Emerging themes in non-coding RNA quality control

Quality control pathways for non-coding RNAs such as tRNAs and rRNAs are widespread. In both prokaryotes and eukaryotes, poly(A) polymerases target aberrant non-coding RNAs for degradation. In yeast, a nuclear complex that includes the poly(A) polymerase Trf4p works together with the exosome in degrading a broad array of non-coding RNAs, several of which are aberrant. Yeast also have additional pathways for the degradation of defective RNAs and other pathways may exist in higher eukaryotes. One possibility is that cells recognize specific, still undiscovered, features common to misfolded RNAs; however, an alternative is that RNA quality control proteins interact with relatively general RNA structures, whereas correctly folded RNAs are sequestered by specific RNA-binding proteins and thus protected from degradation. Recently available structures of protein and ribonucleoprotein complexes involved in non-coding RNA quality control are providing a more detailed understanding of this process.     

竞争性内源RNA的生物学功能及其调控

最新研究表明,RNA之间可以通过竞争结合共同的microRNA反应元件(microRNA response element, MRE)实现相互调节,这种调控模式构成竞争性内源RNA(Competing endogenous RNA, ceRNA)。已发现的ceRNA包括蛋白编码mRNA和非编码RNA,其中后者包括假基因转录物、长链非编码RNA(Long non-coding RNA, lncRNA)、环状RNA(Circular RNA, circRNA)等。文章主要从ceRNA分类的角度,阐述各类ceRNA构成的调控网络发挥的生物学功能在病理和生理相关过程中的作用,以及可能影响ceRNA调控有效性的因素。     

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Protein binding is essential to the transport,decay and regulation of almost all RNA molecules.However,the structural preference of protein binding on RNAs and their cellular functions and dynamics upon changing environmental conditions are poorly understood.Here,we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins(RBPs)and structured RNAs in yeast at single-nucleotide resolution.We found that on average,in terms of percent total lengths,~15%of mRNA untranslated regions(UTRs),~37%of canonical non-coding RNAs(ncRNAs)and~11%of long ncRNAs(lncRNAs)are bound by proteins.The RBP binding sites,in general,tend to occur at single-stranded loops,with evolutionarily conserved signatures,and often facilitate a specific RNA structure conformation in vivo.We found that four nucleotide modifications of tRNA are significantly associated with RBP binding.We also identified various structural motifs bound by RBPs in the UTRs of mRNAs,associated with localization,degradation and stress responses.Moreover,we identified>200 novel lncRNAs bound by RBPs,and about half of them contain conserved secondary structures.We present the first ensemble pattern of RBP binding sites in the structured non-coding regions of a eukaryotic genome,emphasizing their structural context and cellular functions.     

非编码RNA与基因表达调控

近年来,随着对基因组的深入研究,发现真核生物中存在许多形态和功能各异的非编码RNA分子,这类RNA分子并不表达蛋白质,但它们在基因转录水平、转录后水平及翻译水平起了重要的调控作用。具有调控作用的RNA分子种类非常丰富,如长链非编码RNA(long non-coding RNA,lncRNA)、miRNA、PIWI相互作用RNA(PIWI-interacting RNA,piRNA)、内源性小干扰RNA(endogenous small interfering RNA,endo-siRNA)、竞争性内源RNA(competitive endogenous RNA,ceRNA)等,它们使基因表达过程更为丰富、严谨和有序。本文综述几类典型的非编码RNA对基因表达的调节作用,以助于理解细胞中RNA分子调节网络的功能和机制。     

天然反义转录物及其调控基因的表达机制

天然反义转录(NATs)是一组编码蛋白质或非编码蛋白质的RNAs, 与其他(有义)转录物具有互补序列, 可以调节有义链的表达。这种调节可以发生在转录水平或转录后水平, 调节方式有转录干扰、RNA封闭、双链依赖机制或染色质重建(修饰)等。正义链和反义链分别加工成小RNAs调节基因表达, 也是NATs调节基因表达的重要方式, 如piRNAs的“乒乓机制”。实验或计算机研究已经证明了NATs在生物中广泛存在, 是一种重要的基因表达调节方式。文章论述了NATs的重要作用和机理, 重点论述了NATs的调节机制和相关的小RNAs。     

Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq

Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure–function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA–RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA–RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell.