A first version of the Caenorhabditis elegans Promoterome.

An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such "localizome" maps should provide information on where (in what cells or tissues) and when (at what stage of development or under what conditions) genes are expressed. They should also indicate in what cellular compartments the corresponding proteins are localized. Caenorhabditis elegans is particularly suited for the development of a localizome map since all its 959 adult somatic cells can be visualized by microscopy, and its cell lineage has been completely described. Here we address one of the challenges of C. elegans localizome mapping projects: that of obtaining a genome-wide resource of C. elegans promoters needed to generate transgenic animals expressing localization markers such as the green fluorescent protein (GFP). To ensure high flexibility for future uses, we utilized the newly developed MultiSite Gateway system. We generated and validated "version 1.1" of the Promoterome: a resource of approximately 6000 C. elegans promoters. These promoters can be transferred easily into various Gateway Destination vectors to drive expression of markers such as GFP, alone (promoter::GFP constructs), or in fusion with protein-encoding open reading frames available in ORFeome resources (promoter::ORF::GFP).

[1]  T. Ideker,et al.  A new approach to decoding life: systems biology. , 2001, Annual review of genomics and human genetics.

[2]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[3]  M. Chalfie,et al.  Green fluorescent protein as a marker for gene expression. , 1994, Science.

[4]  Marc Vidal,et al.  Integrating Interactome, Phenome, and Transcriptome Mapping Data for the C. elegans Germline , 2002, Current Biology.

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

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

[7]  Elizabeth Casey,et al.  Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. , 2001, Genetics.

[8]  V. Reinke,et al.  A global profile of germline gene expression in C. elegans. , 2000, Molecular cell.

[9]  Hiroaki Kitano,et al.  Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology , 2002, Current Genetics.

[10]  Thomas Blumenthal,et al.  Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. , 2003, Genome research.

[11]  H. Nojima,et al.  High efficiency transformation of Escherichia coli with plasmids. , 1990, Gene.

[12]  M. Vidal.  A Biological Atlas of Functional Maps , 2001, Cell.

[13]  R. Waterston,et al.  Vectors for low copy transformation of C. elegans. , 1990, Nucleic acids research.

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

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

[16]  P. Thuriaux,et al.  A protein-protein interaction map of yeast RNA polymerase III. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Joshua M. Stuart,et al.  A Gene Expression Map for Caenorhabditis elegans , 2001, Science.

[18]  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.

[19]  S. Eimer,et al.  The Caenorhabditis elegans presenilin sel-12 is required for mesodermal patterning and muscle function. , 2002, Developmental biology.

[20]  A. Fire,et al.  Sequence requirements for myosin gene expression and regulation in Caenorhabditis elegans. , 1993, Genetics.

[21]  J. Hartley,et al.  Concerted assembly and cloning of multiple DNA segments using in vitro site-specific recombination: functional analysis of multi-segment expression clones. , 2004, Genome research.

[22]  P. Green,et al.  OSP: a computer program for choosing PCR and DNA sequencing primers. , 1991, PCR methods and applications.

[23]  J. Way,et al.  The mec‐7 beta‐tubulin gene of Caenorhabditis elegans is expressed primarily in the touch receptor neurons. , 1992, The EMBO journal.

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

[25]  M. Vidal,et al.  A gateway-compatible yeast one-hybrid system. , 2004, Genome research.

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

[27]  Y. Kohara,et al.  A multi-well version of in situ hybridization on whole mount embryos of Caenorhabditis elegans. , 1996, Nucleic acids research.

[28]  Paul W. Sternberg,et al.  WormBase: network access to the genome and biology of Caenorhabditis elegans , 2001, Nucleic Acids Res..

[29]  E. O’Shea,et al.  Global analysis of protein localization in budding yeast , 2003, Nature.

[30]  H. Horvitz,et al.  The TRA-1A Sex Determination Protein of C. elegans Regulates Sexually Dimorphic Cell Deaths by Repressing the egl-1 Cell Death Activator Gene , 1999, Cell.

[31]  M. Gerstein,et al.  Subcellular localization of the yeast proteome. , 2002, Genes & development.

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

[33]  I. Hope.  'Promoter trapping' in Caenorhabditis elegans. , 1991, Development.

[34]  S. L. Wong,et al.  A Map of the Interactome Network of the Metazoan C. elegans , 2004, Science.

[35]  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.

[36]  I. Hope,et al.  Promoter trapping identifies real genes in C. elegans , 1998, Molecular and General Genetics MGG.

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

[38]  M. Vidal,et al.  Feasibility of genome-scale construction of promoter::reporter gene fusions for expression in Caenorhabditis elegans using a multisite gateway recombination system. , 2004, Genome research.

[39]  Nicola J. Rinaldi,et al.  Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.

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

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

[42]  Jean Thierry-Mieg,et al.  A global analysis of Caenorhabditis elegans operons , 2002, Nature.

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

[44]  P. Waterhouse,et al.  Construct design for efficient, effective and high-throughput gene silencing in plants. , 2001, The Plant journal : for cell and molecular biology.

[45]  M. Vidal,et al.  A protein–protein interaction map of the Caenorhabditis elegans 26S proteasome , 2001, EMBO reports.

[46]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

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

[48]  Thomas Werner,et al.  Promoters can contribute to the elucidation of protein function. , 2003, Trends in biotechnology.

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