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Series GSE125129 Query DataSets for GSE125129
Status Public on Sep 05, 2019
Title The ChAHP complex counteracts chromatin looping at Ctcf sites that have emerged from recent SINE expansions
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Ctcf and cohesin are key players in the three dimensional organization of chromatin. Whereas genome-wide Ctcf binding has diverged substantially between species due to transposon-mediated motif expansions, demarcation of topologically associating domains (TADs) by Ctcf is remarkably well conserved. Yet, the Ctcf consensus motif poorly predicts TADs and the majority of Ctcf sites are not at TAD boundaries. Here we demonstrate that the ChAHP complex (Chd4, Adnp, HP1) competes with Ctcf for a common set of genomic binding sites. In absence of ChAHP, novel insulated regions are formed at ChAHP bound sites, whereas proximal canonical boundaries are weakened. These data reveal that Ctcf-mediated loop formation is modulated by a distinct zinc-finger protein complex. Strikingly, ChAHP bound loci are mainly situated within evolutionary young SINE B2 transposable elements. This further implicates ChAHP in maintenance of evolutionary conserved spatial chromatin organization by buffering novel Ctcf binding sites that emerged through SINE expansions.
 
Overall design Ctcf, cohesin (Rad21) and H3K27ac ChIPs were performed in biological replicates on independent isogenic wild-type (wt) and Adnp knock-out (AdnpKO) ES cell clones. Hi-C was performed in biological replicates on independent isogenic wild-type (wt) and Adnp knock-out (AdnpKO) ES cell clones. For each biological Hi-C replicate, we performed a technical replicate for which the cells were grown and processed in parallel. 4C experiments were performed in biological duplicates using the same cell lines as for Hi-C.
 
Contributor(s) Mohn F, Kaaij L, Bühler M
Citation(s) 31491387
Submission date Jan 15, 2019
Last update date Nov 08, 2019
Contact name Fabio Mohn
E-mail(s) fabio.mohn@fmi.ch
Organization name Friedrich Miescher Institute for Biomedical Research
Lab Buehler Lab
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (77)
GSM3563950 ChIPseq for Ctcf in wt mES cells, replicate 1
GSM3563951 Input of ChIPseq for Ctcf in wt mES cells, replicate 1
GSM3563952 ChIPseq for Ctcf in wt mES cells, replicate 2
Relations
BioProject PRJNA515300
SRA SRP179647

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
GSE125129_AdnpKO_HiC_allValidPairs_rep1.txt.gz 8.0 Gb (ftp)(http) TXT
GSE125129_AdnpKO_HiC_allValidPairs_rep2.txt.gz 7.0 Gb (ftp)(http) TXT
GSE125129_CtcfPeaks_AdnpKO_merged.bed.gz 1.9 Mb (ftp)(http) BED
GSE125129_CtcfPeaks_wt_merged.bed.gz 1.6 Mb (ftp)(http) BED
GSE125129_Ctcf_ChIP_AdnpKO.bw 220.6 Mb (ftp)(http) BW
GSE125129_Ctcf_ChIP_wt.bw 219.3 Mb (ftp)(http) BW
GSE125129_H3K27ac_ChIP_AdnpKO.bw 346.8 Mb (ftp)(http) BW
GSE125129_H3K27ac_ChIP_wt.bw 341.2 Mb (ftp)(http) BW
GSE125129_RAW.tar 6.3 Gb (http)(custom) TAR (of BW, WIG)
GSE125129_Rad21Peaks_AdnpKO_merged.bed.gz 801.6 Kb (ftp)(http) BED
GSE125129_Rad21Peaks_wt_merged.bed.gz 720.4 Kb (ftp)(http) BED
GSE125129_Rad21_ChIP_AdnpKO.bw 305.2 Mb (ftp)(http) BW
GSE125129_Rad21_ChIP_wt.bw 301.1 Mb (ftp)(http) BW
GSE125129_WT_HiC_allValidPairs_rep1.txt.gz 7.3 Gb (ftp)(http) TXT
GSE125129_WT_HiC_allValidPairs_rep2.txt.gz 7.9 Gb (ftp)(http) TXT
GSE125129_update.xls.gz 15.3 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file
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