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PMID: 17382889 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome.

Cell ·Vol. 128 ·No. 6 ·2007-03-23 ·Pages 1231-45

Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B

Abstract

Insulator elements affect gene expression by preventing the spread of heterochromatin and restricting transcriptional enhancers from activation of unrelated promoters. In vertebrates, insulator's function requires association with the CCCTC-binding factor (CTCF), a protein that recognizes long and diverse nucleotide sequences. While insulators are critical in gene regulation, only a few have been reported. Here, we describe 13,804 CTCF-binding sites in potential insulators of the human genome, discovered experimentally in primary human fibroblasts. Most of these sequences are located far from the transcriptional start sites, with their distribution strongly correlated with genes. The majority of them fit to a consensus motif highly conserved and suitable for predicting possible insulators driven by CTCF in other vertebrate genomes. In addition, CTCF localization is largely invariant across different cell types. Our results provide a resource for investigating insulator function and possible other general and evolutionarily conserved activities of CTCF sites.

MeSH Terms
Animals CCCTC-Binding Factor Cell Line Chromatin Immunoprecipitation Conserved Sequence DNA-Binding Proteins/metabolism Evolution, Molecular Genome, Human Humans Insulator Elements/genetics Oligonucleotide Array Sequence Analysis Repressor Proteins/metabolism U937 Cells Vertebrates/genetics
Chemicals
CCCTC-Binding Factor CTCF protein, human DNA-Binding Proteins Repressor Proteins
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Kim Tae Hoon
Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093-0653, USA. [email protected]
Abdullaev Ziedulla K
Smith Andrew D
Ching Keith A
Loukinov Dmitri I
Green Roland D
Zhang Michael Q
Lobanenkov Victor V
Ren Bing
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Article Info
Journal
Cell
Abbr.
Cell
ISSN
0092-8674
DOI
10.1016/j.cell.2006.12.048
Email
[email protected]
Published
2007-03-23
Pages
1231-45
Language
English
Region
United States
NLM ID
0413066
PMCID
PMC2572726
Subset
IM
Grants
NHGRI NIH HHS · HG001696 · United States
NCI NIH HHS · R33CA105829 · United States
NCI NIH HHS · R21 CA116365 · United States
NCI NIH HHS · F32CA108313 · United States
Intramural NIH HHS · United States
NCI NIH HHS · R33 CA105829 · United States
NHGRI NIH HHS · U01HG003151 · United States
NCI NIH HHS · F32 CA108313 · United States
NCRR NIH HHS · P41 RR008605 · United States
NHGRI NIH HHS · U01 HG003151 · United States
NHGRI NIH HHS · R01 HG001696 · United States
NCI NIH HHS · R21CA116365-01 · United States
NCRR NIH HHS · P41 RR 08605 · United States
Databases
GEO
GSE5559
External Links
PubMed source DOI: 10.1016/j.cell.2006.12.048 PMC Full Text View journal details
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