title: Decoding the genome with an integrative analysis tool: combinatorial CRM Decoder.
abstract: The identification of genome-wide cis-regulatory modules (CRMs) and characterization of their associated epigenetic features are fundamental steps toward the understanding of gene regulatory networks. Although integrative analysis of available genome-wide information can provide new biological insights, the lack of novel methodologies has become a major bottleneck. Here, we present a comprehensive analysis tool called combinatorial CRM decoder (CCD), which utilizes the publicly available information to identify and characterize genome-wide CRMs in a species of interest. CCD first defines a set of the epigenetic features which is significantly associated with a set of known CRMs as a code called 'trace code', and subsequently uses the trace code to pinpoint putative CRMs throughout the genome. Using 61 genome-wide data sets obtained from 17 independent mouse studies, CCD successfully catalogued ∼12 600 CRMs (five distinct classes) including polycomb repressive complex 2 target sites as well as imprinting control regions. Interestingly, we discovered that ∼4% of the identified CRMs belong to at least two different classes named 'multi-functional CRM', suggesting their functional importance for regulating spatiotemporal gene expression. From these examples, we show that CCD can be applied to any potential genome-wide datasets and therefore will shed light on unveiling genome-wide CRMs in various species.
authors: Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
authors: Keunsoo
authors: K
authors: Kang
authors: Joomyeong
authors: J
authors: Kim
authors: Jae Hoon
authors: JH
authors: Chung
authors: Daeyoup
authors: D
authors: Lee
mesh_terms: D000465:Algorithms; D000818:Animals; D023281:Genomics / Q000379:methods; D006657:Histones / Q000378:metabolism; D051379:Mice; D050436:Regulatory Elements, Transcriptional; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D006657:Histones; D014157:Transcription Factors