Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome.
Although a highly accurate sequence of the Caenorhabditis elegans genome has been available for 10 years, the exact transcript structures of many of its protein-coding genes remain unsettled. Approximately two-thirds of the ORFeome has been verified reactively by amplifying and cloning computationally predicted transcript models; still a full third of the ORFeome remains experimentally unverified. To fully identify the protein-coding potential of the worm genome including transcripts that may not satisfy existing heuristics for gene prediction, we developed a computational and experimental platform adapting rapid amplification of cDNA ends (RACE) for large-scale structural transcript annotation. We interrogated 2000 unverified protein-coding genes using this platform. We obtained RACE data for approximately two-thirds of the examined transcripts and reconstructed ORF and transcript models for close to 1000 of these. We defined untranslated regions, identified new exons, and redefined previously annotated exons. Our results show that as much as 20% of the C. elegans genome may be incorrectly annotated. Many annotation errors could be corrected proactively with our large-scale RACE platform.
Salehi-Ashtiani
Kourosh
K
Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. kourosh_salehi-ashtiani@dfci.harvard.edu
Lin
Chenwei
C
Hao
Tong
T
Shen
Yun
Y
Szeto
David
D
Yang
Xinping
X
Ghamsari
Lila
L
Lee
HanJoo
H
Fan
Changyu
C
Murray
Ryan R
RR
Milstein
Stuart
S
Svrzikapa
Nenad
N
Cusick
Michael E
ME
Roth
Frederick P
FP
Hill
David E
DE
Vidal
Marc
M
D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D029742:Caenorhabditis elegans Proteins / Q000235:genetics / Q000378:metabolism*; D003001:Cloning, Molecular; D019295:Computational Biology / Q000379:methods*; D017931:DNA Primers; D018076:DNA, Complementary / Q000235:genetics*; D018509:DNA, Helminth / Q000032:analysis / Q000235:genetics; D005091:Exons; D020869:Gene Expression Profiling; D017238:Genes, Helminth; D016366:Open Reading Frames / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic
D029742:Caenorhabditis elegans Proteins; D017931:DNA Primers; D018076:DNA, Complementary; D018509:DNA, Helminth