Molecular Biology

Reading Chromatin Signatures

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Science  02 Mar 2007:
Vol. 315, Issue 5816, pp. 1194
DOI: 10.1126/science.315.5816.1194d

Regulated gene expression requires a highly choreographed assembly and disassembly of transcription factors to segments of DNA. This process must occur both near gene promoters and at enhancers, which can be present upstream or downstream of the gene being expressed. Specific epigenetic features also mark the degree of activity of the transcribing unit. Genes that are being actively transcribed generally contain nucleosomes with acetylated histone proteins, H3 and H4, as well as methylated H3; in contrast, DNA segments with inactive expression normally have deacetylated histones. Heintzman et al. used a combination of chromatin immunoprecipitation and microarray analysis to map histone modifications, transcription-factor binding, and nucleosome density within 30 Mb of the human genome. The study revealed that active human promoters were nucleosome-depleted. Furthermore, these promoters also showed enrichment of trimethylation of Lys4 of histone H3 (H3K4), whereas the enhancers showed enrichment of monomethylated H3K4.

The authors went on to incorporate these distinct promoter and enhancer chromatin signatures into a computational algorithm. Analysis with this model allowed them to successfully predict the identities of several hundred promoters and enhancers of other genes in the 30-Mb region. — BAP

Nat. Genet. 39, 10.1038/ng1966 (2007).

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