The brave new world of ncRNAs

Progress in understanding how cells interpret their genome has gathered significant momentum in recent years. Of course, the (now historical) catalyst to this was the entry into the genomic age, marked most obviously by the sequencing of the human genome. However, it is the genome-wide application of novel techniques for understanding how this genome is interpreted that has begun to unlock its secrets. In 2007, the international ENCODE consortium reported its initial attempts to annotate, in exhaustive detail, the best understood 1% of the human genome (ENCODE Project Consortium, 2007). The application of such genome-wide efforts to the leading invertebrate model species, Caenorhabditis elegans and Drosophila melanogaster, was published earlier this year (modENCODE Consortium, 2010a, b).

Much has come out of these gargantuan efforts, but one of the most prominent conclusions has been that general speaking, the genome is pervasively transcribed. A whole universe of RNA molecules exist inside cells, and while the extent to which they are functional remains a subject of much debate, it is clear that understanding this universe will yield fundamental insights into cellular, and developmental biology. Against this backdrop, recent work outlining the positive gene regulatory roles of particular populations of non-coding RNAs (ncRNAs) constitute hugely important discoveries. They build upon a landmark study, published in 2009 (Guttman et al. 2009), that for the first time systematically identified a population (~1600) of long multi-exonic ncRNAs in four murine cell lines. Correlative analysis with existing and novel expression datasets suggested putative functions for numerous distinct sets of lincRNAs. At the other end of the size scale, short (<2kb) RNAs, termed enhancer RNAs (eRNAs) have recently been shown to be transcribed from active enhancers in a neuronal cell culture system (Kim et al. 2010). Both of these findings give meaning to the pervasive transcription observed in the ENCODE and MODENCODE studies, but they don’t address the function of such RNA species. Do the RNAs themselves act to govern transcription or cell behaviour, or is it merely the act of transcribing them that is important, perhaps to re-model the local chromatin environment?

This conundrum has begun to be resolved, at least for longer species of ncRNAs, in the last two years. Two papers, one using differentiated cell lines (Ørom et al. 2010), and one in reference to ES cell biology, again from Eric Lander’s group (Guttman et al. 2011), have unequivocally demonstrated the functional importance of ncRNA species themselves. In the first, after using the ENCODE annotations to identify a population of 3019 putative long ncRNAs, a combination of reporter siRNA-mediated knockdown and expression analysis was able to show that the knockdown of particular ncRNAs were in seven cases able to decrease the expression of neighbouring genes, implicating the RNAs as positive regulators of a diversity of developmental processes. In the second study, building on their data set of lincRNAs (Guttman et al. 2009), the authors have demonstrated using short hairpin RNAs that dozens of lincRNAs are fundamental players in promoting and controlling the gene regulatory networks that govern both pluripotency, and differentiation into a range of different lineages. Further, they show that many lincRNAs specifically interact with chromatin regulatory proteins, and present a model that fully integrates ncRNAs into gene regulatory programmes that control cell fate.

Thus, extensive evidence now exists that implicates ncRNAs both in cis and in trans as fundamental controllers of all aspects of cell biology. The implications of such work will be felt across cell and developmental biology. As important as the findings themselves though, has been the illustration that integrating a diversity of epigenetic, comparative genomic and next generation sequencing approaches is capable of revolutionizing our understanding of how phenotype derives from genotype. The stage is set for application of these approaches over the coming years to develop from cell lines to developmental contexts. ncRNAs of all flavours are likely to be of fundamental, and as yet underappreciated, importance.

References

ENCODE Project Consortium (2007) Nature 447: 799-816.

Guttman M et al. (2009) Nature 458: 223 – 227.

Guttman M et al. (2011) Nature 477: 295 – 300.

Kim TK et al. (2010) Nature 465: 182 – 187.

modENCODE Consortium (2010a) Science 330: 1775-1787.

modENCODE Consortium (2010b) Science 330: 1787-1797.

Ørom UA et al. (2010) Cell 143: 46-58.

(5 votes)

Loading...