Cloning and characterization of microRNAs from <i>Brassica napus</i>

Wang, Lei; Wang, Ming-Bo; Tu, Jinxing; Helliwell, Chris A.; Waterhouse, Peter M.; Dennis, E. S.; Fu, Tingdong; Fan, Yanting

doi:10.1016/j.febslet.2007.07.010

Cited by 51 publications

(35 citation statements)

References 55 publications

(59 reference statements)

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“…Most of these known miRNAs (68.3%) were 21 nt in length with the remainder being 20 nt or 22 nt long (Table S1). This is similar to observations of miRNAs from other plant species, indicating that cucumber miRNAs are mostly processed by DCL 1 [30].…”

Section: Resultssupporting

confidence: 89%

A Combined Approach of High-Throughput Sequencing and Degradome Analysis Reveals Tissue Specific Expression of MicroRNAs and Their Targets in Cucumber

Mao

Xia

et al. 2012

PLoS ONE

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MicroRNAs (miRNAs) are endogenous small RNAs playing an important regulatory function in plant development and stress responses. Among them, some are evolutionally conserved in plant and others are only expressed in certain species, tissue or developmental stages. Cucumber is among the most important greenhouse species in the world, but only a limited number of miRNAs from cucumber have been identified and the experimental validation of the related miRNA targets is still lacking. In this study, two independent small RNA libraries from cucumber leaves and roots were constructed, respectively, and sequenced with the high-throughput Illumina Solexa system. Based on sequence similarity and hairpin structure prediction, a total of 29 known miRNA families and 2 novel miRNA families containing a total of 64 miRNA were identified. QRT-PCR analysis revealed that some of the cucumber miRNAs were preferentially expressed in certain tissues. With the recently developed ‘high throughput degradome sequencing’ approach, 21 target mRNAs of known miRNAs were identified for the first time in cucumber. These targets were associated with development, reactive oxygen species scavenging, signaling transduction and transcriptional regulation. Our study provides an overview of miRNA expression profile and interaction between miRNA and target, which will help further understanding of the important roles of miRNAs in cucumber plants.

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Section: Resultssupporting

confidence: 89%

A Combined Approach of High-Throughput Sequencing and Degradome Analysis Reveals Tissue Specific Expression of MicroRNAs and Their Targets in Cucumber

Mao

Xia

et al. 2012

PLoS ONE

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“…Cloning and sequencing of small RNA are the most conventional way of miRNA discovery (Sunkar et al 2005;Tzahi Arazi et al 2005;Wang et al 2007;Carra et al 2009). In recent years, deep sequencing provides masses of data for the dissection and characterization of diverse small RNA populations and the identification of low abundance miRNAs (Lu et al 2005a;Lu et al 2006; Barakat et al 2007;Fahlgren et al 2007), However, the abundance of certain miRNAs depends on the tissue type as well as the treatment to which the tissues were exposed.…”

Section: Introductionmentioning

confidence: 98%

Identification and characterization of microRNAs from citrus expressed sequence tags

Liu

et al. 2010

Tree Genetics & Genomes

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MicroRNAs (miRNAs) are a group of singlestranded noncoding RNAs with general size of 21-24 nucleotides, which negatively regulate gene expression posttranscriptionally by repressing gene translation or degrading targeted mRNAs. Despite the important functions of miRNAs in plants, little is known about miRNAs in citrus. Here we present a study of bioinformatics identification of microRNA precursors in citrus by comparing known plant miRNAs against 560,271 citrus ESTs. Seventy-eight ESTs from ten citrus species and three hybrids were identified as putative miRNA precursors, encoding 51 unique miRNA sequences, representing 28 miRNA families. Blastn search of the putative miRNAs against citrus unigenes and ESTs was performed to identify the target genes. As a result, 36 unigenes and 77 ESTs were identified as putative targets of 25 citrus miRNA families. The putative targets are mainly transcription factors and play important roles in development, metabolism, and stress resistance. To validate the predicted miRNAs, qRT-PCR was applied to detect the tissue-specific expression of nine putative miRNAs in Citrus sinensis cv. Valencia. The cleavage sites on five mRNAs targeted by three miRNA families were mapped by 5′RACE. This study provided information on citrus miRNA precursors, mature miRNAs, and miRNA targets and is helpful for future research of miRNA function in citrus.

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“…The seed oil content varies significantly among B. napus cultivars or under different growth environments. So far, there have been only a few reports on small RNA population and function analysis in B. napus (Wang et al, 2007;Xie et al, 2007;Buhtz et al, 2008;He et al, 2008;Pant et al, 2008Pant et al, , 2009Huang et al, 2010;Wei et al, 2010). In addition, most reports on the oil production mechanisms in B. napus focused on the rapid oil accumulation stage; few studied the gene expression profiles of early embryos, which may have already determined the oil production abilities of B. napus seeds (Li et al, 2006;Sharma et al, 2008;Fu et al, 2009).…”

mentioning

confidence: 99%

Small RNA Profiling in Two Brassica napus Cultivars Identifies MicroRNAs with Oil Production- and Development-Correlated Expression and New Small RNA Classes

Zhao

Wang²,

Fu³

et al. 2011

Plant Physiology

111

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MicroRNAs (miRNAs) and small interfering RNAs are important regulators of plant development and seed formation, yet their population and abundance in the oil crop Brassica napus are still not well understood, especially at different developmental stages and among cultivars with varied seed oil contents. Here, we systematically analyzed the small RNA expression profiles of Brassica napus seeds at early embryonic developmental stages in high-oil-content and low-oil-content B. napus cultivars, both cultured in two environments. A total of 50 conserved miRNAs and 9 new miRNAs were identified, together with some new miRNA targets. Expression analysis revealed some miRNAs with varied expression levels in different seed oil content cultivars or at different embryonic developmental stages. A large number of 23-nucleotide small RNAs with specific nucleotide composition preferences were also identified, which may present new classes of functional small RNAs.

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Cloning and characterization of microRNAs from Brassica napus

Cited by 51 publications

References 55 publications

A Combined Approach of High-Throughput Sequencing and Degradome Analysis Reveals Tissue Specific Expression of MicroRNAs and Their Targets in Cucumber

A Combined Approach of High-Throughput Sequencing and Degradome Analysis Reveals Tissue Specific Expression of MicroRNAs and Their Targets in Cucumber

Identification and characterization of microRNAs from citrus expressed sequence tags

Small RNA Profiling in Two Brassica napus Cultivars Identifies MicroRNAs with Oil Production- and Development-Correlated Expression and New Small RNA Classes

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