Two-dimensional electrophoretic mobility shift assay: Identification and mapping of transcription factor CTCF target sequences within an FXYD5– COX7A1 region of human chromosome 19

An approach for fast identification and mapping of transcription factor binding sites within long genomic sequences is proposed. Using this approach, 10 CCCTC-binding factor (CTCF) binding sites were identified within a 1-Mb FXYD5– COX7A1 human chromosome 19 region. In vivo binding of CTCF to these...

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Bibliographic Details
Published in:Analytical biochemistry 2006-07, Vol.354 (1), p.85-93
Main Authors: Vetchinova, Anna S., Akopov, Sergey B., Chernov, Igor P., Nikolaev, Lev G., Sverdlov, Eugene D.
Format: Article
Language:English
Subjects:
Alu Elements
Binding Sites
CCCTC-Binding Factor
Chromatin Immunoprecipitation - methods
Chromosome Mapping
Chromosomes, Human, Pair 19
CTCF
DNA, Intergenic
DNA-Binding Proteins - analysis
DNA-Binding Proteins - metabolism
Electron Transport Complex IV - genetics
Electrophoretic Mobility Shift Assay - methods
HeLa Cells
Human genome
Humans
Introns
Mapping
Membrane Glycoproteins - genetics
Models, Genetic
Neoplasm Proteins - genetics
Repressor Proteins - analysis
Repressor Proteins - metabolism
Transcription factor
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Summary:An approach for fast identification and mapping of transcription factor binding sites within long genomic sequences is proposed. Using this approach, 10 CCCTC-binding factor (CTCF) binding sites were identified within a 1-Mb FXYD5– COX7A1 human chromosome 19 region. In vivo binding of CTCF to these sites was verified by chromatin immunoprecipitation assay. CTCF binding sites were mapped within gene introns and intergenic regions, and some of them contained Alu-like repeated elements.
ISSN:0003-2697
1096-0309
DOI:10.1016/j.ab.2006.03.052