Genomewide analysis of intronic microRNAs in rice and Arabidopsis

Yang, Guodong; Ke, Yan; Wu, Bingjiang; Wang, Y. H.; Gao, Yingying; Zheng, Chengchao

doi:10.1007/s12041-012-0199-6

Cited by 39 publications

(37 citation statements)

References 45 publications

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“…These detailed analyses on genomic annotation of miRNAs in grapevine can serve as a reference for future research on evolution. We found that the percentage of intragenic miRNAs in grapevine was approximately 0.9 times higher than in rice (23.0 vs. 25.4%) and 0.43 times higher than in A. thaliana (23.0 vs. 52.9%) (Yang et al, 2012). We also found that the proportion of intronic miRNAs in grapevine was approximately 1.1 times higher than in A. thaliana and 2.8 times higher than in rice (Table 3).…”

Section: Analysis Of Intergenic and Intragenic (Intronic Exonic) Micmentioning

confidence: 72%

Genome‐Wide Mapping and Analysis of Grapevine MicroRNAs and Their Potential Target Genes

et al. 2015

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MicroRNAs (miRNAs) are single-stranded, nonprotein-coding, endogenously expressed, small RNAs 19 to 25 nucleotides in length. Recognizing the lack of specific and systematic studies on genome-wide mapping of grapevine (Vitis vinifera L.) miRNAs, we conducted genome-wide mapping of Vv-miRNAs (V. vinifera miRNAs), SB-miRNAs (V. vinifera L. 'Summer Black' miRNAs), and VamiRNAs (V. amurensis Rupr. miRNAs). The mapping results revealed that many of miRNAs located within the intergenic region had independent transcription units. To further validate the mapping results and existence of miRNAs, 12 randomly selected precursors of miRNAs (pre-miRNAs) were successfully cloned and sequenced. Subsequently, 15 conserved and 29 nonconserved intragenic (intronic, exonic) Vv-miRNA genes, 24 nonconserved intragenic SB-miRNA genes, and 23 nonconserved intragenic Va-miRNA genes were labeled on the basis of their locations in host genes, and 15 MIR-NA clusters were detected. Interestingly, five miRNA pairs, namely, Vv-MIR395b and Vv-MIR395c, Vv-MIR482 and Vv-MIRC13, Vv-MIR172a and Va-MIR057, SB-MIR024 and Vv-MIRC35, and Vv-MIRC36 and Va-MIR073 were clustered in the host genes GS-VIVT01011558001, GSVIVT01008132001, GSVIVT01031524001, GSVIVT01028156001, and GSVIVT01024516001, respectively. To validate the existence of target genes and miRNA-guided cleavage sites, 3-end product of four predicted target messenger RNAs were amplified by RNA ligase-mediated 5 rapid amplification of cDNA ends. In addition, we also conducted contrastive analysis on the genomic location of miRNAs and their potential target genes. Results showed that the order of priority of miRNA-target interaction may be less closely related with their genomic location. These findings could benefit some further study on grapevine functional genomics and will provide new insights into the regulatory mechanisms and evolution of miRNAs in Vitis species. ). In addition, the expression levels of miRNAs possess time-dependent and tissue-specific characteristics across species. To date, hundreds of miRNAs have been identified by computational and experimental approaches in many plants (Lu et al., 2005;Zhang et al., 2006aZhang et al., , 2008Zhao et al., 2010;Felippes et al., 2008;Sunkar et al., 2008;Szittya et al., 2008;Song et al., 2009aSong et al., , 2010Yu et al., 2011). Numerous studies also indicated that miRNAs regulated the growth and development of plants by repressing the expression of their target genes through direct cleavage or, in a few Abbreviations: cDNA, complementary DNA; CDS, coding region sequences; ChrUn, unknown chromosome; GSDS, gene structure display server; HMW, high molecular weight; miRNA, microRNA; mRNA, messenger RNA; NCBI, National Center for Biotechnology Information; NCBI, National Center for Biotechnology Information; PCR, polymerase chain reaction; pre-miRNA, precursor of miRNA; RACE, rapid amplification of cDNA ends; RLM-RACE, RNA ligasemediated 5 rapid amplification of cDNA ends; SB-miRNA, Vitis vinifera L. 'Summer Black' miRNA; TU, tra...

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Section: Analysis Of Intergenic and Intragenic (Intronic Exonic) Micmentioning

confidence: 72%

Genome‐Wide Mapping and Analysis of Grapevine MicroRNAs and Their Potential Target Genes

et al. 2015

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“…A number of miRNA genes in plants reside within an intron of protein coding genes and are coexpressed and processed with the host protein-coding gene Yan et al, 2012;Yang et al, 2012a). AS of primary transcripts due to IR and exon skipping of several plant miRNAs has been reported (Aukerman and Sakai, 2003;Kurihara and Watanabe, 2004;Hirsch et al, 2006;Szarzynska et al, 2009).…”

Section: Coupling Of As To Mrna Stability Through Nmdmentioning

confidence: 99%

“…Dicerlike1 (DCL1), a key endonuclease in biogenesis of miRNA from primiRNA (Rogers and Chen, 2013b), has 20 exons and contains an MBS for miR162 that is interrupted by intron 12. AS in this intron generates four isoforms (DCL1-1 to DCL1-4), and one of these four isoform contains an MBS (Yang et al, 2012a). Hence, regulated AS of DCL1 pre-mRNAs would affect regulation of DCL1 protein levels.…”

Section: Coupling Of As To Mrna Stability Through Nmdmentioning

confidence: 99%

Complexity of the Alternative Splicing Landscape in Plants

et al. 2013

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Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.

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“…Introns of protein-coding genes, where MIR genes are hosted are referred to as mirtrons. Until date, they have been discovered in invertebrates and mammals (Berezikov et al 2007), and, more recently, in rice and Arabidopsis (Yang et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Regulation of NBS-LRR genes by MicroRNAs in wheat: Computational identification of candidate MIR-2118 genes and evidence of flexibility

Khalfallah

Bouktila

Habachi-Houimli

et al. 2017

Cereal Research Communications

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Plant microRNAs are crucial for post-transcriptional regulation of gene expression, with some of them particularly involved in regulating several disease resistance (R) genes. This study is a computational screening for microRNAs potentially involved in the regulation of disease resistance in bread wheat Triticum aestivum, through the genome and transcriptome of this crop species. We used plant miRNAs of the superfamily miR-482/2118 to find complementarities with the expressed sequence tags (ESTs) coding NBS-LRR proteins of the bread wheat. This analysis revealed a vast recognition potential, highlighting highly variable miRNA-mRNA hybridization schemes. Precursors of miR-2118/482 sequences that showed a potential for recognizing wheat NBS-LRR ESTs were used as input for similarity search in the T. aestivum transcriptome shotgun assemblies (TSA) database, enabling the identification of a couple of wheat TSA sequences (JV952948.1 and JV851699.1) that were predicted to adopt a stable miRNA/miRNA* duplex structure. The genomic regions corresponding to both predicted tae-miR-2118 genes were determined on wheat chromosomes 2DL and 5AS. The findings of the present study will contribute to a better understanding of R gene expression regulation in wheat.

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Genomewide analysis of intronic microRNAs in rice and Arabidopsis

Cited by 39 publications

References 45 publications

Genome‐Wide Mapping and Analysis of Grapevine MicroRNAs and Their Potential Target Genes

Genome‐Wide Mapping and Analysis of Grapevine MicroRNAs and Their Potential Target Genes

Complexity of the Alternative Splicing Landscape in Plants

Regulation of NBS-LRR genes by MicroRNAs in wheat: Computational identification of candidate MIR-2118 genes and evidence of flexibility

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