Comparative analysis of miRNAs and their targets across four plant species (original) (raw)
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Conservation and divergence of plant microRNA genes
The Plant Journal, 2006
MicroRNA (miRNA) is one class of newly identified, small, non-coding RNAs that play versatile and important roles in post-transcriptional gene regulation. All miRNAs have similar secondary hairpin structures; many of these are evolutionarily conserved. This suggests a powerful approach to predict the existence of new miRNA orthologs or homologs in other species. We developed a comprehensive strategy to identify new miRNA homologs by mining the repository of available ESTs. A total of 481 miRNAs, belonging to 37 miRNA families in 71 different plant species, were identified from more than 6 million EST sequences in plants. The potential targets of the EST-predicted miRNAs were also elucidated from the EST and protein databases, providing additional evidence for the real existence of these miRNAs in the given plant species. Some plant miRNAs were physically clustered together, suggesting that these miRNAs have similar gene expression patterns and are transcribed together as a polycistron, as observed among animal miRNAs. The uracil nucleotide is dominant in the first position of 5¢ mature miRNAs. Our results indicate that many miRNA families are evolutionarily conserved across all major lineages of plants, including mosses, gymnosperms, monocots and eudicots. Additionally, the number of miRNAs discovered was directly related to the number of available ESTs and not to evolutionary relatedness to Arabidopsis thaliana, indicating that miRNAs are conserved and little phylogenetic signal exists in the presence or absence of these miRNAs. Regulation of gene expression by miRNAs appears to have existed at the earliest stages of plant evolution and has been tightly constrained (functionally) for more than 425 million years.
Scientific reports, 2015
microRNAs (miRNAs), a class of endogenously produced small non-coding RNAs of 20-21 nt length, processed from precursor miRNAs, regulate many developmental processes by negatively regulating the target genes in both animals and plants. The coevolutionary pattern of a miRNA family and their targets underscores its functional conservation or diversification. The miR167 regulates various aspects of plant development in Arabidopsis by targeting ARF6 and ARF8. The evolutionary conservation or divergence of miR167s and their target genes are poorly understood till now. Here we show the evolutionary relationship among 153 MIR167 genes obtained from 33 diverse plant species. We found that out of the 153 of miR167 sequences retrieved from the "miRBase", 27 have been annotated to be processed from the 3' end, and have diverged distinctively from the other miR167s produced from 5' end. Our analysis reveals that gma-miR167h/i and mdm-miR167a are processed from 3' end and h...
Plant miRNAs: biogenesis, organization and origins
MicroRNAs, or miRNAs, are posttranscriptional regulators of gene expression. A wealth of observations and findings suggest highly complex, multicomponent, and intermingled pathways governing miRNA biogenesis and miRNA-mediated gene silencing. Plant miRNA genes are usually found as individual entities scattered around the intergenic and—to a much lesser extent—intragenic space, while miRNA gene clusters, formed by tandem or segmental duplications, also exist in plant genomes. Genome duplications are proposed to contribute to miRNA family expansions, as well. Evolutionarily young miRNAs retaining extensive homology to their loci of origin deliver important clues into miRNA origins and evolution. Additionally, imprecisely processed miRNAs evidence noncanonical routes of biogenesis, which may affect miRNA expression levels or targeting capabilities. Majority of the knowledge regarding miRNAs comes from model plant species. As ongoing research progressively expands into nonmodel systems, our understanding of miRNAs and miRNA-related pathways changes which opens up new perspectives and frontiers in miRNA research.
PLoS ONE, 2007
In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep sequencing and computational methods to identify, profile and analyze non-conserved MIRNA genes in Arabidopsis thaliana. 48 nonconserved MIRNA families, nearly all of which were represented by single genes, were identified. Sequence similarity analyses of miRNA precursor foldback arms revealed evidence for recent evolutionary origin of 16 MIRNA loci through inverted duplication events from protein-coding gene sequences. Interestingly, these recently evolved MIRNA genes have taken distinct paths. Whereas some non-conserved miRNAs interact with and regulate target transcripts from gene families that donated parental sequences, others have drifted to the point of non-interaction with parental gene family transcripts. Some young MIRNA loci clearly originated from one gene family but form miRNAs that target transcripts in another family. We suggest that MIRNA genes are undergoing relatively frequent birth and death, with only a subset being stabilized by integration into regulatory networks.
A Family of MicroRNAs Present in Plants and Animals W OA
Although many miRNAs are deeply conserved within each kingdom, none are known to be conserved between plants and animals. We identified Arabidopsis thaliana miR854 and miR855, two microRNAs (miRNAs) with multiple binding sites in the 39 untranslated region (39UTR) of OLIGOURIDYLATE binding PROTEIN1b (At UBP1b), forming miRNA:mRNA interactions similar to those that cause translational repression/mRNA cleavage in animals. At UBP1b encodes a member of a heterogeneous nuclear RNA binding protein (hnRNP) family. The 39UTR of At UBP1b is sufficient to repress reporter protein expression in tissues expressing miR854 or miR855 (rosette leaves and flowers, respectively) but not where both miRNAs are absent (cauline leaves). Intergenic regions containing sequences closely resembling miR854 are predicted to fold into stable miRNA precursors in animals, and members of the miR854 family are expressed in Caenorhabditis elegans, Mus musculus, and Homo sapiens, all with imperfect binding sites in the 39UTR of genes encoding the T cell Intracellular Antigen-Related protein, an hnRNP of the UBP1 family. Potential binding sites for miR854 are absent from UBP1-like genes in fungi lacking the miRNA biogenetic machinery. Our results indicate that plants and animals share miRNAs of the miR854 family, suggesting a common origin of these miRNAs as regulators of basal transcriptional mechanisms.
Recent Insights into Plant miRNA Biogenesis: Multiple Layers of miRNA Level Regulation
Plants
MicroRNAs are small RNAs, 20–22 nt long, the main role of which is to downregulate gene expression at the level of mRNAs. MiRNAs are fundamental regulators of plant growth and development in response to internal signals as well as in response to abiotic and biotic factors. Therefore, the deficiency or excess of individual miRNAs is detrimental to particular aspects of a plant’s life. In consequence, the miRNA levels must be appropriately adjusted. To obtain proper expression of each miRNA, their biogenesis is controlled at multiple regulatory layers. Here, we addressed processes discovered to influence miRNA steady-state levels, such as MIR transcription, co-transcriptional pri-miRNA processing (including splicing, polyadenylation, microprocessor assembly and activity) and miRNA-encoded peptides synthesis. MiRNA stability, RISC formation and miRNA export out of the nucleus and out of the plant cell also define the levels of miRNAs in various plant tissues. Moreover, we show the evol...
Plant micrornas: New players in functional genomics
2013
Introduction MicroRNAs (miRNAs) are endogenous, small, noncoding RNA molecules playing crucial roles in the regulation of gene expression at the post-transcriptional level in eukaryotes and viruses (Carrington and Ambros 2003; Bartel 2004; Schwab et al. 2005; Unver et al. 2009). These regulatory small RNA molecules achieve their roles through sequence-specific interactions with complementary sites of target mRNA that lead to their degradation (cleavage) or translational repression. Plant miRNAs are approximately 21-24 nucleotides in length, generally having a high degree of complementarity (nearperfect) between miRNAs and their targets, whereas animal miRNAs usually display partial complementarities to their targets; however, that is not the only difference between plant and animal miRNAs (Millar and Waterhouse 2005; Axtell et al. 2011). Although miRNAs share similarities in general, plant pre-miRNAs have larger and more variable stem-loop structures. Mature plant miRNAs often recognize a single target site in the coding region, pair their target sites with near-perfect complementarity, and guide the mRNA to cleavage, suggesting that plant miRNAs may act like siRNAs due to this specificity (Yang et al. 2007). To date, a total of 21,643 mature miRNAs have been identified from 168 species including viruses, a filamentous brown alga (Ectocarpus siliculosus), a diatome (Phaeodactylum tricornutum), a soil-living amoeba (Dictyostelium discoideum), a green alga (Chlamydomonas reinhardtii), plants, and animals. Identified miRNAs have been deposited in the publicly available miRNA database (miRBase v18 release November 2011; http://www. mirbase.org) (Kozomara and Griffiths-Jones 2011). Now, totally 4014 miRNAs belonging to 52 plant species have been loaded since the discovery of miRNAs in plants in 2002 (Park et al. 2002; Reinhart et al. 2002). 2. Biogenesis of plant miRNA The miRNAs are expressed from their own genes located in the intergenic (between protein-coding genes) or intragenic region (within protein-coding genes, in an exonic or intronic manner) on the chromosomes (Lagos-Quintana et al. 2001; Wang and Blelloch 2009). In plants, most miRNA genes are intergenic and transcribed individually from their own region, but a few genes are organized into polycistronic transcription units and cotranscribed from a single promoter at the end of a miRNA gene cluster (Bartel 2004; He and Hannon 2004; Voinnet 2009). It has been also reported that most miRNA genes in plants and animals have TATA box motifs upstream of their transcription start sites (TSSs), which are transcribed, 3´-poly-adenylated, and 5´ capped by RNA Polymerase II (POL II) like most protein-coding genes (Houbaviy et al. 2005; Xie et al. 2005; Megraw et al. 2006). Biogenesis of plant miRNAs requires a multiple biological process Abstract: MicroRNAs (miRNAs) are small, endogenously expressed, and nonprotein coding RNAs that regulate gene expression via post-transcriptional inhibition and cleavage. To date, several plant miRNAs have been identified via direct cloning, high-throughput sequencing, and bioinformatics analyses. The miRNAs participate in RNA-induced gene silencing complex, and specifically repress the target gene transcripts. Thus, miRNAs regulate the expression of genes playing diverse roles in plants, such as root initiation, leaf morphology, flower development, and response to environmental stimuli. A number of miRNAs have been identified and functionally characterized in eukaryotes. In this review, we discuss the functional roles of miRNAs in plant development as well as stress response to biotic and abiotic environmental factors. Additionally, we present brief information about miRNA detection and discovery techniques.
MicroRNAs and their regulatory roles in animals and plants
Journal of Cellular Physiology, 2007
microRNAs (miRNAs) are an abundant class of newly identified endogenous non-protein-coding small RNAs. They exist in animals, plants, and viruses, and play an important role in gene silencing. Translational repression, mRNA cleavage, and mRNA decay initiated by miRNA-directed deadenylation of targeted mRNAs are three mechanisms of miRNA-guided gene regulation at the posttranscriptional levels. Many miRNAs are highly conserved in animals and plants, suggesting that they play an essential function in plants and animals. Lots of investigations indicate that miRNAs are involved in multiple biological processes, including stem cell differentiation, organ development, phase change, signaling, disease, cancer, and response to biotic and abiotic environmental stresses. This review provides a general background and current advance on the discovery, history, biogenesis, genomics, mechanisms, and functions of miRNAs.