CTCFBSDB

A CTCF-binding site database for characterization of vertebrate genomic insulators

Lei Bao, Mi Zhou, Yan Cui

Research output: Contribution to journalArticle

80 Citations (Scopus)

Abstract

Recent studies on transcriptional control of gene expression have pinpointed the importance of long-range interactions and three-dimensional organization of chromatins within the nucleus. Distal regulatory elements such as enhancers may activate transcription over long distances; hence, their action must be restricted within appropriate boundaries to prevent illegitimate activation of non-target genes. Insulators are DNA elements with enhancer-blocking and/or chromatin-bordering functions. In vertebrates, the versatile transcription regulator CCCTC-binding factor (CTCF) is the only identified trans -acting factor that confers enhancer-blocking insulator activity. CTCF-binding sites were found to be commonly distributed along the vertebrate genomes. We have constructed a CTCF-binding site database (CTCFBSDB) to characterize experimentally identified and computationally predicted CTCF-binding sties. Biological knowledge and data from multiple resources have been integrated into the database, including sequence data, genetic polymorphisms, function annotations, histone methylation profiles, gene expression profiles and comparative genomic information. A web-based user interface was implemented for data retrieval, analysis and visualization. In silico prediction of CTCF-binding motifs is provided to facilitate the identification of candidate insulators in the query sequences submitted by users. The database can be accessed at http://insulatordb.utmem.edu/.

Original languageEnglish (US)
JournalNucleic Acids Research
Volume36
Issue numberSUPPL. 1
DOIs
StatePublished - Jan 1 2008

Fingerprint

Vertebrates
Binding Sites
Databases
Chromatin
Hordeolum
Insulator Elements
Trans-Activators
Information Storage and Retrieval
Genetic Polymorphisms
Transcriptome
Computer Simulation
Histones
Methylation
Genome
Gene Expression
DNA
Genes
CCCTC-binding factor

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

CTCFBSDB : A CTCF-binding site database for characterization of vertebrate genomic insulators. / Bao, Lei; Zhou, Mi; Cui, Yan.

In: Nucleic Acids Research, Vol. 36, No. SUPPL. 1, 01.01.2008.

Research output: Contribution to journalArticle

@article{98b01d2f4d72407bb581a2f1debdcfe5,
title = "CTCFBSDB: A CTCF-binding site database for characterization of vertebrate genomic insulators",
abstract = "Recent studies on transcriptional control of gene expression have pinpointed the importance of long-range interactions and three-dimensional organization of chromatins within the nucleus. Distal regulatory elements such as enhancers may activate transcription over long distances; hence, their action must be restricted within appropriate boundaries to prevent illegitimate activation of non-target genes. Insulators are DNA elements with enhancer-blocking and/or chromatin-bordering functions. In vertebrates, the versatile transcription regulator CCCTC-binding factor (CTCF) is the only identified trans -acting factor that confers enhancer-blocking insulator activity. CTCF-binding sites were found to be commonly distributed along the vertebrate genomes. We have constructed a CTCF-binding site database (CTCFBSDB) to characterize experimentally identified and computationally predicted CTCF-binding sties. Biological knowledge and data from multiple resources have been integrated into the database, including sequence data, genetic polymorphisms, function annotations, histone methylation profiles, gene expression profiles and comparative genomic information. A web-based user interface was implemented for data retrieval, analysis and visualization. In silico prediction of CTCF-binding motifs is provided to facilitate the identification of candidate insulators in the query sequences submitted by users. The database can be accessed at http://insulatordb.utmem.edu/.",
author = "Lei Bao and Mi Zhou and Yan Cui",
year = "2008",
month = "1",
day = "1",
doi = "10.1093/nar/gkm875",
language = "English (US)",
volume = "36",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "SUPPL. 1",

}

TY - JOUR

T1 - CTCFBSDB

T2 - A CTCF-binding site database for characterization of vertebrate genomic insulators

AU - Bao, Lei

AU - Zhou, Mi

AU - Cui, Yan

PY - 2008/1/1

Y1 - 2008/1/1

N2 - Recent studies on transcriptional control of gene expression have pinpointed the importance of long-range interactions and three-dimensional organization of chromatins within the nucleus. Distal regulatory elements such as enhancers may activate transcription over long distances; hence, their action must be restricted within appropriate boundaries to prevent illegitimate activation of non-target genes. Insulators are DNA elements with enhancer-blocking and/or chromatin-bordering functions. In vertebrates, the versatile transcription regulator CCCTC-binding factor (CTCF) is the only identified trans -acting factor that confers enhancer-blocking insulator activity. CTCF-binding sites were found to be commonly distributed along the vertebrate genomes. We have constructed a CTCF-binding site database (CTCFBSDB) to characterize experimentally identified and computationally predicted CTCF-binding sties. Biological knowledge and data from multiple resources have been integrated into the database, including sequence data, genetic polymorphisms, function annotations, histone methylation profiles, gene expression profiles and comparative genomic information. A web-based user interface was implemented for data retrieval, analysis and visualization. In silico prediction of CTCF-binding motifs is provided to facilitate the identification of candidate insulators in the query sequences submitted by users. The database can be accessed at http://insulatordb.utmem.edu/.

AB - Recent studies on transcriptional control of gene expression have pinpointed the importance of long-range interactions and three-dimensional organization of chromatins within the nucleus. Distal regulatory elements such as enhancers may activate transcription over long distances; hence, their action must be restricted within appropriate boundaries to prevent illegitimate activation of non-target genes. Insulators are DNA elements with enhancer-blocking and/or chromatin-bordering functions. In vertebrates, the versatile transcription regulator CCCTC-binding factor (CTCF) is the only identified trans -acting factor that confers enhancer-blocking insulator activity. CTCF-binding sites were found to be commonly distributed along the vertebrate genomes. We have constructed a CTCF-binding site database (CTCFBSDB) to characterize experimentally identified and computationally predicted CTCF-binding sties. Biological knowledge and data from multiple resources have been integrated into the database, including sequence data, genetic polymorphisms, function annotations, histone methylation profiles, gene expression profiles and comparative genomic information. A web-based user interface was implemented for data retrieval, analysis and visualization. In silico prediction of CTCF-binding motifs is provided to facilitate the identification of candidate insulators in the query sequences submitted by users. The database can be accessed at http://insulatordb.utmem.edu/.

UR - http://www.scopus.com/inward/record.url?scp=38549161074&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=38549161074&partnerID=8YFLogxK

U2 - 10.1093/nar/gkm875

DO - 10.1093/nar/gkm875

M3 - Article

VL - 36

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - SUPPL. 1

ER -