MicroRNAs in farm animals

MicroRNAs (miRNAs) are a class of ∼22 nucleotide-long small noncoding RNAs that target mRNAs for translational repression or degradation. miRNAs target mRNAs by base-pairing with the 3′-untranslated regions (3′-UTRs) of mRNAs. miRNAs are present in various species, from animals to plants. In this review, we summarize the identification, expression, and function of miRNAs in four important farm animal species: cattle, chicken, pig and sheep. In each of these species, hundreds of miRNAs have been identified through homology search, small RNA cloning and next generation sequencing. Real-time RT-PCR and microarray experiments reveal that many miRNAs are expressed in a tissue-specific or spatiotemporal-specific manner in farm animals. Limited functional studies suggest that miRNAs have important roles in muscle development and hypertrophy, adipose tissue growth, oocyte maturation and early embryonic development in farm animals. Increasing evidence suggests that single-nucleotide polymorphisms in miRNA target sites or miRNA gene promoters may contribute to variation in production or health traits in farm animals.     

Heavy metal-regulated new microRNAs from rice

MicroRNAs (miRNAs) are a novel class of short, endogenous non-coding small RNAs that have the ability to base pair with their target mRNAs to repress their translation or induce their degradation in both plants and animals. To identify heavy metal stress-regulated novel miRNAs, we constructed a library of small RNAs from rice seedlings that were exposed to toxic levels of cadmium (Cd²⁺). Sequencing of the library and subsequent analysis revealed 19 new miRNAs representing six families. These cloned new rice miRNAs have sequence conservation neither in Arabidopsis nor in any other species. Most of the new rice miRNAs were up- or down-regulated in response to the metal exposure. On the base of sequence complementarity, a total of 34 miRNA targets were predicted, of which 23 targets are functionally annotated and the other 11 records belong to unknown proteins. Some predicted targets of miRNAs are associated with the regulation of the response to heavy metal-induced stresses. In addition to the new miRNAs, we detected nine previously reported miRNAs and 56 other novel endogenous small RNAs in rice. These findings suggest that the number of new miRNAs in rice is unsaturated and some of them may play critical roles in plant responses to environmental stresses.     

MicroRNAs: something important between the genes

Non-coding small endogenous RNAs, of 21-24 nucleotides in length, have recently emerged as important regulators of gene expression in both plants and animals. At least three categories of small RNAs exist in plants: short interfering RNAs (siRNAs) deriving from viruses or transgenes and mediating virus resistance or transgene silencing via RNA degradation; siRNAs deriving from transposons or transgene promoters and controlling transposon and transgene silencing probably via chromatin changes; and microRNAs (miRNAs) deriving from intergenic regions of the genome and regulating the expression of endogenous genes either by mRNA cleavage or translational repression. The disruption of miRNA-mediated regulation causes developmental abnormalities in plants, demonstrating that miRNAs play an important role in the regulation of developmental decisions.     

Genomics of microRNA

Discovered just over a decade ago, microRNA (miRNA) is now recognized as one of the major regulatory gene families in eukaryotic cells. Hundreds of miRNAs have been found in animals, plants and viruses, and there are certainly more to come. Through specific base-pairing with mRNAs, these tiny approximately 22-nt RNAs induce mRNA degradation or translational repression, or both. Because a miRNA can target numerous mRNAs, often in combination with other miRNAs, miRNAs operate highly complex regulatory networks. In this article, we summarize the current status of miRNA gene mining and miRNA expression profiling. We also review up-to-date knowledge of miRNA gene structure and the biogenesis mechanism. Our focus is on animal miRNAs.     

MicroRNA-223 is a key factor in osteoclast differentiation

MicroRNAs (miRNAs) are a class of noncording RNAs that control gene expression by translational inhibition and messenger RNAs (mRNAs) degradation in plants and animals. Although miRNAs have been implicated in developmental and homeostatic events of vertebrates and invertebrates, the role of miRNAs in bone metabolism has not been explored. Here, we show that microRNA-223 (miR-223) is expressed in RAW264.7 cells, mouse osteoclast precursor cell lines, and plays a critical role in osteoclast differentiation. We constructed miR-223 short interfering RNA (siRNA) or precursor miR-223 (pre-miR-223) overexpression retroviral vectors, and established miR-223 knockdown by siRNA or pre-miR-223 overexpression in stably infected RAW264.7 cells. Tartrate-resistant acid phosphatase (TRAP)-positive multinucleated cells were observed in miR-223 knockdown cells as well as control cells. In contrast, pre-miR-223 overexpression completely blocked TRAP-positive multinucleated cell formation compared with control cells. Apoptotic cells were not observed in this study. Our results indicate that miR-223 plays an essential role during osteoclast differentiation, and miR-223 might be a viable therapeutic target for a range of bone metabolic disorders with excess osteoclast activity.     

MicroRNAs: genomics, biogenesis, mechanism, and function

MicroRNAs (miRNAs) are endogenous approximately 22 nt RNAs that can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes.     

siRNA and miRNA processing: new functions for Cajal bodies

In diverse eukaryotes, micro-RNAs (miRNAs) and small interfering RNAs (siRNAs) regulate important processes that include mRNA inactivation, viral defense, chromatin modification, and transposon silencing. Recently, nucleolus-associated Cajal bodies in plants have been implicated as sites of siRNA and miRNA biogenesis, whereas in animals siRNA and miRNA dicing occurs in the cytoplasm. The plant nucleolus also contains proteins of the nonsense-mediated mRNA decay pathway that in animals are found associated with cytoplasmic processing bodies (P-bodies). P-bodies also function in the degradation of mRNAs subjected to miRNA and siRNA targeting. Collectively, these observations suggest interesting variations in the way siRNAs and miRNAs can accomplish their similar functions in plants and animals.     

果蝇miRNA的结构与功能及研究策略

miRNA是一类在动植物基因组中广泛存在的小分子非编码RNA, 作为真核细胞转录后水平上基因表达的关键调控者, 它通过与靶基因mRNA的特定位点结合, 抑制mRNA的翻译或诱导mRNA的降解, 从而介导生物体的许多重要生理活动。本文简要总结了模式昆虫黑腹果蝇Drosophila melanogaster miRNA的鉴定情况, 综述了miRNA的结构特征、生物合成途径和作用机制。miRNA可能同时调节成百上千个靶标, 其生物功能主要体现为: 调节细胞分化与凋亡, 调节器官和神经系统的发育, 控制肌肉分化, 保持能量动态平衡, 调节昆虫变态或综合调节作用。miRNA具有“低丰度、短序列、难富集”的特点, miRNA基因的获得和功能鉴定研究的基本策略是实验生物学和生物信息学方法的有机结合。鉴定新miRNA及其靶标, 深入研究其生物功能和基因进化等可能成为今后一段时间昆虫miRNA研究的重要内容。     

Common functions for diverse small RNAs of land plants

Endogenous small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), are critical components of plant gene regulation. Some abundant miRNAs involved in developmental control are conserved between anciently diverged plants, while many other less-abundant miRNAs appear to have recently emerged in the Arabidopsis thaliana lineage. Using large-scale sequencing of small RNAs, we extended the known diversity of miRNAs in basal plants to include 88 confidently annotated miRNA families in the moss Physcomitrella patens and 44 in the lycopod Selaginella moellendorffii. Cleavage of 29 targets directed by 14 distinct P. patens miRNA families and a trans-acting siRNA (ta-siRNA) was experimentally confirmed. Despite a core set of 12 miRNA families also expressed in angiosperms, weakly expressed and apparently lineage-specific miRNAs accounted for the majority of miRNA diversity in both species. Nevertheless, the molecular functions of several of these lineage-specific small RNAs matched those of angiosperms, despite dissimilarities in the small RNA sequences themselves, including small RNAs that mediated negative feedback regulation of the miRNA pathway and miR390-dependent ta-siRNAs that guided the cleavage of AUXIN RESPONSE FACTOR mRNAs. Diverse, lineage-specific, small RNAs can therefore perform common biological functions in plants.     

GW182 family proteins are crucial for microRNA-mediated gene silencing

microRNAs (miRNAs) are a conserved class of small RNAs approximately 22 nucleotides in length. They regulate the expression of a large number of mRNAs in animals and plants through the miRNA-induced silencing complex (miRISC). The conserved GW182 family of proteins has recently been identified, and its members have been shown to be associated with miRISC and to be required for miRNA-mediated gene silencing. These proteins have also been localized to processing bodies that are cytoplasmic messenger ribonucleoprotein (mRNP) aggregates containing mRNA decay factors, translational repressors and untranslated mRNAs. Therefore, these properties of GW182 family proteins support the hypothesis that the formation of untranslatable messenger ribonuclear protein particles is one important mechanism of miRNA-mediated gene silencing.     

Short leader sequences may be transferred from small RNAs to pre-mature mRNAs by trans-splicing in Euglena.

Very closely related short sequences are present at the 5' end of cytoplasmic mRNAs in Euglena as evidenced by comparison of cDNA sequences and hybrid-arrested translation experiments. By cloning Euglena gracilis nuclear DNA and isolating the rbcS gene (encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase), we have shown that the short leader sequence does not flank the nuclear gene sequence. The leader sequences were found to constitute the 5' extremities of a family of small RNAs. Sequencing six members of this family revealed a striking similarity to vertebrate U snRNAs. We propose that a trans-splicing mechanism transfers the spliced leader (SL) sequence from these small RNAs (SL RNAs) to pre-mature mRNAs. Transfer of leader sequences to mRNAs by trans-splicing has been shown only in trypanosomes where cis-splicing is unknown, and in nematodes where not more than 10% of the mRNAs have leader sequences. Our results strongly suggest that Euglena is a unique organism in which both a widespread trans-splicing and a cis-splicing mechanism co-exist.     

The role of small RNAs in abiotic stress

It was recently discovered that plants respond to environmental stress not only with a specific gene expression programme at the mRNA and protein level but also small RNAs as response modulators play an important role. The small RNAs lead to cleavage or translational inhibition of mRNAs via complementary target sites. Different examples are described where small RNAs have been shown to be involved in stress responses. A link between hormonal action and small RNA activities has frequently been observed thus coupling exogenous factors with endogenous transmitters. Using the CDT-1 gene from the desiccation tolerant plant Craterostigma plantagineum as an example, it is discussed that generation of novel small RNAs could be an evolutionary pathway in plants to adapt to extreme environments.     

Transcriptome and miRNAs analyses enhance our understanding of the evolutionary advantages of polyploidy

Polyploid organisms have more than two sets of chromosomes, including autopolyploid via intraspecific genome doubling, and allopolyploid via merging genomes of distinct species by hybridization. Polyploid organisms are widespread in plants, indicating that polyploidy has some evolutionary advantages over its diploid ancestor. Actually, polyploidy is always tightly associated with hybrid vigor and adaptation to adverse environmental conditions. However, why polyploidy can develop such advantages is poorly known. MicroRNAs (miRNAs) are endogenous ～21?nt small RNAs which can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. MicroRNAs are essential for cell development, differentiation, signal transduction, and show an adaptive response to biotic and abiotic stresses. Environmental stresses cause plants to over- or under-express certain miRNAs or synthesize new miRNAs to cope with stress. We have here reviewed our current knowledge on the molecular mechanisms, which can account for the evolutionary advantages of polyploidy over its diploid ancestor from genome-wide gene expression and microRNAs expression perspectives.