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

    • 1 Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
    • 2 Graduate School of the Chinese Academy of Science, Beijing 100080, China;
    • 3 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA;
    • 4 Harvard School of Public Health, Boston, Massachusetts 02115, USA;
    • 5 Affymetrix, Inc., Santa Clara, California 95051, USA;
    • 6 Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Science, Beijing 100080, China;
    • 7 Chinese National Human Genome Center, Beijing 100176, China
Published September 4, 2007. Vol 17 Issue 10, pp. 1471-1477. https://doi.org/10.1101/gr.6611807
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Abstract

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 ∼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 ∼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.

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