Abundance of Long NcRNAs
A recent study found only one-fifth of transcription across the human genome is associated with protein-coding genes (Kapranov 2007), indicating at least four-times more long non-coding than coding RNA sequences. However, it is large-scale complementary DNA (cDNA) sequencing projects such as FANTOM (Functional Annotation of Mammalian cDNA) that reveal the complexity of this transcription (Carninci 2005). The FANTOM3 project identified ~35,000 non-coding transcripts from ~10,000 distinct loci that bear many signatures of mRNAs, including 5’capping, splicing, and poly-adenylation, but have little or no open reading frame (ORF) (Carninci 2005). While the abundance of long ncRNAs was unanticipated, this number, nevertheless, represents a conservative lower estimate, since it omitted many singleton transcripts and non-polyadenylated transcripts (tiling array data shows more than 40% of transcripts are non-polyadenylated) (Cheng 2005). However, unambiguously identifying ncRNAs within these cDNA libraries is challenging, since it can be difficult to distinguish protein-coding transcripts from non-coding transcripts.
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