Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray.

The number of annotated protein coding genes in the genome of Caenorhabditis elegans is similar to that of other animals, but the extent of its non-protein-coding transcriptome remains unknown. Expression profiling on whole-genome tiling microarrays applied to a mixed-stage C. elegans population verified the expression of 71% of all annotated exons. Only a small fraction (11%) of the polyadenylated transcription is non-annotated and appears to consist of approximately 3200 missed or alternative exons and 7800 small transcripts of unknown function (TUFs). Almost half (44%) of the detected transcriptional output is non-polyadenylated and probably not protein coding, and of this, 70% overlaps the boundaries of protein-coding genes in a complex manner. Specific analysis of small non-polyadenylated transcripts verified 97% of all annotated small ncRNAs and suggested that the transcriptome contains approximately 1200 small (<500 nt) unannotated noncoding loci. After combining overlapping transcripts, we estimate that at least 70% of the total C. elegans genome is transcribed.

[1]  A. Coulson,et al.  Genomics in C. elegans: so many genes, such a little worm. , 2005, Genome research.

[2]  G. Phillips,et al.  Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Wolfgang Huber,et al.  A high-resolution map of transcription in the yeast genome. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Thomas E. Royce,et al.  Global Identification of Human Transcribed Sequences with Genome Tiling Arrays , 2004, Science.

[5]  Stuart K. Kim,et al.  Global analysis of dauer gene expression in Caenorhabditis elegans , 2003, Development.

[6]  Jun Wang,et al.  Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture , 2005, Genome Biology.

[7]  John Bracht,et al.  Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. , 2004, RNA.

[8]  T. Gingeras,et al.  TUF Love for “Junk” DNA , 2006, Cell.

[9]  P. Stadler,et al.  Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. , 2006, Journal of experimental zoology. Part B, Molecular and developmental evolution.

[10]  M. Gerstein,et al.  Design optimization methods for genomic DNA tiling arrays. , 2005, Genome research.

[11]  Stijn van Dongen,et al.  miRBase: microRNA sequences, targets and gene nomenclature , 2005, Nucleic Acids Res..

[12]  Juancarlos Chan,et al.  WormBase: a cross-species database for comparative genomics , 2003, Nucleic Acids Res..

[13]  Boris Lenhard,et al.  RNAdb—a comprehensive mammalian noncoding RNA database , 2004, Nucleic Acids Res..

[14]  Jun Wang,et al.  Genome-wide transcription analyses in rice using tiling microarrays , 2006, Nature Genetics.

[15]  P. Burcham,et al.  Genome-wide transcriptional responses to acrolein. , 2008, Chemical research in toxicology.

[16]  Kimberly Van Auken,et al.  WormBase: a comprehensive data resource for Caenorhabditis biology and genomics , 2004, Nucleic Acids Res..

[17]  Sin Lam Tan,et al.  Complex Loci in Human and Mouse Genomes , 2006, PLoS genetics.

[18]  Joseph M. Dale,et al.  Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome , 2003, Science.

[19]  Paul T. Groth,et al.  The ENCODE (ENCyclopedia Of DNA Elements) Project , 2004, Science.

[20]  S. Cawley,et al.  Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. , 2004, Genome research.

[21]  G. Helt,et al.  Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution , 2005, Science.

[22]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[23]  W. J. Kent,et al.  Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. , 2000, Genome research.

[24]  J. Mattick.  RNA regulation: a new genetics? , 2004, Nature Reviews Genetics.

[25]  S. P. Fodor,et al.  Large-Scale Transcriptional Activity in Chromosomes 21 and 22 , 2002, Science.

[26]  Yan Cui,et al.  Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray , 2006, Nucleic acids research.

[27]  Yi Zhao,et al.  NONCODE: an integrated knowledge database of non-coding RNAs , 2004, Nucleic Acids Res..

[28]  J. Rinn,et al.  The transcriptional activity of human Chromosome 22. , 2003, Genes & development.

[29]  Sean R Eddy,et al.  C. elegans noncoding RNA genes. , 2005, WormBook : the online review of C. elegans biology.

[30]  Jürgen Brosius,et al.  Evolution of small nucleolar RNAs in nematodes , 2006, Nucleic acids research.

[31]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[32]  Baoyan Bai,et al.  Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression. , 2005, Genome research.

[33]  V. Reinke,et al.  Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Srinka Ghosh,et al.  Biological function of unannotated transcription during the early development of Drosophila melanogaster , 2006, Nature Genetics.