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Mapping the C-elegans noncoding transcriptome with a whole-genome tiling microarray
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DOI：10.1101/gr.6611807.png)
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Abstract
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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 similar to 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 similar to 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.
Keywords:
CAENORHABDITIS-ELEGANS
GENE-EXPRESSION
SEQUENCES
RNAS
IDENTIFICATION
DATABASE
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