Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans

B. Sönnichsen; L. B. Koski; A. Walsh; P. Marschall; B. Neumann; M. Brehm; A. M. Alleaume; J. Artelt; P. Bettencourt; E. Cassin; M. Hewitson; C. Holz; M. Khan; S. Lazik; C. Martin; B. Nitzsche; M. Ruer; J. Stamford; M. Winzi; R. Heinkel; M. Röder; J. Finell; H. Häntsch; S. J M Jones; M. Jones; F. Piano; K. C. Gunsalus; K. Oegema; P. Gönczy; A. Coulson; A. A. Hyman; C. J. Echeverri

doi:10.1038/nature03353

Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans

B. Sönnichsen, L. B. Koski, A. Walsh, P. Marschall, B. Neumann, M. Brehm, A. M. Alleaume, J. Artelt, P. Bettencourt, E. Cassin, M. Hewitson, C. Holz, M. Khan, S. Lazik, C. Martin, B. Nitzsche, M. Ruer, J. Stamford, M. Winzi, R. HeinkelM. Röder, J. Finell, H. Häntsch, S. J M Jones, M. Jones, F. Piano, K. C. Gunsalus, K. Oegema, P. Gönczy, A. Coulson, A. A. Hyman, C. J. Echeverri

Research output: Contribution to journal › Article › peer-review

Abstract

A key challenge of functional genomics today is to generate well-annotated data sets that can be interpreted across different platforms and technologies. Large-scale functional genomics data often fail to connect to standard experimental approaches of gene characterization in individual laboratories. Furthermore, a lack of universal annotation standards for phenotypic data sets makes it difficult to compare different screening approaches. Here we address this problem in a screen designed to identify all genes required for the first two rounds of cell division in the Caenorhabditis elegans embryo. We used RNA-mediated interference to target 98% of all genes predicted in the C. elegans genome in combination with differential interference contrast time-lapse microscopy. Through systematic annotation of the resulting movies, we developed a phenotypic profiling system, which shows high correlation with cellular processes and biochemical pathways, thus enabling us to predict new functions for previously uncharacterized genes.

Original language	English (US)
Pages (from-to)	462-469
Number of pages	8
Journal	Nature
Volume	434
Issue number	7032
DOIs	https://doi.org/10.1038/nature03353
State	Published - Mar 24 2005

ASJC Scopus subject areas

General

Access to Document

10.1038/nature03353

Cite this

Sönnichsen, B., Koski, L. B., Walsh, A., Marschall, P., Neumann, B., Brehm, M., Alleaume, A. M., Artelt, J., Bettencourt, P., Cassin, E., Hewitson, M., Holz, C., Khan, M., Lazik, S., Martin, C., Nitzsche, B., Ruer, M., Stamford, J., Winzi, M., ... Echeverri, C. J. (2005). Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature, 434(7032), 462-469. https://doi.org/10.1038/nature03353

Sönnichsen, B, Koski, LB, Walsh, A, Marschall, P, Neumann, B, Brehm, M, Alleaume, AM, Artelt, J, Bettencourt, P, Cassin, E, Hewitson, M, Holz, C, Khan, M, Lazik, S, Martin, C, Nitzsche, B, Ruer, M, Stamford, J, Winzi, M, Heinkel, R, Röder, M, Finell, J, Häntsch, H, Jones, SJM, Jones, M, Piano, F , Gunsalus, KC, Oegema, K, Gönczy, P, Coulson, A, Hyman, AA & Echeverri, CJ 2005, 'Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans', Nature, vol. 434, no. 7032, pp. 462-469. https://doi.org/10.1038/nature03353

@article{0e017fc832f94d2bbf5bdb6e5fb14d4b,

title = "Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans",

abstract = "A key challenge of functional genomics today is to generate well-annotated data sets that can be interpreted across different platforms and technologies. Large-scale functional genomics data often fail to connect to standard experimental approaches of gene characterization in individual laboratories. Furthermore, a lack of universal annotation standards for phenotypic data sets makes it difficult to compare different screening approaches. Here we address this problem in a screen designed to identify all genes required for the first two rounds of cell division in the Caenorhabditis elegans embryo. We used RNA-mediated interference to target 98% of all genes predicted in the C. elegans genome in combination with differential interference contrast time-lapse microscopy. Through systematic annotation of the resulting movies, we developed a phenotypic profiling system, which shows high correlation with cellular processes and biochemical pathways, thus enabling us to predict new functions for previously uncharacterized genes.",

author = "B. S{\"o}nnichsen and Koski, {L. B.} and A. Walsh and P. Marschall and B. Neumann and M. Brehm and Alleaume, {A. M.} and J. Artelt and P. Bettencourt and E. Cassin and M. Hewitson and C. Holz and M. Khan and S. Lazik and C. Martin and B. Nitzsche and M. Ruer and J. Stamford and M. Winzi and R. Heinkel and M. R{\"o}der and J. Finell and H. H{\"a}ntsch and Jones, {S. J M} and M. Jones and F. Piano and Gunsalus, {K. C.} and K. Oegema and P. G{\"o}nczy and A. Coulson and Hyman, {A. A.} and Echeverri, {C. J.}",

note = "Funding Information: Acknowledgements We thank M. Srayko, C. Cowan, L. Pelletier and W. B. Wood for critical reading of the manuscript, and M. Volkmer and S. Schloissnig for their help on the completion of the online Phenobank database. This work was supported in part by the German government through a DLR grant. A.C. was supported by the MRC, UK.",

year = "2005",

month = mar,

day = "24",

doi = "10.1038/nature03353",

language = "English (US)",

volume = "434",

pages = "462--469",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7032",

}

TY - JOUR

T1 - Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans

AU - Sönnichsen, B.

AU - Koski, L. B.

AU - Walsh, A.

AU - Marschall, P.

AU - Neumann, B.

AU - Brehm, M.

AU - Alleaume, A. M.

AU - Artelt, J.

AU - Bettencourt, P.

AU - Cassin, E.

AU - Hewitson, M.

AU - Holz, C.

AU - Khan, M.

AU - Lazik, S.

AU - Martin, C.

AU - Nitzsche, B.

AU - Ruer, M.

AU - Stamford, J.

AU - Winzi, M.

AU - Heinkel, R.

AU - Röder, M.

AU - Finell, J.

AU - Häntsch, H.

AU - Jones, S. J M

AU - Jones, M.

AU - Piano, F.

AU - Gunsalus, K. C.

AU - Oegema, K.

AU - Gönczy, P.

AU - Coulson, A.

AU - Hyman, A. A.

AU - Echeverri, C. J.

N1 - Funding Information: Acknowledgements We thank M. Srayko, C. Cowan, L. Pelletier and W. B. Wood for critical reading of the manuscript, and M. Volkmer and S. Schloissnig for their help on the completion of the online Phenobank database. This work was supported in part by the German government through a DLR grant. A.C. was supported by the MRC, UK.

PY - 2005/3/24

Y1 - 2005/3/24

N2 - A key challenge of functional genomics today is to generate well-annotated data sets that can be interpreted across different platforms and technologies. Large-scale functional genomics data often fail to connect to standard experimental approaches of gene characterization in individual laboratories. Furthermore, a lack of universal annotation standards for phenotypic data sets makes it difficult to compare different screening approaches. Here we address this problem in a screen designed to identify all genes required for the first two rounds of cell division in the Caenorhabditis elegans embryo. We used RNA-mediated interference to target 98% of all genes predicted in the C. elegans genome in combination with differential interference contrast time-lapse microscopy. Through systematic annotation of the resulting movies, we developed a phenotypic profiling system, which shows high correlation with cellular processes and biochemical pathways, thus enabling us to predict new functions for previously uncharacterized genes.

AB - A key challenge of functional genomics today is to generate well-annotated data sets that can be interpreted across different platforms and technologies. Large-scale functional genomics data often fail to connect to standard experimental approaches of gene characterization in individual laboratories. Furthermore, a lack of universal annotation standards for phenotypic data sets makes it difficult to compare different screening approaches. Here we address this problem in a screen designed to identify all genes required for the first two rounds of cell division in the Caenorhabditis elegans embryo. We used RNA-mediated interference to target 98% of all genes predicted in the C. elegans genome in combination with differential interference contrast time-lapse microscopy. Through systematic annotation of the resulting movies, we developed a phenotypic profiling system, which shows high correlation with cellular processes and biochemical pathways, thus enabling us to predict new functions for previously uncharacterized genes.

UR - http://www.scopus.com/inward/record.url?scp=15844431376&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=15844431376&partnerID=8YFLogxK

U2 - 10.1038/nature03353

DO - 10.1038/nature03353

M3 - Article

C2 - 15791247

AN - SCOPUS:15844431376

SN - 0028-0836

VL - 434

SP - 462

EP - 469

JO - Nature

JF - Nature

IS - 7032

ER -

Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this