Computational identification of novel family members of microRNA genes in Arabidopsis thaliana and Oryza sativa.

MicroRNAs (miRNAs) are a class of endogenous small RNAs that play important regulatory roles in both animals and plants. miRNA genes have been intensively studied in animals, but not in plants. In this study, we adopted a homology search approach to identify homologs of previously validated plant miRNAs in Arabidopsis thaliana and Oryza sativa. We identified 20 potential miRNA genes in Arabidopsis and 40 in O. sativa, providing a relatively complete enumeration of family members for these miRNAs in plants. In addition, a greater number of Arabidopsis miRNAs (MIR168, MIR159 and MIR172) were found to be conserved in rice. With the novel homologs, most of the miRNAs have closely related fellow miRNAs and the number of paralogs varies in the different miRNA families. Moreover, a probable functional segment highly conserved on the elongated stem of pre-miRNA fold-backs of MIR319 and MIR159 family was identified. These results support a model of variegated miRNA regulation in plants, in which miRNAs with different functional elements on their pre-miRNA fold-backs can differ in their function or regulation, and closely related miRNAs can be diverse in their specificity or competence to downregulate target genes. It appears that the sophisticated regulation of miRNAs can achieve complex biological effects through qualitative and quantitative modulation of gene expression profiles in plants.

Li Y ，Li W ，Jin YX 《ACTA BIOCHIMICA ET BIOPHYSICA SINICA》

Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice.

To understand the expansion of multicopy microRNA (miRNA) families in plants, we localized the reported miRNA genes from Arabidopsis and rice to their chromosomes, respectively, and observed that 37% of 117 miRNA genes from Arabidopsis and 35% of 173 miRNA genes from rice were segmental duplications in the genome. In order to characterize whether the expression diversification has occurred among plant multicopy miRNA family members, we designed PCR primers targeting 48 predicted miRNA precursors from 10 families in Arabidopsis and rice. Results from RT-PCR data suggest that the transcribed precursors of members within the same miRNA family were present at different expression levels. In addition, although miR160 and miR162 sequences were conserved in Arabidopsis and rice, we found that the expression patterns of these genes differed between the two species. These data suggested that expression diversification has occurred in multicopy miRNA families, increasing our understanding of the expression regulation of miRNAs in plants.

Jiang D ，Yin C ，Yu A ，Zhou X ，Liang W ，Yuan Z ，Xu Y ，Yu Q ，Wen T ，Zhang D ... -  《CELL RESEARCH》

Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes.

MicroRNAs (miRNAs) are an extensive class of tiny RNA molecules that regulate the expression of target genes by means of complementary base pair interactions. Although the first miRNAs were discovered in Caenorhabditis elegans, >300 miRNAs were recently documented in animals and plants, both by cloning methods and computational predictions. We present a genome-wide computational approach to detect miRNA genes in the Arabidopsis thaliana genome. Our method is based on the conservation of short sequences between the genomes of Arabidopsis and rice (Oryza sativa) and on properties of the secondary structure of the miRNA precursor. The method was fine-tuned to take into account plant-specific properties, such as the variable length of the miRNA precursor sequences. In total, 91 potential miRNA genes were identified, of which 58 had at least one nearly perfect match with an Arabidopsis mRNA, constituting the potential targets of those miRNAs. In addition to already known transcription factors involved in plant development, the targets also comprised genes involved in several other cellular processes, such as sulfur assimilation and ubiquitin-dependent protein degradation. These findings considerably broaden the scope of miRNA functions in plants.

Bonnet E ，Wuyts J ，Rouzé P ，Van de Peer Y ... -  《-》

Genomic analysis of rice microRNA promoters and clusters.

MicroRNAs (miRNAs) are endogenous single-stranded non-coding small RNAs with a length of about 21 nt, that negatively regulate development and stresses. Rice miRNAs are representative of the monocot miRNAs, and many of them are non-conserved in Arabidopsis and the other plant species. Previous studies have shown that a majority of plant miRNAs are expressed from independent transcription units, whereas some others are transcribed with their host genes. Despite of the fact that a growing number of rice miRNAs are discovered, little is known about the transcriptional regulation of miRNA genes. In this study, we performed genomic analysis of rice miRNA transcripts surrounding the regions of promoter/transcription start site (TSS) and TATA-box, and organization of miRNA clusters. We detected 249 promoters for 212 rice pre-miRNA sequences via bioinformatics approach and found that the conserved rice miRNA genes have a greater proportion of promoters than the non-conserved miRNA genes. We further globally analyzed the genomic organization of pri-miRNAs and found that 52 rice miRNA genes appear in 18 clusters. Alignment of the miRNA sequences in these clusters shows a number of miRNA paralogs within the cluster. The data obtained may aid our understanding of the specific sequences upstream of pre-miRNAs and the functional implications of miRNA clusters in rice plants.

Cui X ，Xu SM ，Mu DS ，Yang ZM ... -  《-》

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 (Cd(2+)). 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.

Huang SQ ，Peng J ，Qiu CX ，Yang ZM ... -  《-》