发现具有潜在调控特征的序列。

Discovering sequences with potential regulatory characteristics.

作者信息

Bina Minou, Wyss Phillip, Lazarus Sheryl A, Shah Syed R, Ren Wenhui, Szpankowski Wojciech, Crawford Gregory E, Park Sang P, Song Xiaohui C

机构信息

Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.

出版信息

Genomics. 2009 Apr;93(4):314-22. doi: 10.1016/j.ygeno.2008.11.008. Epub 2008 Dec 30.

DOI:10.1016/j.ygeno.2008.11.008

PMID:19084590

Abstract

We developed a computational model to explore the hypothesis that regulatory instructions are context dependent and conveyed through specific 'codes' in human genomic DNA. We provide examples of correlation of computational predictions to reported mapped DNase I hypersensitive segments in the HOXA locus in human chromosome 7. The examples show that statistically significant 9-mers from promoter regions may occur in sequences near and upstream of transcription initiation sites, in intronic regions, and within intergenic regions. Additionally, a subset of 9-mers from coding sequences appears frequently, as clusters, in regulatory regions dispersed in noncoding regions in genomic DNA. The results suggest that the computational model has the potential of decoding regulatory instructions to discover candidate transcription factor binding sites and to discover candidate epigenetic signals that appear in both coding and regulatory regions of genes.

摘要

我们开发了一种计算模型，以探究调控指令依赖于上下文并通过人类基因组DNA中的特定“密码”进行传递这一假说。我们提供了计算预测与人类7号染色体HOXA基因座中报道的定位DNase I超敏片段之间相关性的示例。这些示例表明，来自启动子区域的具有统计学意义的9聚体可能出现在转录起始位点附近和上游的序列、内含子区域以及基因间区域中。此外，来自编码序列的9聚体子集经常以簇的形式出现在基因组DNA非编码区域中分散的调控区域。结果表明，该计算模型具有解码调控指令以发现候选转录因子结合位点以及发现出现在基因编码区和调控区的候选表观遗传信号的潜力。