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 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.
Vetchinova
Anna S
AS
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
Akopov
Sergey B
SB
Chernov
Igor P
IP
Nikolaev
Lev G
LG
Sverdlov
Eugene D
ED
D020087:Alu Elements; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D047369:Chromatin Immunoprecipitation / Q000379:methods; D002874:Chromosome Mapping; D002888:Chromosomes, Human, Pair 19; D021901:DNA, Intergenic; D004268:DNA-Binding Proteins / Q000032:analysis / Q000378:metabolism*; D003576:Electron Transport Complex IV / Q000235:genetics*; D024202:Electrophoretic Mobility Shift Assay / Q000379:methods*; D006367:HeLa Cells; D006801:Humans; D007438:Introns; D007473:Ion Channels; D008562:Membrane Glycoproteins / Q000235:genetics*; D008840:Microfilament Proteins; D008957:Models, Genetic; D009363:Neoplasm Proteins / Q000235:genetics*; D012097:Repressor Proteins / Q000032:analysis / Q000378:metabolism*
D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D021901:DNA, Intergenic; D004268:DNA-Binding Proteins; C451410:FXYD5 protein, human; D007473:Ion Channels; D008562:Membrane Glycoproteins; D008840:Microfilament Proteins; D009363:Neoplasm Proteins; D012097:Repressor Proteins; C513901:COX7A1 protein, human; D003576:Electron Transport Complex IV