Evolutionary patterns of non-coding RNAs

Abstract

A plethora of new functions of non-coding RNAs have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and Manuscript January 2005RNA modification to translational regulation. Nevertheless, very little is known about the evolution of this "Modern RNA World" and its components. In this contribution we attempt to provide at least a cursory overview of the diversity of non-coding RNAs and functional RNA motifs in non-translated regions of regular messenger RNAs (mRNAs) with an emphasis on evolutionary questions. This survey is complemented by an in-depth analysis of examples from different classes of RNAs focusing mostly on their evolution in the vertebrate lineage. We present a survey of Y RNA genes in vertebrates, studies of the molecular evolution of the U7 snRNA, the snoRNAs E1/U17, E2, and E3, the Y RNA family, the let-7 microRNA family, and the mRNA-like evf-1 gene. We furthermore discuss the statistical distribution of microRNAs in metazoans, which suggests an explosive increase in the microRNA repertoire in vertebrates. The analysis of the transcription of non-coding RNAs (ncRNAs) suggests that small RNAs in general are genetically mobile in the sense that their association with a hostgene (e.g. when transcribed from introns of a mRNA) can change on evolutionary time scales. The let-7 family demonstrates, that even the mode of transcription (as intron or as exon) can change among paralogous ncRNA.

Evolution of plant microRNA gene families

“…Was the evolutionary history of these genes with tiny final products similar to their protein-coding counterparts? Since the evolution of animal miRNA gene families has been a subject of many papers [14,30,31], in this review, we attempt to summarize the recent progress in the evolutionary study of miRNA gene families in plant genomes.…”

RNAs everywhere: genome‐wide annotation of structured RNAs

“…A wide variety of different approaches to perform homology searches based on both sequence and structure have been proposed in the last few years in order to utilize the strong conservation of secondary structure in many ncRNA families, see (Bompfünewerer et al, 2005) for a recent more extensive summary of this topic. Stochastic context free grammars (SCFGs) can be used to construct covariance models from a multiple alignment with structural annotation as in infernal (Eddy, 2002).…”

“…A few examples of functional ncRNAs that changed their host genes have been reported, see e.g. (Rodriguez et al, 2004;Bompfünewerer et al, 2005). Only a hand full of mlncRNAs are annotated in databases as in Y2K (Erdmann et al, 1999(Erdmann et al, , 2000 or RNAdb (Pang et al, 2005), while most cDNAs that lack a CDS remain functionally unassigned (Carninci et al, 2005).…”

Identification of miRNAs in sorghum by using bioinformatics approach

“…18,[66][67][68][69][70] Some clusters are so compact where multiple miRNAs are aligned in the same orientation and transcribed as a polycistronic transcript. 68,71,72 Clusters are conserved across vertebrates: from teleost fish to human. 73 However in plants, only few miRNA cluster have been found.…”