Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans

G3: Genes, Genomes, Genetics

Guoyan Zhao²  Gary D. Stormo²  Larry Schriefer²  Ting Wang²  Nnamdi Ihuegbu²  Mo Lee¹ 

[1]Brigham Young University, Provo, Utah 84602Brigham Young University, Provo, Utah 84602Brigham Young University, Provo, Utah 84602

[2]Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110

关键词: cis-regulatory element;    cis-regulatory module;    transcription factor;    transcriptional regulation;    Caenorhabditis elegans;   

DOI  :  10.1534/g3.111.001081

学科分类：生物科学（综合）

来源: Genetics Society of America

【 摘 要 】

Transcriptional regulation, a primary mechanism for controlling the development of multicellular organisms, is carried out by transcription factors (TFs) that recognize and bind to their cognate binding sites. In Caenorhabditis elegans, our knowledge of which genes are regulated by which TFs, through binding to specific sites, is still very limited. To expand our knowledge about the C. elegans regulatory network, we performed a comprehensive analysis of the C. elegans, Caenorhabditis briggsae, and Caenorhabditis remanei genomes to identify regulatory elements that are conserved in all genomes. Our analysis identified 4959 elements that are significantly conserved across the genomes and that each occur multiple times within each genome, both hallmarks of functional regulatory sites. Our motifs show significant matches to known core promoter elements, TF binding sites, splice sites, and poly-A signals as well as many putative regulatory sites. Many of the motifs are significantly correlated with various types of experimental data, including gene expression patterns, tissue-specific expression patterns, and binding site location analysis as well as enrichment in specific functional classes of genes. Many can also be significantly associated with specific TFs. Combinations of motif occurrences allow us to predict the location of cis-regulatory modules and we show that many of them significantly overlap experimentally determined enhancers. We provide access to the predicted binding sites, their associated motifs, and the predicted cis-regulatory modules across the whole genome through a web-accessible database and as tracks for genome browsers.

【 授权许可】

Unknown