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 ... -  《-》

Genomic analysis of silkworm microRNA promoters and clusters.

MicroRNAs (miRNAs) are endogenous single-stranded RNAs of 18-22 nt in length, which can regulate the complementary mRNAs at the post-transcriptional level by cleavage or repression of translation of the target mRNAs. Studies have shown that the majority of animal miRNAs are transcribed from independent transcription units, and someare transcribed together with their host genes. However, the nature of the primary transcript of intergenic miRNAs remains unknown. Silkworm (Bombyx mori) miRNAs are representative of those of the Lepidoptera insects and many of them are conserved in Caenorhabditis elegans and other animal species. To date, little is known about the transcriptional regulation of silkworm miRNA genes. We performed the genomic analysis on the silkworm miRNA transcripts around the promoter region including the transcription start site (TSS) and the TATA-box, and on the organization of the miRNA cluster. In 73 pre-miRNAs from the silkworm 131 promoters were detected via a bioinformatics approach. Among them the portion of non-conserved promoters is greater than that of the conserved ones. The genomic organization of pre-miRNAs of the silkworm was globally analyzed and it was determined that 11 of them we reorganized into five clusters. Sequence alignment showed that paralogs existed for some of the miRNAs in the cluster. These results may increase the understanding of the specific sequences upstream of the pre-miRNAs and of the functional implications of miRNA clusters in the silkworm.

Huang Y ，Shen XJ ，Zou Q ，Huang JS ，Tang SM ... -  《-》

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》

Selection and mutation on microRNA target sequences during rice evolution.

MicroRNAs (miRNAs) posttranscriptionally down-regulate gene expression by binding target mRNAs. Analysis of the evolution of miRNA binding sites is helpful in understanding the co-evolution between miRNAs and their targets. To understand this process in plants a comparative analysis of miRNA-targeted duplicated gene pairs derived from a well-documented whole genome duplication (WGD) event in combination with a population genetics study of six experimentally validated miRNA binding sites in rice (O. sativa) was carried out. Of the 1,331 pairs of duplicate genes from the WGD, 41 genes (29 pairs) were computationally predicted to be miRNA targets. Sequence substitution analysis indicated that the synonymous substitution rate was significantly lower in the miRNA binding sites than their 5' and 3' flanking regions. Of the 29 duplicated gene pairs, 17 have only one paralog been targeted by a miRNA. This could be due to either gain of a miRNA binding site after the WGD or because one of the duplicated genes has escaped from being a miRNA target after the WGD (loss of miRNA binding site). These possibilities were distinguished by separating miRNAs conserved in both dicots and monocot plants from rice-specific miRNAs and by phylogenetic analysis of miRNA target gene families. The gain/loss rate of miRNA binding sites was estimated to be 3.0 x 10(-9) gain/loss per year. Most (70.6%) of the gains/losses were due to nucleotide mutation. By analysis of cultivated (O. sativa; n = 30) and wild (O. rufipogon; n = 15) rice populations, no segregating site was observed in six miRNA binding sites whereas 0.12-0.20 SNPs per 21-nt or 1.53-1.80 x 10(-3) of the average pairwise nucleotide diversity (pi) were found in their flanking regions. Both molecular evolution and population genetics support the hypothesis that conservation of miRNA binding sites is maintained by purifying selection through elimination of deleterious alleles. Nucleotide mutations play a major role in the gain/loss of miRNA binding sites during evolution.

Guo X ，Gui Y ，Wang Y ，Zhu QH ，Helliwell C ，Fan L ... -  《BMC GENOMICS》