title: A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels.
abstract: Gene expression is regulated at multiple levels, including transcription and translation, as well as mRNA and protein stability. Although systems-level functions of transcription factors and microRNAs are rapidly being characterized, few studies have focused on the posttranscriptional gene regulation by RNA binding proteins (RBPs). RBPs are important to many aspects of gene regulation. Thus, it is essential to know which genes encode RBPs, which RBPs regulate which gene(s), and how RBP genes are themselves regulated. Here we provide a comprehensive compendium of RBPs from the nematode Caenorhabditis elegans (wRBP1.0). We predict that as many as 887 (4.4%) of C. elegans genes may encode RBPs ~250 of which likely function in a gene-specific manner. In addition, we find that RBPs, and most notably gene-specific RBPs, are themselves enriched for binding and modification by regulatory proteins, indicating the potential for extensive regulation of RBPs at many different levels. wRBP1.0 will provide a significant contribution toward the comprehensive delineation of posttranscriptional regulatory networks and will provide a resource for further studies regulation by RBPs.
authors: Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
authors: Alex M
authors: AM
authors: Tamburino
authors: Sean P
authors: SP
authors: Ryder
authors: Albertha J M
authors: AJ
authors: Walhout
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D029742:Caenorhabditis elegans Proteins / Q000235:genetics / Q000378:metabolism*; D005786:Gene Expression Regulation; D016678:Genome; D035683:MicroRNAs / Q000378:metabolism; D010766:Phosphorylation; D012333:RNA, Messenger / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D012984:Software; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; D029742:Caenorhabditis elegans Proteins; D035683:MicroRNAs; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D014157:Transcription Factors
keywords: C. elegans; RBP; RNA binding protein; gene expression; regulation; systems biology
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