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Genome-wide mapping cis-regulatory sequence elements in the human genome using Nuclease-Hypersensitive-CGH technique

ABSTRACT: Cis-regulatory sequences are the key elements for understanding global, context-dependent gene expression program in response to environmental challenges. Because of uncertainty in their location relative to gene, nuclease hypersensitivity has been used as the robust experimental approach for identifying these regulatory elements. We used oligonucleotide array chip and 454 sequencing platform to map the nuclease-hypersensitive sites (NHSS) in MCF-7 cell genome. Small DNA fragments released after very mild micrococcal nuclease treatment were found to be highly associated with promoter, transcription factor binding sites, regulatory potential and gene expression. In addition, sequencing data reveal three classes of novel NHSS not reported previously: 1) those containing regular repeat of NHSS (RNHSS), 2) those containing mitochondria sequence inserts (MNHSS), and 3) those containing highly clustered NHSS (CNHSS). Blatting analysis shows that these novel NHSS are highly associated with genome rearrangements and creation of novel genes during primate genome evolution. Repeated genes/ESTs in RNHSS are often widely expressed in human adult and fetal tissues. The majority of NHSS is sensitive to alpha-amanitin treatment with the exception of RNHSS and some genes with amanitin-insensitive expression. We suggest that study of these novel classes of NHSS may be crucial for understanding primate genome evolution.

ORGANISM(S): Homo sapiens

PROVIDER: GSE12650 | GEO | 2008/09/05

SECONDARY ACCESSION(S): PRJNA113053

REPOSITORIES: GEO

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Genome-wide mapping cis-regulatory sequence elements in the human genome using Nuclease-Hypersensitive-CGH technique

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