Regulatory RNAs in mammals

RNA degradome--its biogenesis and functions

RNA degradation is among the most fundamental processes that occur in living cells. The continuous decay of RNA molecules is associated not only with nucleotide turnover, but also with transcript maturation and quality control. The efficiency of RNA decay is ensured by a broad spectrum of both specific and non-specific ribonucleases. Some of these ribonucleases participate mainly in processing primary transcripts and in RNA quality control. Others preferentially digest mature, functional RNAs to yield a variety of molecules that together constitute the RNA degradome. Recently, it has become increasingly clear that the composition of the cellular RNA degradome can be modulated by numerous endogenous and exogenous factors (e.g. by stress). In addition, instead of being hydrolyzed to single nucleotides, some intermediates of RNA degradation can accumulate and function as signalling molecules or participate in mechanisms that control gene expression. Thus, RNA degradation appears to be not only a process that contributes to the maintenance of cellular homeostasis but also an underestimated source of regulatory molecules.

Alternative polyadenylation: a mechanism maximizing transcriptome diversity in higher eukaryotes

Based on comparative genome analyses, the increases in protein-coding gene number could not account for the increases of morphological and behavioral complexity of higher eukaryotes. Transcriptional regulations, alternative splicing and the involvement of non-coding RNA in gene expression regulations have been credited for the drastic increase of transcriptome complexity. However, an emerging theme of another mechanism that contributes to the formation of alternative mRNA 3'-ends is alternative polyadenylation (APA). First, recent studies indicated that APA is a wide spread phenomenon across the transcriptomes of higher eukaryotes and being regulated by developmental and environmental cues. Secondly, our characterization of the Arabidopsis polyadenylation factors suggested that plant polyadenylation has also evolved to regulate the expression of specific genes by means of APA and therefore the specific biological functions. Finally, Phylogenetic analyses of eukaryotic polyadenylation factors from several organisms revealed that the number of polyadenylation factors tends to increase in higher eukaryotes, which provides the potential for their functional differentiation in regulating gene expression through APA. Based on above evidence, we, thus, hypothesize that APA, serving as an additional mechanism, contributes to the complexity of higher eukaryotes.

Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum

A large portion of the eukaryotic genome is transcribed as noncoding RNAs (ncRNAs). While once thought of primarily as "junk," recent studies indicate that a large number of these RNAs play central roles in regulating gene expression at multiple levels. The increasing diversity of ncRNAs identified in the eukaryotic genome suggests a critical nexus between the regulatory potential of ncRNAs and the complexity of genome organization. We provide an overview of recent advances in the identification and function of eukaryotic ncRNAs and the roles played by these RNAs in chromatin organization, gene expression, and disease etiology.