Systematic analysis of dynamic miRNA-target interactions during C. elegans development

Zhang, L., Hammell, M., Kudlow, B. A., Ambros, V., Han, M. (September 2009) Systematic analysis of dynamic miRNA-target interactions during C. elegans development. Development, 136 (18). pp. 3043-55. ISSN 0950-1991

URL: http://www.ncbi.nlm.nih.gov/pubmed/19675127
DOI: 10.1242/dev.039008

Abstract

Although microRNA (miRNA)-mediated functions have been implicated in many aspects of animal development, the majority of miRNA::mRNA regulatory interactions remain to be characterized experimentally. We used an AIN/GW182 protein immunoprecipitation approach to systematically analyze miRNA::mRNA interactions during C. elegans development. We characterized the composition of miRNAs in functional miRNA-induced silencing complexes (miRISCs) at each developmental stage and identified three sets of miRNAs with distinct stage-specificity of function. We then identified thousands of miRNA targets in each developmental stage, including a significant portion that is subject to differential miRNA regulation during development. By identifying thousands of miRNA family-mRNA pairs with temporally correlated patterns of AIN-2 association, we gained valuable information on the principles of physiological miRNA::target recognition and predicted 1589 high-confidence miRNA family::mRNA interactions. Our data support the idea that miRNAs preferentially target genes involved in signaling processes and avoid genes with housekeeping functions, and that miRNAs orchestrate temporal developmental programs by coordinately targeting or avoiding genes involved in particular biological functions.

Item Type: Paper
Uncontrolled Keywords: 3' Untranslated Regions Animals *Caenorhabditis elegans/genetics/growth & development Caenorhabditis elegans Proteins/genetics/metabolism Carrier Proteins/genetics/metabolism Gene Expression Profiling *Gene Expression Regulation, Developmental MicroRNAs/genetics/*metabolism Oligonucleotide Array Sequence Analysis RNA, Messenger/genetics/*metabolism Recombinant Fusion Proteins/genetics/metabolism
Subjects: organism description > animal > C elegans
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA
CSHL Authors:
Communities: CSHL labs > Hammell M. lab
Depositing User: Matt Covey
Date: September 2009
Date Deposited: 06 Nov 2014 17:38
Last Modified: 06 Nov 2014 17:38
PMCID: PMC2730362
Related URLs:
URI: http://repository.cshl.edu/id/eprint/30881

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