Despite all of the attention to the non-coding transcriptome lately, our knowledge about what most long intergenic non-coding RNA (lncRNA) transcripts do – if indeed they do anything at all, still has more holes than a Dunkin’ Donut shop. Luckily there are folks out there willing to step in to take on the dirty job of filling in those gaps, and trying to pin down the function of all those different flavors of lincRNAs and macroRNAs.
Oxford’s Ana Marques and Chris Ponting reasoned that checking out non-coding RNA evolution over time would generate clues to figuring out if they’re important, and maybe even how they might work. So they went to work scoping out how fast the DNA for these sequences has been mutating.
They compared two species of non-coding transcripts: lncRNAs, found by their association with chromatin markers for transcription; and macroRNAs, which were sequenced from cDNA libraries, and which don’t share with lincRNA enrichment for H3K36me3. Some similarities and differences they found include:
- Both lincRNAs and macroRNAs are under more selective pressure than their neighbors, but less than protein coding regions.
- The selective pressure is not evenly distributed between TSSs and coding regions.
- macroRNAs can more readily form secondary structures, and may be likely to act in trans.
- lncRNAs exhibit short regions of more intense constraint, and may prefer to act in cis.
See what this all might mean in Genome Biology, November 2009.