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Comprehensive, high resolution analysis of cis-acting regulatory networks at the alpha globin locus (HTS)


ABSTRACT: We have combined the 4C chromosome conformation capture protocol with high throughput, genome-wide sequence analysis to characterise in full a cis-acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10-1000kb), the 4C approach provides a comprehensive, high resolution analysis of a specific locus with the aim of defining, in detail, all cis- regulatory elements controlling a single gene or gene cluster. Using the human M-NM-1-globin locus as a model we detected all known local and long-range interactions with this gene cluster. In addition we identified two interactions with genes located 300 kb (NME4) and 625 kb (FAM173a) from the M-NM-1-globin cluster. Using paired-end sequencing it was possible for the first time to identify interactions between specific subsets of cis-regulatory elements in populations of cells and within individual cells. Two biological replicates of 4C amplification from the promoters of the human HBA gene promoters. Sequenced as paired end fragments usinig Illumina GAII

ORGANISM(S): Homo sapiens

SUBMITTER: Richard Gibbons 

PROVIDER: E-GEOD-42382 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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High-resolution analysis of cis-acting regulatory networks at the α-globin locus.

Hughes Jim R JR   Lower Karen M KM   Dunham Ian I   Taylor Stephen S   De Gobbi Marco M   Sloane-Stanley Jacqueline A JA   McGowan Simon S   Ragoussis Jiannis J   Vernimmen Douglas D   Gibbons Richard J RJ   Higgs Douglas R DR  

Philosophical transactions of the Royal Society of London. Series B, Biological sciences 20130506 1620


We have combined the circular chromosome conformation capture protocol with high-throughput, genome-wide sequence analysis to characterize the cis-acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10-1000 kb), the 4C approach provides a comprehensive, high-resolution analysis of a specific locus with the aim of defining, in detail, the cis-regulatory elements controlling a single gene or gene cluster. Using the human α-globin locus as a  ...[more]

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