Program in Molecular Medicine Publications and Presentations Copyright (c) 2013 University of Massachusetts Medical School All rights reserved. http://escholarship.umassmed.edu/pmm_pp Recent documents in Program in Molecular Medicine Publications and Presentations en-us Thu, 16 May 2013 11:01:25 PDT 3600 Systematic analysis of dynamic miRNA-target interactions during C. elegans development http://escholarship.umassmed.edu/pmm_pp/3 http://escholarship.umassmed.edu/pmm_pp/3 Wed, 16 Jun 2010 06:42:00 PDT 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.

]]> Liang Zhang et al. 3' Untranslated Regions Animals *Caenorhabditis elegans Caenorhabditis elegans Proteins Carrier Proteins Gene Expression Profiling *Gene Expression Regulation, Developmental MicroRNAs Oligonucleotide Array Sequence Analysis RNA, Messenger Recombinant Fusion Proteins Inhibiting miRNA in Caenorhabditis elegans using a potent and selective antisense reagent http://escholarship.umassmed.edu/pmm_pp/1 http://escholarship.umassmed.edu/pmm_pp/1 Wed, 16 Jun 2010 06:41:59 PDT BACKGROUND: Antisense reagents can serve as efficient and versatile tools for studying gene function by inhibiting nucleic acids in vivo. Antisense reagents have particular utility for the experimental manipulation of the activity of microRNAs (miRNAs), which are involved in the regulation of diverse developmental and physiological pathways in animals. Even in traditional genetic systems, such as the nematode Caenorhabditis elegans, antisense reagents can provide experimental strategies complementary to mutational approaches. Presently no antisense reagents are available for inhibiting miRNAs in the nematode C. elegans.

RESULTS: We have developed a new class of fluorescently labelled antisense reagents to inhibit miRNAs in developing worms. These reagents were synthesized by conjugating dextran with 2'-O-methyl oligoribonucleotide. The dextran-conjugated antisense reagents can be conveniently introduced into the germline of adult hermaphrodites and are transmitted to their progeny, where they efficiently and specifically inhibit a targeted miRNA in different tissues, including the hypodermis, the vulva and the nervous system. We show that these reagents can be used combinatorially to inhibit more than one miRNA in the same animal.

CONCLUSION: This class of antisense reagents represents a new addition to the toolkit for studying miRNA in C. elegans. Combined with numerous mutants or reporter stains available, these reagents should provide a convenient approach to examine genetic interactions that involve miRNA, and may facilitate studying functions of miRNAs, especially ones whose deletion strains are difficult to generate.See related research article: http://jbiol.com/content/9/3/20.

]]> Genhua Zheng et al. Caenorhabditis elegans Caenorhabditis elegans Proteins MicroRNAs RNA, Antisense In the tradition of science: an interview with Victor Ambros http://escholarship.umassmed.edu/pmm_pp/2 http://escholarship.umassmed.edu/pmm_pp/2 Wed, 16 Jun 2010 06:41:59 PDT Victor R. Ambros Animals History, 20th Century History, 21st Century Molecular Biology Science United States