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Series GSE103651 Query DataSets for GSE103651
Status Public on Oct 30, 2017
Title Molecular Mechanism of Directional CTCF Recognition of a Diverse Range of Genomic Sites
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary CTCF, a conserved 3D genome architecture protein, determines proper genome-wide chromatin looping interactions through directional binding to specific sequence elements of four modules within numerous CTCF-binding sites (CBSs) by its 11 zinc fingers (ZFs). Here, we report the crystal structures of four human CTCF-CBS complexes of the protocadherin (Pcdh) clusters, and show that directional CTCF binding to cognate CBSs of the Pcdh enhancers and promoters is achieved through inserting its ZF3, ZFs 4-7, and ZFs 9-11 into the major groove along CBSs, resulting in a sequence-specific recognition of module 4, modules 2-3, and module 1, respectively, with ZF8 as a spacer element for variable distances between modules 1 and 2. In addition, the base-contact with the asymmetric “A” in the central position of modules 2-3, is essential for directional recognition of the CBSs with symmetric core sequences and lack of module 1. Furthermore, CTCF tolerates base changes at specific positions within the degenerated CBS sequences, permitting genome-wide CTCF binding to a diverse range of CBSs. Together, these complex structures provide important insights into the molecular mechanisms for the directionality, diversity, flexibility, dynamics, and conservation of multivalent CTCF binding to its cognate sites across the entire human genome
 
Overall design Examination of CTCF binding sites in 293T cell.
 
Contributor(s) Zhang M, Wu Q
Citation(s) 29076501
Submission date Sep 08, 2017
Last update date May 15, 2019
Contact name Zhang Mo
E-mail(s) zhangmo@sjtu.edu.cn
Organization name SJTU
Street address Dong Chuan Road 800
City Shang Hai
ZIP/Postal code 200240
Country China
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (2)
GSM2777335 CTCF_ChIP-nexus Rep1
GSM2777336 CTCF_ChIP-nexus Rep2
Relations
BioProject PRJNA403847
SRA SRP117176

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
GSE103651_CTCF_MACE.border_pair.txt.gz 542.9 Kb (ftp)(http) TXT
GSE103651_CTCF_MACS_peaks.txt.gz 748.9 Kb (ftp)(http) TXT
GSE103651_RAW.tar 60.9 Mb (http)(custom) TAR (of BW)
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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