Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library.

The recently completed Caenorhabditis elegans genome sequence allows application of high-throughput (HT) approaches for phenotypic analyses using RNA interference (RNAi). As large phenotypic data sets become available, "phenoclustering" strategies can be used to begin understanding the complex molecular networks involved in development and other biological processes. The current HT-RNAi resources represent a great asset for phenotypic profiling but are limited by lack of flexibility. For instance, existing resources do not take advantage of the latest improvements in RNAi technology, such as inducible hairpin RNAi. Here we show that a C. elegans ORFeome resource, generated with the Gateway cloning system, can be used as a starting point to generate alternative HT-RNAi resources with enhanced flexibility. The versatility inherent to the Gateway system suggests that additional HT-RNAi libraries can now be readily generated to perform gene knockdowns under various conditions, increasing the possibilities for phenome mapping in C. elegans.

[1]  A. Fire,et al.  Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference. , 2000, Molecular cell.

[2]  Gary Ruvkun,et al.  Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes , 2003, Nature.

[3]  F. Collins,et al.  The Human Genome Project: Lessons from Large-Scale Biology , 2003, Science.

[4]  Marc Vidal,et al.  Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. , 2004, Molecular cell.

[5]  L. Stein,et al.  RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans , 2000, Current Biology.

[6]  Kimberly Van Auken,et al.  WormBase: a multi-species resource for nematode biology and genomics , 2004, Nucleic Acids Res..

[7]  M. Vidal,et al.  Combined Functional Genomic Maps of the C. elegans DNA Damage Response , 2002, Science.

[8]  P. Zipperlen,et al.  Roles for 147 embryonic lethal genes on C.elegans chromosome I identified by RNA interference and video microscopy , 2001, The EMBO journal.

[9]  Gregory J. Hannon,et al.  Insight Review Articles , 2022 .

[10]  M. Vidal,et al.  C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions. , 2004, Genome research.

[11]  Stephen J. Elledge,et al.  The univector plasmid-fusion system, a method for rapid construction of recombinant DNA without restriction enzymes , 1998, Current Biology.

[12]  Andrew G Fraser,et al.  Genome-Wide RNAi of C. elegans Using the Hypersensitive rrf-3 Strain Reveals Novel Gene Functions , 2003, PLoS biology.

[13]  Hilla Peretz,et al.  Ju n 20 03 Schrödinger ’ s Cat : The rules of engagement , 2003 .

[14]  J. Hartley,et al.  DNA cloning using in vitro site-specific recombination. , 2000, Genome research.

[15]  S. Brenner.  The genetics of Caenorhabditis elegans. , 1974, Genetics.

[16]  Y. Dong,et al.  Systematic functional analysis of the Caenorhabditis elegans genome using RNAi , 2003, Nature.

[17]  J. Berg.  Genome sequence of the nematode C. elegans: a platform for investigating biology. , 1998, Science.

[18]  F. Piano,et al.  Gene Clustering Based on RNAi Phenotypes of Ovary-Enriched Genes in C. elegans , 2002, Current Biology.

[19]  T. Moore,et al.  Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans , 2001, Nature Genetics.

[20]  Marc Vidal,et al.  WorfDB: the Caenorhabditis elegans ORFeome Database , 2003, Nucleic Acids Res..

[21]  M. Vidal,et al.  ORFeome projects: gateway between genomics and omics. , 2004, Current opinion in chemical biology.

[22]  P. Zipperlen,et al.  Functional genomic analysis of C. elegans chromosome I by systematic RNA interference , 2000, Nature.

[23]  Sebastian A. Leidel,et al.  Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III , 2000, Nature.

[24]  Kristin C. Gunsalus,et al.  RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects , 2004, Nucleic Acids Res..

[25]  Yuji Kohara,et al.  Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi , 2001, Current Biology.

[26]  Jeffrey M Good,et al.  Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans. , 2003, Genome research.

[27]  J. Hudson,et al.  C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression , 2003, Nature Genetics.

[28]  Andrew G Fraser,et al.  Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAi. , 2003, Genes & development.

[29]  A. Fire,et al.  Specific interference by ingested dsRNA , 1998, Nature.

[30]  Erik M. Jorgensen,et al.  The art and design of genetic screens: Caenorhabditis elegans , 2002, Nature Reviews Genetics.

[31]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[32]  N. Perrimon,et al.  Genome-Wide RNAi Analysis of Growth and Viability in Drosophila Cells , 2004, Science.

[33]  M Mochii,et al.  Use of cDNA subtraction and RNA interference screens in combination reveals genes required for germ-line development in Caenorhabditis elegans , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[34]  C. Mello,et al.  RNAi in C. elegans: Soaking in the Genome Sequence , 1998, Science.

[35]  Gary Ruvkun,et al.  A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity , 2003, Nature Genetics.

[36]  M. Vidal,et al.  GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. , 2000, Methods in enzymology.

[37]  S. Elledge,et al.  Towards genetic genome projects: genomic library screening and gene-targeting vector construction in a single step , 2002, Nature Genetics.

[38]  Nektarios Tavernarakis,et al.  Heritable and inducible genetic interference by double-stranded RNA encoded by transgenes , 2000, Nature Genetics.

[39]  M. Vidal,et al.  Protein interaction mapping in C. elegans using proteins involved in vulval development. , 2000, Science.

[40]  Julie Ahringer,et al.  A Genome-Wide Screen Identifies 27 Genes Involved in Transposon Silencing in C. elegans , 2003, Current Biology.

[41]  David E Hill,et al.  A first version of the Caenorhabditis elegans Promoterome. , 2004, Genome research.