NIKULOVA, Anna A; FAVOROV, Alexander V; SUTORMIN, Roman A; MAKEEV, Vsevolod J; MIRONOV, Andrey A

doi:10.1093/nar/gks235

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NIKULOVA, Anna A
Lomonosov Moscow State University = Université d'État Lomonossov de Moscou [Moscou] [MSU]
Institute for Information Transmission Problems [IITP]

FAVOROV, Alexander V
Johns Hopkins University School of Medicine [Baltimore]

SUTORMIN, Roman A
Lomonosov Moscow State University = Université d'État Lomonossov de Moscou [Moscou] [MSU]

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Nucleic Acids Research. 2012-03-15, vol. 40, n° 12, p. 1-10

Oxford University Press

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Identification of transcriptional regulatory regions and tracing their internal organization are important for understanding the eukaryotic cell machinery. Cis-regulatory modules (CRMs) of higher eukaryotes are believed to possess a regulatory 'grammar', or preferred arrangement of binding sites, that is crucial for proper regulation and thus tends to be evolutionarily conserved. Here, we present a method CORECLUST (COnservative REgulatory CLUster STructure) that predicts CRMs based on a set of positional weight matrices. Given regulatory regions of orthologous and/or co-regulated genes, CORECLUST constructs a CRM model by revealing the conserved rules that describe the relative location of binding sites. The constructed model may be consequently used for the genome-wide prediction of similar CRMs, and thus detection of co-regulated genes, and for the investigation of the regulatory grammar of the system. Compared with related methods, CORECLUST shows better performance at identification of CRMs conferring muscle-specific gene expression in vertebrates and early-developmental CRMs in Drosophila.< Leer menos

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CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.

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