Characteristic comparison between two types of miRNA precursors in metazoan species

MicroRNAs (miRNAs) are a class of small non-coding RNAs discovered in recent years, which are found to play important regulatory roles in various organisms. As the number of experimentally validated miRNAs is rapidly increasing, systematic analysis on the characteristics of these known miRNAs is necessary and indispensable, especially for computational prediction of new miRNAs. We extensively analyzed precursor sequences for all experimentally validated mature miRNAs in metazoan species, focusing on the characteristics at the level of primary sequences and secondary structures. An observation over the secondary structures of 2729 miRNA precursors (pre-miRNAs) reveals that these hairpin structures can be approximately classified into two types: one with a hairpin loop, and the other with multiple loops. Interestingly, the two types of pre-miRNAs show significant differences in both sequence and structure characteristics, and our study indicates that separate consideration on each type of pre-miRNAs is more reasonable, especially in computational prediction. Besides, we develop a new criterion called mAMFE which shows robust discriminative power in distinguishing pre-miRNAs against other RNAs, thus can potentially serve as a discriminative feature in prediction of new pre-miRNAs.     

A deeply conserved,noncanonical miRNA hosted by ribosomal DNA

Advances in small RNA sequencing technologies and comparative genomics have fueled comprehensive microRNA (miRNA) gene annotations in humans and model organisms. Although new miRNAs continue to be discovered in recent years, these have universally been lowly expressed, recently evolved, and of debatable endogenous activity, leading to the general assumption that virtually all biologically important miRNAs have been identified. Here, we analyzed small RNAs that emanate from the highly repetitive rDNA arrays of Drosophila. In addition to endo-siRNAs derived from sense and antisense strands of the pre-rRNA sequence, we unexpectedly identified a novel, deeply conserved, noncanonical miRNA. Although this miRNA is widely expressed, this miRNA was not identified by previous studies due to bioinformatics filters removing such repetitive sequences. Deep-sequencing data provide clear evidence for specific processing with precisely defined 5′ and 3′ ends. Furthermore, we demonstrate that the mature miRNA species is incorporated in the effector complexes and has detectable trans regulatory activity. Processing of this miRNA requires Dicer-1, whereas the Drosha–Pasha complex is dispensable. The miRNA hairpin sequence is located in the internal transcribed spacer 1 region of rDNA and is highly conserved among Dipteran species that were separated from their common ancestor ∼100 million years ago. Our results suggest that biologically active miRNA genes may remain unidentified even in well-studied organisms.     

Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide

Argonaute (AGO) proteins recruit small RNAs to form the core of RNAi effector complexes. Arabidopsis encodes ten AGO proteins and a large network of small RNAs. How these small RNAs are sorted into specific AGO complexes remains largely unknown. We have cataloged small RNAs resident in four AGO complexes. We found that AGO2 and AGO4 preferentially recruit small RNAs with a 5' terminal adenosine, whereas AGO1 harbors microRNAs (miRNAs) that favor a 5' terminal uridine. AGO5 predominantly binds small RNAs that initiate with cytosine. Changing the 5' terminal nucleotide of an miRNA predictably redirected it into a different AGO complex and alters its biological activity. These results reveal a role for small RNA sequences in assorting among AGO complexes. This suggests that specialization of AGO complexes might involve remodeling the 5' end-binding pocket to accept certain small RNA sequences, perhaps explaining the evolutionary drive for miRNAs to initiate with uridine.     

Role of miRNA and miRNA processing factors in development and disease

Mature microRNAs (miRNAs) are single-stranded RNA molecules of 17-24 nucleotides (nt) in length that are encoded in the genomes of plants and animals. The seminal discoveries of miRNA made in C. elegans have led the way to the rampant discoveries being made today in this field. Since each miRNA is predicted and in some cases confirmed to regulate multiple genes, the potential regulatory circuitry afforded by miRNAs is thought to be enormous and could amount to regulation of >30% of all human genes. Due to the sequences of many of the miRNAs being highly homologous among organisms, the huge potential of miRNAs to regulate gene expression, and the hints of miRNAs being useful in both diagnostics and therapeutics, it is no wonder these small RNAs are gaining such popularity in both the academic and industrial settings. It is now becoming clear that the miRNA gene class represents a very important gene regulatory network. This article reviews the initial discoveries of miRNA that began in the nematode C. elegans, and extends into what is known about miRNAs and miRNA processing factors in mouse development and human disease.     

微RNA抑制物:竞争性内源RNA和人工miRNA吸附物

microRNA(miRNA)是一类细胞内源性的小片段非编码RNA家族,通过与靶基因3′非翻译区(3′untranslated region,3′UTR)结合,对基因表达进行转录后水平的负性调控,参与多种生理和病理学过程。对细胞内成熟体miRNA的功能抑制机制之一是抑制物与miRNA互补结合,从而阻止其与靶基因的结合。这类抑制物主要包括细胞内天然存在的竞争性内源RNA(competing endogenous RNA,ce RNA),以及人工合成或载体表达的外源性miRNA吸附物。本文分别对这两种机制的作用方式进行综述,并对二者的相似点和不同点进行总结。     

SNPs in human miRNA genes affect biogenesis and function

MicroRNAs (miRNAs) are 21–25-nucleotide-long, noncoding RNAs that are involved in translational regulation. Most miRNAs derive from a two-step sequential processing: the generation of pre-miRNA from pri-miRNA by the Drosha/DGCR8 complex in the nucleus, and the generation of mature miRNAs from pre-miRNAs by the Dicer/TRBP complex in the cytoplasm. Sequence variation around the processing sites, and sequence variations in the mature miRNA, especially the seed sequence, may have profound affects on miRNA biogenesis and function. In the context of analyzing the roles of miRNAs in Schizophrenia and Autism, we defined at least 24 human X-linked miRNA variants. Functional assays were developed and performed on these variants. In this study we investigate the affects of single nucleotide polymorphisms (SNPs) on the generation of mature miRNAs and their function, and report that naturally occurring SNPs can impair or enhance miRNA processing as well as alter the sites of processing. Since miRNAs are small functional units, single base changes in both the precursor elements as well as the mature miRNA sequence may drive the evolution of new microRNAs by altering their biological function. Finally, the miRNAs examined in this study are X-linked, suggesting that the mutant alleles could be determinants in the etiology of diseases.     

Argonaute loading improves the 5' precision of both MicroRNAs and their miRNA* strands in flies

MicroRNAs (miRNAs) are short regulatory RNAs that direct repression of their mRNA targets. The miRNA "seed"-nucleotides 2-7-establishes target specificity by mediating target binding. Accurate processing of the miRNA 5' end is thought to be under strong selective pressure because a shift by just one nucleotide in the 5' end of a miRNA alters its seed sequence, redefining its repertoire of targets (Figure 1). Animal miRNAs are produced by the sequential cleavage of partially double-stranded precursors by the RNase III endonucleases Drosha and Dicer, thereby generating a transitory double-stranded intermediate comprising the miRNA paired to its partially complementary miRNA strand. Here, we report that in flies, the 5' ends of miRNAs and miRNA strands are typically more precisely defined than their 3' ends. Surprisingly, the precision of the 5' ends of both miRNA and miRNA sequences increases after Argonaute2 (Ago2) loading. Our data imply that either many miRNA sequences are under evolutionary pressure to maintain their seed sequences-that is, they have targets-or that secondary constraints, such as the sequence requirements for loading small RNAs into functional Argonaute complexes, narrow the range of miRNA and miRNA 5' ends that accumulate in flies.     

水稻MicroRNA的预测及实验验证

根据已报道水稻pre-miRNA的序列与结构信息,利用支持向量机（support vector machine, SVM）方法在miRNA前体上预测成熟区,产生一个模型——mature-SVM.它预测水稻成熟区的敏感性和特异性分别为86.7% 和100%;然后,用这个模型对从水稻基因组中筛选出的46.501条pre-miRNA进行成熟链预测,此外再根据miRNA的作用原理用blast程序所进一步的筛选,得到了127条pre-miRNA及成熟miRNA;除去其中已知的21条,最后得到106条候选的新的水稻miRNA. 从中随机挑取10条进行Northern验证,结果有4条miRNA得到确认.     

人源microRNA分子表达库的构建

microRNA(miRNA)是一类长度为22nt左右的单链非编码小RNA分子,通过与靶mRNA分子结合而沉默其表达.目前,虽然在多种生物中发现了大量的miRNA,但对它们的功能还知之甚少.为了深入研究miRNA的功能,构建了一个包括170多种人源miRNA表达载体的miRNA分子表达库,并对部分表达载体采用RNA印迹及双荧光素酶分析技术进行验证.实验证明:这些miRNA表达载体在HEK-293细胞内可以高水平表达miRNA前体和成熟的miRNA,并且能抑制含有相应靶位点的报告基因的表达.这些结果表明:该miRNA表达库可以表达功能miRNA,并可用于miRNA功能的筛选和研究.     

In vivo structure-function analysis of human Dicer reveals directional processing of precursor miRNAs

Dicer is an RNase III family endoribonuclease and haploinsufficient tumor suppressor that processes mature miRNAs from the 5' (5p) or 3' (3p) arm of hairpin precursors. In murine Dicer knockout fibroblasts, we expressed human Dicer with point mutations in the RNase III, helicase, and PAZ domains and characterized miRNA expression by Northern blot and massively parallel sequencing of small RNAs. We report that inactivation of the RNase IIIA domain results in complete loss of 3p-derived mature miRNAs, but only partial reduction in 5p-derived mature miRNAs. Conversely, inactivation of the RNase IIIB domain by mutation of D1709, a residue mutated in a subset of nonepithelial ovarian cancers, results in complete loss of 5p-derived mature miRNAs, including the tumor-suppressive let-7 family, but only partial reduction in 3p-derived mature miRNAs. Mutation of the PAZ domain results in global reduction of miRNA processing, while mutation of the Walker A motif in the helicase domain of Dicer does not alter miRNA processing. These results provide insight into the biochemical activity of human Dicer in vivo and, furthermore, suggest that mutation of the clinically relevant residue D1709 within the RNase IIIB results in a uniquely miRNA-haploinsufficient state in which the let-7 family of tumor suppressor miRNAs is lost while a complement of 3p-derived miRNAs remains expressed.