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1.
MicroRNAs (miRNAs) are small RNAs, generally of 20–23 nt, that down-regulate target gene expression during development, differentiation,
growth, and metabolism. In Populus, extensive studies of miRNAs involved in cold, heat, dehydration, salinity, and mechanical stresses have been performed;
however, there are few reports profiling the miRNA expression patterns during pathogen stress. We obtained almost 38 million
raw reads through Solexa sequencing of two libraries from Populus inoculated and uninoculated with canker disease pathogen. Sequence analyses identified 74 conserved miRNA sequences belonging
to 37 miRNA families from 154 loci in the Populus genome and 27 novel miRNA sequences from 35 loci, including their complementary miRNA* strands. Intriguingly, the miRNA*
of three conserved miRNAs were more abundant than their corresponding miRNAs. The overall expression levels of conserved miRNAs
increased when subjected to pathogen stress, and expression levels of 33 miRNA sequences markedly changed. The expression
trends determined by sequencing and by qRT-PCR were similar. Finally, nine target genes for three conserved miRNAs and 63
target genes for novel miRNAs were predicted using computational analysis, and their functions were annotated. Deep sequencing
provides an opportunity to identify pathogen-regulated miRNAs in trees, which will help in understanding the regulatory mechanisms
of plant defense responses during pathogen infection. 相似文献
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Cloning and characterization of microRNAs from wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) 总被引:8,自引:0,他引:8
Background
MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. So far, identification of miRNAs has been limited to a few model plant species, such as Arabidopsis, rice and Populus, whose genomes have been sequenced. Wheat is one of the most important cereal crops worldwide. To date, only a few conserved miRNAs have been predicted in wheat and the computational identification of wheat miRNAs requires the genome sequence, which is unknown. 相似文献4.
杨惠琴;蒋晶;刘明英;乔桂荣;姜彦成;卓仁英 《植物研究》2013,33(5):599-604
在构建盐胁迫下青杨microRNA文库中发现了ptc-miR801,为探索植物在盐胁迫条件下ptc-miR801参与胁迫应答的机制,本实验构建了植物表达载体pCAM2300-ami801,经根癌农杆菌EHA105介导、花序侵染法获得拟南芥转基因植株。RT-PCR半定量结果显示ptc-miR801可以在转基因拟南芥中超表达且NaCl胁迫下ptc-miRNA801转基因植株种子萌发率和根长显著高于野生型,说明ptc-miR801超表达增强了转基因拟南芥耐盐性。该试验为进一步研究miR801在杨树胁迫应答机制中的作用奠定基础。 相似文献
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Mature microRNAs (miRNAs) with a length of 20–24 nucleotides are endogenous, small, non-coding RNAs. They program the RNA-induced
silencing complex (RISC) to inhibit translation of the mRNAs carrying the sites complementary to these miRNAs. When the RISC
contains Ago3, the mRNA translation is inhibited; however, in the case of Ago2, the mRNA can be also cleaved in the center
of mRNA/miRNA heteroduplex. Using the earlier developed system ACTIVITY, we have analyzed the published data on the affinity
of mature human miRNA sequences for the Ago2 and Ago3 proteins. It has been found that the higher the abundance of YRHB tetranucleotides
near the miRNA 3′-end, the higher the miRNA affinity for both proteins (r = 0.613, α < 0.025) and that the miRNA binding to Ago2 increases relative to that Ago3 with the abundance of RHHK tetranucleotides
near the miRNA center (r=0.501, α < 0.05). These two patterns allowed us to propose equations for predicting the affinity of mature miRNAs for the
Ago2 and Ago3 proteins and to reliably predict the affinity of canonical (α < 0.00025) and noncanonical (α < 0.05) miRNAs
for each protein using independent data. 相似文献
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Qiulei Lang ChunZhi Jin Leiyu Lai Junli Feng Shaoning Chen Jishuang Chen 《Molecular biology reports》2011,38(3):1523-1531
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Identification of microRNA in the developing chick immune organs 总被引:1,自引:0,他引:1
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MicroRNA biogenesis and function in higher plants 总被引:1,自引:0,他引:1
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Feng Wang Nathan R. Johnson Ceyda Coruh Michael J. Axtell 《Nucleic acids research》2016,44(15):7395-7405
Plant small RNAs are subject to various modifications. Previous reports revealed widespread 3′ modifications (truncations and non-templated tailing) of plant miRNAs when the 2′-O-methyltransferase HEN1 is absent. However, non-templated nucleotides in plant heterochromatic siRNAs have not been deeply studied, especially in wild-type plants. We systematically studied non-templated nucleotide patterns in plant small RNAs by analyzing small RNA sequencing libraries from Arabidopsis, tomato, Medicago, rice, maize and Physcomitrella. Elevated rates of non-templated nucleotides were observed at the 3′ ends of both miRNAs and endogenous siRNAs from wild-type specimens of all species. ‘Off-sized’ small RNAs, such as 25 and 23 nt siRNAs arising from loci dominated by 24 nt siRNAs, often had very high rates of 3′-non-templated nucleotides. The same pattern was observed in all species that we studied. Further analysis of 24 nt siRNA clusters in Arabidopsis revealed distinct patterns of 3′-non-templated nucleotides of 23 nt siRNAs arising from heterochromatic siRNA loci. This pattern of non-templated 3′ nucleotides on 23 nt siRNAs is not affected by loss of known small RNA 3′-end modifying enzymes, and may result from modifications added to longer heterochromatic siRNA precursors. 相似文献
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Genetic evidence for 18S rRNA binding and an Rps19p assembly function of yeast nucleolar protein Nep1p 总被引:3,自引:0,他引:3
The nucleolar protein Nep1 and its human homologue were previously shown to be involved in the maturation of 18S rRNA and to interfere directly or indirectly with a methylation reaction. Here, we report that the loss-of-function mutation Δsnr57 and multicopy expression of the ribosomal 40S subunit protein 19 (Rps19p) can partially suppress the Saccharomyces cerevisiae Δnep1 growth defect. SnR57 mediates 2′-O-ribose-methylation of G1570 in the 18S rRNA. By performing a three-hybrid screen, we isolated several short RNA sequences with strong binding affinity to Nep1p. All isolated RNAs shared a six-nucleotide consensus motif C/UUCAAC. Furthermore, one of the isolated RNAs exactly corresponded to nucleotides 1553–1577 of the 18S rRNA, which includes G1570, the site of snR57-dependent 18S rRNA methylation. From protein–protein crosslink data and the cryo-EM map of the S.
cerevisiae small ribosomal subunit, we suggest that Rps19p is localized in close vicinity to the Nep1p 18S rRNA binding site. Our results suggest that Nep1p binds adjacent to helix 47 of the 18S rRNA and possibly supports the association of Rps19p to pre-ribosomal particles. 相似文献
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Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation 总被引:12,自引:0,他引:12
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Background
The microRNAs (miRNAs) are an extensive class of small noncoding RNAs (18 to 25 nucleotides) with probable roles in the regulation of gene expression. In Caenorhabditis elegans, lin-4 and let-7 miRNAs control the timing of fate specification of neuronal and hypodermal cells during larval development. lin-4, let-7 and other miRNA genes are conserved in mammals, and their potential functions in mammalian development are under active study. 相似文献16.
To date, the majority of plant small RNAs (sRNA) have been identified in rice, poplar and Arabidopsis. To identify novel tomato sRNAs potentially involved in tomato specific processes such as fruit development and/or ripening,
we cloned 4,018 sRNAs from tomato fruit tissue at the mature green stage. From this pool of sRNAs, we detected tomato homologues
of nine known miRNAs, including miR482; a poplar miRNA not conserved in Arabidopsis or rice. We identified three novel putative miRNAs with flanking sequence that could be folded into a stem-loop precursor
structure and which accumulated as 19-24nt RNA. One of these putative miRNAs (Put-miRNA3) exhibited significantly higher expression
in fruit compared with leaf tissues, indicating a specific role in fruit development processes. We also identified nine sRNAs
that accumulated as 19–24nt RNA species in tomato but genome sequence was not available for these loci. None of the nine sRNAs
or three putative miRNAs possessed a homologue in Arabidopsis that had a precursor with a predicted stem-loop structure or that accumulated as a sRNA species, suggesting that the 12 sRNAs
we have identified in tomato may have a species specific role in this model fruit species.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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Biological role of MicroRNA-103 based on expression profile and target genes analysis in pigs 总被引:1,自引:0,他引:1
MicroRNAs (miRNAs) are endogenously expressed RNAs consisting of 20–24 nucleotides. These molecules are thought to repress
protein translation by binding to target mRNAs. However, biological functions have not been assigned to most of the 175 porcine
miRNAs registered in miRBase (release 15.0). In an effort to uncover miR-103 important in pigs, we examined the integrative
tissue expression profile and gene ontology (GO) term enrichment of predicted target genes to determine the global biological
functions of miR-103. Our results demonstrated that miR-103 is involved in various biological processes including brain development,
lipid metabolism, adipocyte differentiation, hematopoiesis, and immunity. Moreover, we also experimentally verified effects
of miR-103 in porcine preadipocytes. miR-103 levels increased in differentiating adipocytes, and inhibition of miR-103 effectively
inhibited preadipocyte differentiation. In addition, mRNA levels of the putative miR-103 target RAI14 were higher in miR-103 inhibitor-treated adipocytes. These results demonstrate that miR-103 is involved in porcine preadipocyte
differentiation and may act through the putative target gene RAI14. In a word, our data provide new insights into the global biological role of miR-103. 相似文献
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