Long non-coding RNA research isn’t just a load of HOTAIR; since their initial discovery long non-coding RNAs have revealed their importance in regulating the genome. One such insight is the observation that lncRNA express antisense transcripts, which are abundantly found either partially or completely overlapping with transcripts from the opposite strand. These have been shown to function in a cis orientation to augment overall transcription of the sense transcript.
Evidence suggests that antisense transcripts are capable of exerting gene regulation in many layers including epigenetic control, transcriptional regulation, imprinting, alternative splicing, translation and RNA editing . However, the exact mechanism behind antisense-mediated gene expression regulation remains vastly under-explored.
Previously, antisense transcription has been shown to promote R-loop formation. R loops form a more stable RNA:DNA hybrid structure that displaces one DNA strand from a DNA:DNA duplex. Almost all R loops originate from the transcription of a C-rich template strand by an RNA polymerase, which generates a G-rich strand. Notably, R loops have been at the forefront of current research due to their purported role in transcriptional regulation.
A team of researchers led by Manel Esteller and Sonia Guil ventured into the under-explored territory of antisense-mediated transcriptional regulation to decipher the underlying mechanism behind antisense functionality. To accomplish this, the researchers use a head-to-head antisense transcript of the vimentin gene (VIM-AS1) in a series of regulatory experiments including hypermethylation of VIM promoter and VIM-AS1 knockdown.
Using several tumor and normal samples as well as diverse cell lines, the team found:
- VIM-AS1 transcript is enriched in the nucleus and may possess nuclear function.
- The abundance of VIM mRNA is 2-3 fold higher than that of VIM-AS1 transcript consistent with general estimates of sense to antisense abundance.
- Hypermethylation of the VIM promoter resulted in sense and antisense transcript silencing.
- VIM-AS1 RNA knockdown resulted in VIM silencing, possibly via promoter hypermethylation.
- VIM-AS1 transcript forms an R-loop structure that when disrupted repress the transcription of VIM.
- Transcription of VIM-AS1 and R-loop formation maintains an open chromatin conformation possibly making VIM template strand accessible to transcriptional factors.
The researchers conclude that their findings “imply a positive role for R-loop formation by a head-to-head antisense transcript in the regulation of sense transcript expression”.
Get in the loop of this exciting new research over in PNAS, April 2015.