The dark matter rises: the expanding world of regulatory RNAs

Abstract

The ability to sequence genomes and characterize their products has begun to reveal the central role for regulatory RNAs in biology, especially in complex organisms. It is now evident that the human genome contains not only protein-coding genes, but also tens of thousands of non-protein coding genes that express small and long ncRNAs (non-coding RNAs). Rapid progress in characterizing these ncRNAs has identified a diverse range of subclasses, which vary widely in size, sequence and mechanism-of-action, but share a common functional theme of regulating gene expression. ncRNAs play a crucial role in many cellular pathways, including the differentiation and development of cells and organs and, when mis-regulated, in a number of diseases. Increasing evidence suggests that these RNAs are a major area of evolutionary innovation and play an important role in determining phenotypic diversity in animals.

Influenza A virus preferentially snatches noncoding RNA caps

“…In addition, we find that promoter-associated csRNAs are snatched by IAV. Coupled with increased recognition for the roles of noncoding RNAs in cellular regulation (Clark et al 2013), our findings that noncoding and csRNAs are preferential targets of IAV cap-snatching suggest their possible impact on the host-virus interaction.…”

Key Levels of Biocommunication

“…RNA editing especially can transmit environmental information to the epigenome and therefore enable neuronal plasticity with learning and memory (Qureshi and Mehler, 2012). Additionally, non-coding RNAs can undergo nuclear-cytoplasmic, nuclear-mitochondrial, and axodendritic trafficking via ribonucleoprotein complexes that promote the spatiotemporal distribution and function of various combinations of ncRNAs, mRNAs, and RNA-binding proteins Mattick, 2013a, 2013b;Clark et al, 2013).…”

Corrigendum and follow-up: Whole genome sequencing of multiple CRISPR-edited mouse lines suggests no excess mutations

“…Additionally, there have been multiple reports of miRNAs in the nucleus, making it even more likely that Cas9 may be associating with crRNA-like endogenous sequences within the same subcellular compartment as DNA. 7 Furthermore, precursors of siRNAs, another type of small ncRNA, are transcripts with long stem-loop structures, a vital structure of the crRNA. All these ncRNA species are seen in substantially high numbers of embryogenesis.…”

“…6 This included long-distance template-switching events that resulted in mutations far away from the breakpoint junctions. 6 Most of the mammalian genome (some approximations nearing 75% of bases) is transcribed, even though only 1-2% encodes for proteins 7 , whereas 80-95% of prokaryote genomes encode proteins. 8 The rest of the transcriptome is comprised of tens of thousands of non-coding RNAs (ncRNAs).…”