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Series GSE156868 Query DataSets for GSE156868
Status Public on Aug 30, 2020
Title Molecular basis of CTCF binding polarity in genome folding
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Current models propose that boundaries of mammalian topologically associating domains (TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by cohesin. While the orientation of CTCF motifs determines which pairs of CTCF sites preferentially stabilize loops, the molecular basis of this polarity remains mysterious. Here we report that CTCF positions cohesin but does not control its overall binding dynamics on chromatin by single molecule live imaging. Using an inducible complementation system, we found that CTCF mutants lacking the N-terminus cannot insulate TADs properly. Cohesin remained at CTCF sites in this mutant, albeit with reduced enrichment. Given that the orientation of the CTCF motif presents the CTCF N-terminus towards cohesin as it translocates from the interior of TADs, these observations explain how the orientation of CTCF binding sites determines the genomic distribution of chromatin loops.
 
Overall design ChIP-seq, Hi-C and 5C in mouse ES cells harboring an auxin-inducible degron on endogenous CTCF alleles and expressing dox-inducible mutant CTCF transgenes. WT parental cells are E14tg2a (129 X,Y background).
 
Contributor(s) Nora EP, Caccianini L, Fudenberg G, So K, Kameswaran V, Nagle A, Uebersohn A, Hajj B, Le Saux A, Coulon A, Mirny LA, Pollard KS, Dahan M, Bruneau BG
Citation(s) 33154377
Submission date Aug 25, 2020
Last update date Nov 16, 2020
Contact name Elphege Nora
Organization name University of California San Francisco
Department Cardiovascular Research Institute
Lab Elphege Nora
Street address 555 Mission Bay Boulevard South
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (161)
GSM4745685 ENHIC1; Hi-C_untagged_untreated_rep1
GSM4745686 ENHIC2; Hi-C_untagged_untreated_rep2
GSM4745687 ENHIC3; Hi-C_CTCF-AID_auxin2days_rep1
Relations
BioProject PRJNA660128
SRA SRP279308

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE156868_FLAG_ChIP-seq_peaks_in_cells_expressing_full-length_FLAG-CTCF__EN133.10_auxin+dox2days_.bed.gz 391.8 Kb (ftp)(http) BED
GSE156868_RAW.tar 563.7 Mb (http)(custom) TAR (of COOL, TXT)
GSE156868_Reference_genome_for_mapping_5C_ligation_products.fasta.gz 6.2 Mb (ftp)(http) FASTA
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Raw data are available in SRA
Processed data provided as supplementary file
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