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Series GSE33819 Query DataSets for GSE33819
Status Public on Nov 19, 2011
Title A genome-wide map of CTCF multivalency redefines the CTCF code
Organisms Mus musculus; Mus spretus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The “CTCF code” hypothesis posits that CTCF pleotropic functions are driven by recognition of diverse DNA sequences through combinatorial use of its 11 zinc fingers (ZFs). This model however is supported by in vitro binding studies of a limited number of sequences. To directly test CTCF multivalency in vivo we here define ZF binding requirements at ~50,000 genomic sites in primary lymphocytes. We find that CTCF reads sequence diversity through ZF clustering. ZFs4-7 anchor CTCF to ~80% of targets containing the 20bp core motif. Non-conserved flanking sequences are recognized by ZFs1-2 and ZFs8- 11 clusters, which also stabilize CTCF broadly. Alternatively, CTCF employ ZFs9-11 to associate with a second phylogenetically-conserved upstream motif at ~15% of its sites. Individually, ZFs increase overall binding affinity and chromatin residence time. Unexpectedly, we also uncover a conserved downstream DNA motif that destabilizes CTCF occupancy. CTCF thus associates with a wide array of DNA modules via combinatorial clustering of its 11 ZFs.
Overall design ChIP-Seq of wt and mutant CTCF in activated mouse B cells. For the comparison of wt and mutant CTCF binding profiles, CTCF fused to a biotag was overexpressed in the presence of the endogenous wt CTCF copies together with BirA. The exongenous CTCF was then precipitated using streptavidin beads. For the comparison of wt CTCF binding in Mus musculus C57BL/6 and Mus spretus, endogenous CTCF was precipitated with an anti-CTCF antibody. All these experiments were carried out in triplicate. In addition, several overexpressed mutants were subjected to exonuclease treatment prior to sequencing (ChIP-Exo).
Web link
Contributor(s) Nakahashi H, Kwon KK, Resch W, Vian L, Dose M, Stavreva D, Hakim O, Pruett N, Nelson S, Yamane A, Qian J, Dubois W, Welsh S, Phair RD, Pugh F, Lobanenkov V, Hager GL, Casellas R
Citation(s) 21113164, 23707059
Submission date Nov 18, 2011
Last update date May 15, 2019
Contact name Seolkyoung Jung
Organization name NIH
Department NIAMS
Lab biodata mining and discovery section
Street address 10 Center Dr
City bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (3)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17106 Illumina HiSeq 2000 (Mus spretus)
Samples (45)
GSM836458 CTCF/activated B cells/wt
GSM1132317 CTCFbiotag/Mus musculus:activated B/R339W/rep_a
GSM1132318 CTCFbiotag/Mus musculus:activated B/R339W/rep_b
SRA SRP009414
BioProject PRJNA148151

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Supplementary file Size Download File type/resource
GSE33819_RAW.tar 1.0 Gb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data included within Sample table
Processed data provided as supplementary file

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