Long Non-coding RNA - Genomic Organization of Long NcRNAs

Genomic Organization of Long NcRNAs

The current landscape of the mammalian genome is described as numerous ‘foci’ of transcription that are separated by long stretches of intergenic space (Carninci 2005). While long ncRNAs are located and transcribed within the intergenic stretches, the majority are transcribed as complex, interlaced networks of overlapping sense and antisense transcripts that often includes protein-coding genes (Kapranov 2007). Genomic sequences within these transcriptional foci are often shared within a number of different coding and non-coding transcripts in the sense and antisense directions (Birney 2007) giving rise to a complex hierarchy of overlapping isoforms. For example, 3012 out of 8961 cDNAs previously annotated as truncated coding sequences within FANTOM2 were later designated as genuine ncRNA variants of protein-coding cDNAs (Carninci 2005). While the abundance and conservation of these interleaved arrangements suggest they have biological relevance, the complexity of these foci frustrates easy evaluation.

The GENCODE consortium has collated and analysed a comprehensive set of human lncRNA annotations and their genomic organisation, modifications, cellular locations and tissue expression profiles. Their analysis indicates human lncRNAs show a bias toward two-exon transcripts.