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Evolution and functional diversification of MIRNA genes 总被引:1,自引:0,他引:1
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Plant microRNA: a small regulatory molecule with big impact 总被引:20,自引:0,他引:20
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Computational identification of miRNA and targets from expressed sequence tags of coffee (Coffea arabica) 总被引:1,自引:0,他引:1
Arzuba Akter Md. Muzahidul Islam Shakhinur Islam Mondal Zabed Mahmud Nurnabi Azad Jewel Sabiha Ferdous Md. Ruhul Amin Md. Mahfuzur Rahman 《Saudi Journal of Biological Sciences》2014,21(1):3-12
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Shih-Hsin Chang Petrus Tang Cheng-Hung Lai Ming-Ling Kuo Lian-Chen Wang 《Memórias do Instituto Oswaldo Cruz》2013,108(6):699-706
Angiostrongylus cantonensis is an important causative agent of
eosinophilic meningitis and eosinophilic meningoencephalitis in humans.
MicroRNAs (miRNAs) are small non-coding RNAs that participate in a wide range of
biological processes. This study employed a deep-sequencing approach to study
miRNAs from young adults of A. cantonensis. Based on 16,880,456
high-quality reads, 252 conserved mature miRNAs including 10 antisense miRNAs
that belonging to 90 families, together with 10 antisense miRNAs were identified
and characterised. Among these sequences, 53 miRNAs from 25 families displayed
50 or more reads. The conserved miRNA families were divided into four groups
according to their phylogenetic distribution and a total of nine families
without any members showing homology to other nematodes or adult worms were
identified. Stem-loop real-time polymerase chain reaction analysis of
aca-miR-1-1 and aca-miR-71-1 demonstrated that their level of expression
increased dramatically from infective larvae to young adults and then decreased
in adult worms, with the male worms exhibiting significantly higher levels of
expression than female worms. These findings provide information related to the
regulation of gene expression during the growth, development and pathogenesis of
young adults of A. cantonensis. 相似文献
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与转基因方法相比,基因瞬时表达系统在基因表达研究上具有快速便捷的特点。为检验水稻mi RNA与靶标基因之间的调控关系,将MIRNA基因与GFP/靶标序列融合基因(或GFP/靶标突变序列融合基因)构建在同一瞬时表达载体上,并转化水稻原生质体,通过观察含有GFP/靶标序列融合基因和GFP/靶标突变序列融合基因的载体之间的荧光强度差异,以及通过q RT-PCR方法检测靶标和非靶标m RNA水平差异来验证mi RNA对靶标基因的调控。用osa MIR156和osa MIR397及其靶标序列对实验设计方法进行验证,荧光显微观察和q RT-PCR检测证明,osami R156和osami R397能降低相应靶标序列GFP融合基因的转录物水平和GFP荧光水平。此种水稻原生质体瞬时表达方法用于在体内进行大规模mi RNA靶标基因检测。由于其他近缘单子叶植物很可能与水稻有近似的小RNA加工系统,因此对于其他单子叶植物mi RNA功能研究也将有很好的应用前景。 相似文献
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Damien Formey Luis Pedro I?iguez Pablo Peláez Yong-Fang Li Ramanjulu Sunkar Federico Sánchez José Luis Reyes Georgina Hernández 《BMC genomics》2015,16(1)
Background
MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21, the most used miRNA database, and no phasiRNAs have been identified for the model legume Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs for this organism and, particularly, we suggest new protagonists in the symbiotic nodulation events.Results
We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families. Degradome data allowed us to identify a total of 181 targets for these miRNAs. We reveal two regulatory networks involving conserved miRNAs: those known to play crucial roles in the establishment of nodules, and novel miRNAs present only in common bean, suggesting a specific role for these sequences. In addition, we identified 125 loci that potentially produce phased small RNAs, with 47 of them having all the characteristics of being triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study.Conclusions
We provide here a set of new small RNAs that contribute to the broader knowledge of the sRNAome of Phaseolus vulgaris. Thanks to the identification of the miRNA targets from degradome analysis and the construction of regulatory networks between the mature microRNAs, we present here the probable functional regulation associated with the sRNAome and, particularly, in N2-fixing symbiotic nodules.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1639-5) contains supplementary material, which is available to authorized users. 相似文献17.
The RNA interference machinery has served as a guardian of eukaryotic genomes since the divergence from prokaryotes. Although the basic components have a shared origin, silencing pathways directed by small RNAs have evolved in diverse directions in different eukaryotic lineages. Micro (mi)RNAs regulate protein-coding genes and play vital roles in plants and animals, but less is known about their functions in other organisms. Here, we report, for the first time, deep sequencing of small RNAs from the social amoeba Dictyostelium discoideum. RNA from growing single-cell amoebae as well as from two multicellular developmental stages was sequenced. Computational analyses combined with experimental data reveal the expression of miRNAs, several of them exhibiting distinct expression patterns during development. To our knowledge, this is the first report of miRNAs in the Amoebozoa supergroup. We also show that overexpressed miRNA precursors generate miRNAs and, in most cases, miRNA* sequences, whose biogenesis is dependent on the Dicer-like protein DrnB, further supporting the presence of miRNAs in D. discoideum. In addition, we find miRNAs processed from hairpin structures originating from an intron as well as from a class of repetitive elements. We believe that these repetitive elements are sources for newly evolved miRNAs. 相似文献
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Xie Ge Yong Zhang Jianhao Jiang Yi Zhong Xiaonan Yang Zhiqian Li Yongping Huang Anjiang Tan 《International journal of biological sciences》2013,9(1):1-15
The current identification of microRNAs (miRNAs) in insects is largely dependent on genome sequences. However, the lack of available genome sequences inhibits the identification of miRNAs in various insect species. In this study, we used a miRNA database of the silkworm Bombyx mori as a reference to identify miRNAs in Helicoverpa armigera and Spodoptera litura using deep sequencing and homology analysis. Because all three species belong to the Lepidoptera, the experiment produced reliable results. Our study identified 97 and 91 conserved miRNAs in H. armigera and S. litura, respectively. Using the genome of B. mori and BAC sequences of H. armigera as references, 1 novel miRNA and 8 novel miRNA candidates were identified in H. armigera, and 4 novel miRNA candidates were identified in S. litura. An evolutionary analysis revealed that most of the identified miRNAs were insect-specific, and more than 20 miRNAs were Lepidoptera-specific. The investigation of the expression patterns of miR-2a, miR-34, miR-2796-3p and miR-11 revealed their potential roles in insect development. miRNA target prediction revealed that conserved miRNA target sites exist in various genes in the 3 species. Conserved miRNA target sites for the Hsp90 gene among the 3 species were validated in the mammalian 293T cell line using a dual-luciferase reporter assay. Our study provides a new approach with which to identify miRNAs in insects lacking genome information and contributes to the functional analysis of insect miRNAs. 相似文献
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Jones-Rhoades MW 《Plant molecular biology》2012,80(1):3-16
MicroRNAs (miRNAs) are a class of small, non-coding RNAs that regulate gene expression in eukaryotic cells. The past decade has seen an explosion in our understanding of the sets of miRNA genes encoded in the genomes in different species of plants and the mechanisms by which miRNAs interact with target RNAs. A subset of miRNA families (and their binding sites in target RNAs) are conserved between angiosperms and basal plants, suggesting they predate the divergence of existing lineages of plants. However, the majority of miRNA families expressed by any given plant species have a narrow phylogenetic distribution. As a group, these "young" miRNAs genes appear to be evolutionarily fluid and lack clearly understood biological function. The goal of this review is to summarize our understanding of the sets of miRNA genes and miRNA targets that exist in various plant species and to discuss hypotheses that explain the patterns of conservation and divergence observed among microRNAs in plants. 相似文献