. Additionally, by comparing changes in CTCF binding with changes in gene expression during differentiation, we show that LowOc and HighOc sites are associated with distinct regulatory functions. In sum, these results suggest that the regulatory control of CTCF’s binding and function is dependent in part upon specific motifs within its DNA binding site.
Overall design Mouse E14 ES cells were differentiated in vitro for 4.5 days using retinoic acid. ChIP-seq for CTCF and an IgG control was performed from cells collected before and after differentiation. For undifferentiated cells, data were generated in two biological replicates.
Contributor(s) Plasschaert RN, Vigneau S, Tempera I, Gupta R, Maksimoska J, Everett L, Davuluri R, Mamorstein R, Lieberman PM, Schultz D, Hannenhalli S, Bartolomei MS
Citation(s) 24121688
Submission date Jul 19, 2012
Last update date May 15, 2019
Contact name Sebastien Vigneau
Phone +1-857-540-5439
Organization name Dana-Farber Cancer Institute
Department Cancer Biology
Lab Alexander Gimelbrant
Street address 450 Brookline Avenue
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (7)
GSM970264 CTCF_ChIPSeq_Undifferentiated
GSM970265 IgG_ChIPSeq_Undifferentiated
GSM970266 CTCF_ChIPSeq_Differentiated
This SubSeries is part of SuperSeries:
GSE39523 Differences in CTCF binding site sequence are associated with unique regulatory and functional trends during embryonic stem cell differentiation
BioProject PRJNA171028
SRA SRP014478

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
GSE39502_Equations.pdf.gz 10.2 Kb (ftp)(http) PDF
GSE39502_RAW.tar 909.0 Mb (http)(custom) TAR (of BED, TSV, WIG)
GSE39502_ctcf_peaks_differentiated.tsv.gz 88.6 Kb (ftp)(http) TSV
GSE39502_ctcf_peaks_undifferentiated.tsv.gz 152.6 Kb (ftp)(http) TSV
GSE39502_ctcf_peaks_undifferentiated_rep2.tsv.gz 244.3 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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