High-throughput in Vivo Analysis of Gene Expression in Caenorhabditis Elegans

Overview

Journal PLoS Biol

Specialty Biology

Date 2007 Sep 14

PMID 17850180

Citations 235

Authors

Rebecca Hunt-Newbury

Ryan Viveiros

Robert Johnsen

Allan Mah

Dina Anastas

Lily Fang

Erin Halfnight

David Lee

John Lin

Adam Lorch

Sheldon McKay

H Mark Okada

Jie Pan

Ana K Schulz

Domena Tu

Kim Wong

Z Zhao

Andrey Alexeyenko

Thomas Burglin

Eric Sonnhammer

Ralf Schnabel

Steven J Jones

Marco A Marra

David L Baillie

Donald G Moerman

Affiliations

Soon will be listed here.

Abstract

Using DNA sequences 5' to open reading frames, we have constructed green fluorescent protein (GFP) fusions and generated spatial and temporal tissue expression profiles for 1,886 specific genes in the nematode Caenorhabditis elegans. This effort encompasses about 10% of all genes identified in this organism. GFP-expressing wild-type animals were analyzed at each stage of development from embryo to adult. We have identified 5' DNA regions regulating expression at all developmental stages and in 38 different cell and tissue types in this organism. Among the regulatory regions identified are sequences that regulate expression in all cells, in specific tissues, in combinations of tissues, and in single cells. Most of the genes we have examined in C. elegans have human orthologs. All the images and expression pattern data generated by this project are available at WormAtlas (http://gfpweb.aecom.yu.edu/index) and through WormBase (http://www.wormbase.org).

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References

Chen L, Krause M, Draper B, Weintraub H, Fire A . Body-wall muscle formation in Caenorhabditis elegans embryos that lack the MyoD homolog hlh-1. Science. 1992; 256(5054):240-3. DOI: 10.1126/science.1314423. View

Krause M, Fire A, HARRISON S, Priess J, Weintraub H . CeMyoD accumulation defines the body wall muscle cell fate during C. elegans embryogenesis. Cell. 1990; 63(5):907-19. DOI: 10.1016/0092-8674(90)90494-y. View

Chen L, Krause M, Sepanski M, Fire A . The Caenorhabditis elegans MYOD homologue HLH-1 is essential for proper muscle function and complete morphogenesis. Development. 1994; 120(6):1631-41. DOI: 10.1242/dev.120.6.1631. View

Dolphin C, Hope I . Caenorhabditis elegans reporter fusion genes generated by seamless modification of large genomic DNA clones. Nucleic Acids Res. 2006; 34(9):e72. PMC: 1464416. DOI: 10.1093/nar/gkl352. View

Sulston J, Schierenberg E, White J, Thomson J . The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev Biol. 1983; 100(1):64-119. DOI: 10.1016/0012-1606(83)90201-4. View

Harris T, Lee R, Schwarz E, Bradnam K, Lawson D, Chen W . WormBase: a cross-species database for comparative genomics. Nucleic Acids Res. 2003; 31(1):133-7. PMC: 165500. DOI: 10.1093/nar/gkg053. View

Sulston J, Horvitz H . Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev Biol. 1977; 56(1):110-56. DOI: 10.1016/0012-1606(77)90158-0. View

Muyrers J, Zhang Y, Stewart A . Techniques: Recombinogenic engineering--new options for cloning and manipulating DNA. Trends Biochem Sci. 2001; 26(5):325-31. DOI: 10.1016/s0968-0004(00)01757-6. View

Blumenthal T . Trans-splicing and polycistronic transcription in Caenorhabditis elegans. Trends Genet. 1995; 11(4):132-6. DOI: 10.1016/s0168-9525(00)89026-5. View

10.

Wilm T, Demel P, Koop H, Schnabel H, Schnabel R . Ballistic transformation of Caenorhabditis elegans. Gene. 1999; 229(1-2):31-5. DOI: 10.1016/s0378-1119(99)00043-8. View

11.

Lynch A, Briggs D, Hope I . Developmental expression pattern screen for genes predicted in the C. elegans genome sequencing project. Nat Genet. 1995; 11(3):309-13. DOI: 10.1038/ng1195-309. View

12.

Rozen S, Skaletsky H . Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 1999; 132:365-86. DOI: 10.1385/1-59259-192-2:365. View

13.

Praitis V, Casey E, Collar D, Austin J . Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. Genetics. 2001; 157(3):1217-26. PMC: 1461581. DOI: 10.1093/genetics/157.3.1217. View

14.

Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis S . Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2003; 3(12):RESEARCH0088. PMC: 151190. DOI: 10.1186/gb-2002-3-12-research0088. View

15.

Lein E, Hawrylycz M, Ao N, Ayres M, Bensinger A, Bernard A . Genome-wide atlas of gene expression in the adult mouse brain. Nature. 2006; 445(7124):168-76. DOI: 10.1038/nature05453. View

16.

Moerman D, Hutter H, Mullen G, Schnabel R . Cell autonomous expression of perlecan and plasticity of cell shape in embryonic muscle of Caenorhabditis elegans. Dev Biol. 1996; 173(1):228-42. DOI: 10.1006/dbio.1996.0019. View

17.

SENGUPTA P, Chou J, Bargmann C . odr-10 encodes a seven transmembrane domain olfactory receptor required for responses to the odorant diacetyl. Cell. 1996; 84(6):899-909. DOI: 10.1016/s0092-8674(00)81068-5. View

18.

Fukushige T, Brodigan T, Schriefer L, Waterston R, Krause M . Defining the transcriptional redundancy of early bodywall muscle development in C. elegans: evidence for a unified theory of animal muscle development. Genes Dev. 2006; 20(24):3395-406. PMC: 1698447. DOI: 10.1101/gad.1481706. View

19.

Sarov M, Schneider S, Pozniakovski A, Roguev A, Ernst S, Zhang Y . A recombineering pipeline for functional genomics applied to Caenorhabditis elegans. Nat Methods. 2006; 3(10):839-44. DOI: 10.1038/nmeth933. View

20.

McGhee J, Sleumer M, Bilenky M, Wong K, McKay S, Goszczynski B . The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol. 2006; 302(2):627-45. DOI: 10.1016/j.ydbio.2006.10.024. View