Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans.
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.
Sönnichsen
B
B
Cenix BioScience GmbH, Tatzberg 47-51, D-01307 Dresden, Germany. soennichsen@cenix-bioscience.com
Koski
L B
LB
Walsh
A
A
Marschall
P
P
Neumann
B
B
Brehm
M
M
Alleaume
A-M
AM
Artelt
J
J
Bettencourt
P
P
Cassin
E
E
Hewitson
M
M
Holz
C
C
Khan
M
M
Lazik
S
S
Martin
C
C
Nitzsche
B
B
Ruer
M
M
Stamford
J
J
Winzi
M
M
Heinkel
R
R
Röder
M
M
Finell
J
J
Häntsch
H
H
Jones
S J M
SJ
Jones
M
M
Piano
F
F
Gunsalus
K C
KC
Oegema
K
K
Gönczy
P
P
Coulson
A
A
Hyman
A A
AA
Echeverri
C J
CJ
D000818:Animals; D017173:Caenorhabditis elegans / Q000196:embryology* / Q000235:genetics* / Q000502:physiology; D029742:Caenorhabditis elegans Proteins / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology; D047108:Embryonic Development / Q000235:genetics*; D017238:Genes, Helminth / Q000235:genetics; D016678:Genome; D023281:Genomics; D010641:Phenotype; D034622:RNA Interference; D018510:RNA, Helminth / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
D029742:Caenorhabditis elegans Proteins; D018510:RNA, Helminth; D012333:RNA, Messenger