Molecular characterization of miRNA genes and their expression in Dimocarpus longan Lour

A genome-wide analysis of longan miRNA genes was conducted, and full-length pri-miRNA transcripts were cloned. Bioinformatics and expression analyses contributed to the functional characterization of longan miRNA genes. MicroRNAs are important for the post-transcriptional regulation of target genes. However, little is known about the transcription and regulation of miRNA genes in longan (Dimocarpus longan Lour.). In this study, 80 miRNA precursors (pre-miRNA) were predicted, and their secondary structure, size, conservation, and diversity were analyzed. Furthermore, the full-length cDNA sequences of 13 longan primary miRNAs (pri-miRNAs) were amplified by RLM-RACE and SMART-RACE and analyzed, which revealed that longan pri-miRNA transcripts have multiple transcription start sites (TSSs) and the downstream pre-miRNAs are polymorphic. Accordingly, the longan pri-miRNAs and protein-encoding genes may have similar transcriptional specificities. An analysis of the longan miRNA gene promoter elements indicated that the three most abundant cis-acting elements were light-responsive, stress-responsive, and hormone-responsive elements. A quantitative real-time PCR assay elucidated the potential spatial and temporal expression patterns of longan pre-miRNAs during the early stages of somatic embryogenesis (SE) and in different longan organs/tissues. This is the first report regarding the molecular characterization of miRNA genes and their expression profiles in longan. The generated data may serve as a foundation for future research aimed at clarifying the longan miRNA gene functions.

New insights into tomato microRNAs

Cultivated tomato, Solanum lycopersicum, is one of the most common fruits in the global food industry. Together with the wild tomato Solanum pennellii, it is widely used for developing better cultivars. MicroRNAs affect mRNA regulation, inhibiting its translation and/or promoting its degradation. Important proteins involved in these processes are ARGONAUTE and DICER. This study aimed to identify and characterize the genes involved in the miRNA processing pathway, miRNA molecules and target genes in both species. We validated the presence of pathway genes and miRNA in different NGS libraries and 6 miRNA families using quantitative RT-PCR. We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. Of these, 29 and 32 participate in miRNA processing pathways, respectively. We identified 343 mature miRNAs, 226 pre-miRNAs in 87 families, including 192 miRNAs, which were not previously identified, belonging to 38 new families in S. lycopersicum. In S. pennellii, we found 388 mature miRNAs and 234 pre-miRNAs contained in 85 families. All miRNAs found in S. pennellii were unpublished, being identified for the first time in our study. Furthermore, we identified 2471 and 3462 different miRNA target in S. lycopersicum and S. pennellii, respectively.

Identification and expression analysis of a microRNA cluster derived from pre-ribosomal RNA in Papaver somniferum L. and Papaver bracteatum L

Opium poppy (Papaver somniferum L.) is one of the ancient medical crops, which produces several important alkaloids such as morphine, noscapine, sanguinarine and codeine. MicroRNAs are endogenous non-coding RNAs that play important regulatory roles in plant diverse biological processes. Many plant miRNAs are encoded as single transcriptional units, in contrast to animal miRNAs, which are often clustered. Herein, using computational approaches, a total of 22 miRNA precursors were identified, which five of them were located as a clustered in pre-ribosomal RNA. Afterward, the transcript level of the precursor and the mature of clustered miRNAs in two species of the Papaveraceae family, i.e. P. somniferum L. and P. bracteatum L, were quantified by RT-PCR. With respect to obtained results, these clustered miRNAs were expressed differentially in different tissues of these species. Moreover, using target prediction and Gene Ontology (GO)-based on functional classification indicated that these miRNAs might play crucial roles in various biological processes as well as metabolic pathways. In this study, we discovered the clustered miRNA derived from pre-rRNA, which may shed some light on the importance of miRNAs in the plant kingdom.

Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis

MicroRNAs (miRNAs) comprise a class of short noncoding RNA molecules that play diverse developmental and physiological roles by controlling mRNA abundance and protein output of the vast majority of transcripts. Despite the importance of miRNAs in regulating gene function, we still lack a complete understanding of how miRNAs themselves are transcriptionally regulated. To fill this gap, we predicted regulatory sequences by searching for abundant short motifs located upstream of miRNAs in eight species of Caenorhabditis nematodes. We identified three conserved motifs across the Caenorhabditis phylogeny that show clear signatures of purifying selection from comparative genomics, patterns of nucleotide changes in motifs of orthologous miRNAs, and correlation between motif incidence and miRNA expression. We then validated our predictions with transgenic green fluorescent protein reporters and site-directed mutagenesis for a subset of motifs located in an enhancer region upstream of let-7 We demonstrate that a CT-dinucleotide motif is sufficient for proper expression of GFP in the seam cells of adult C. elegans, and that two other motifs play incremental roles in combination with the CT-rich motif. Thus, functional tests of sequence motifs identified through analysis of molecular evolutionary signatures provide a powerful path for efficiently characterizing the transcriptional regulation of miRNA genes.

Genome-wide identification and in silico characterisation of microRNAs, their targets and processing pathway genes in Phaseolus vulgaris L

Common bean (Phaseolus vulgaris L., Fabaceae) is a globally important staple crop, which is an important source of calories, protein and essential micronutrients. At the genomic level little is known regarding the small non-coding RNAs within the common bean genome. One of the most important classes of such small non-coding RNAs is microRNAs (miRNAs), which control mRNA and protein expression levels in many eukaryotes. Computational methods have been applied to identify putative miRNAs in the genomes of different organisms. In this study, our objective was to comprehensively identify and characterise miRNAs from the genome and transcriptome of P. vulgaris, including both mature and precursor miRNA forms. We also sought to identify the putative proteins involved in miRNA processing and the likely target genes of common bean miRNAs. We identified 221 mature miRNAs and 136 precursor miRNAs distributed across 52 different miRNA families in the P. vulgaris genome. Amongst these, we distinguished 129 novel mature miRNAs and 123 miRNA precursors belonging to 24 different miRNA families. We also identified 31 proteins predicted to participate in the miRNA-processing pathway in P. vulgaris. Finally, we also identified 483 predicted miRNA targets, including many which corroborate results from other species, suggesting that miRNA regulatory systems are evolutionarily conserved and important for plant development. Our results expand the study of miRNAs and their target genes in common bean, and provide new opportunities to understand their roles in the biology of this important staple crop.

Inferring plant microRNA functional similarity using a weighted protein-protein interaction network

BACKGROUND

MiRNAs play a critical role in the response of plants to abiotic and biotic stress. However, the functions of most plant miRNAs remain unknown. Inferring these functions from miRNA functional similarity would thus be useful. This study proposes a new method, called PPImiRFS, for inferring miRNA functional similarity.

RESULTS

The functional similarity of miRNAs was inferred from the functional similarity of their target gene sets. A protein-protein interaction network with semantic similarity weights of edges generated using Gene Ontology terms was constructed to infer the functional similarity between two target genes that belong to two different miRNAs, and the score for functional similarity was calculated using the weighted shortest path for the two target genes through the whole network. The experimental results showed that the proposed method was more effective and reliable than previous methods (miRFunSim and GOSemSim) applied to Arabidopsis thaliana. Additionally, miRNAs responding to the same type of stress had higher functional similarity than miRNAs responding to different types of stress.

CONCLUSIONS

For the first time, a protein-protein interaction network with semantic similarity weights generated using Gene Ontology terms was employed to calculate the functional similarity of plant miRNAs. A novel method based on calculating the weighted shortest path between two target genes was introduced.

Identification of miRNAs involved in pear fruit development and quality

Background

MicroRNAs (miRNAs) are a class of small, endogenous RNAs that take part in regulating genes through mediating gene expressions at the post-transcriptional level in plants. Previous studies have reported miRNA identification in various plants ranging from model plants to perennial fruit trees. However, the role of miRNAs in pear (Pyrus bretschneideri) fruit development is not clear. Here, we investigated the miRNA profiles of pear fruits from different time stages during development with Illumina HiSeq 2000 platform and bioinformatics analysis. Quantitative real-time PCR was used to validate the expression levels of miRNAs.

Results

Both conserved and species-specific miRNAs in pear have been identified in this study. Total reads, ranging from 19,030,925 to 25,576,773, were obtained from six small RNA libraries constructed for different stages of fruit development after flowering. Comparative profiling showed that an average of 90 miRNAs was expressed with significant differences between various developmental stages. KEGG pathway analysis on 2,216 target genes of 188 known miRNAs and 1,127 target genes of 184 novel miRNAs showed that miRNAs are widely involved in the regulation of fruit development. Among these, a total of eleven miRNAs putatively participate in the pathway of lignin biosynthesis, nine miRNAs were identified to take part in sugar and acid metabolism, and MiR160 was identified to regulate auxin response factor.

Conclusion

Comparative analysis of miRNAomes during pear fruit development is presented, and miRNAs were proved to be widely involved in the regulation of fruit development and formation of fruit quality, for example through lignin synthesis, sugar and acid metabolism, and hormone signaling. Combined with computational analysis and experimental confirmation, the research contributes valuable information for further functional research of microRNA in fruit development for pear and other species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-953) contains supplementary material, which is available to authorized users.

A genome-wide identification and characterization of mircoRNAs and their targets in 'Suli' pear (Pyrus pyrifolia white pear group)

MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that are endogenous regulators of gene expression. miRNAs play a crucial role in cells via degradation of target mRNAs or by inhibition of target protein translation. In the present study, 186 new potentially conserved pear miRNAs belonging to 37 families were identified. The length of mature miRNAs ranged from 19 to 24 nt, and most of the miRNAs (154 out of 186) were 21 nt in length. The length of pre-miRNAs in pear was also found to vary from 62 to 282 nt with an average of 105 ± 43 nt. The potential miRNAs belonged to 29 clusters involving 20 different miRNA families. Using these potential miRNAs, we further scoured of the pear genome and found 326 potential target genes, which included transcription factors, stress responsive genes, and the genes involved in transmembrane transport and signal transduction. Gene ontology analysis of these potential targets suggested that 47 biological processes were potentially regulated by miRNAs, including oxidation-reduction, stress response, transport, etc. KEGG pathway analysis showed that the identified miRNAs were found in 15 metabolism networks which were related to starch and sucrose metabolism, and ascorbate and aldarate metabolism, among others. Our study will help in the further understanding of the essential role of miRNAs in growth and development and stress response of pear.

Links between the oncoprotein YB-1 and small non-coding RNAs in breast cancer

Background

The nucleic acid-binding protein YB-1, a member of the cold-shock domain protein family, has been implicated in the progression of breast cancer and is associated with poor patient survival. YB-1 has sequence similarity to LIN28, another cold-shock protein family member, which has a role in the regulation of small noncoding RNAs (sncRNAs) including microRNAs (miRNAs). Therefore, to investigate whether there is an association between YB-1 and sncRNAs in breast cancer, we investigated whether sncRNAs were bound by YB-1 in two breast cancer cell lines (luminal A-like and basal cell-like), and whether the abundance of sncRNAs and mRNAs changed in response to experimental reduction of YB-1 expression.

Results

RNA-immunoprecipitation with an anti-YB-1 antibody showed that several sncRNAs are bound by YB-1. Some of these were bound by YB-1 in both breast cancer cell lines; others were cell-line specific. The small RNAs bound by YB-1 were derived from various sncRNA families including miRNAs such as let-7 and miR-320, transfer RNAs, ribosomal RNAs and small nucleolar RNAs (snoRNA). Reducing YB-1 expression altered the abundance of a number of transcripts encoding miRNA biogenesis and processing proteins but did not alter the abundance of mature or precursor miRNAs.

Conclusions

YB-1 binds to specific miRNAs, snoRNAs and tRNA-derived fragments and appears to regulate the expression of miRNA biogenesis and processing machinery. We propose that some of the oncogenic effects of YB-1 in breast cancer may be mediated through its interactions with sncRNAs.

Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum): Characterization of flax miRNA genes

MicroRNAs (miRNAs) are small (20-24 nucleotide long) endogenous regulatory RNAs that play important roles in plant growth and development. They regulate gene expression at the post-transcriptional level by translational repression or target degradation and gene silencing. In this study, we identified 116 conserved miRNAs belonging to 23 families from the flax (Linum usitatissimum L.) genome using a computational approach. The precursor miRNAs varied in length; while most of the mature miRNAs were 21 nucleotide long, intergenic and showed conserved signatures of RNA polymerase II transcripts in their upstream regions. Promoter region analysis of the flax miRNA genes indicated prevalence of MYB transcription factor binding sites. Four miRNA gene clusters containing members of three phylogenetic groups were identified. Further, 142 target genes were predicted for these miRNAs and most of these represent transcriptional regulators. The miRNA encoding genes were expressed in diverse tissues as determined by digital expression analysis as well as real-time PCR. The expression of fourteen miRNAs and nine target genes was independently validated using the quantitative reverse transcription PCR (qRT-PCR). This study suggests that a large number of conserved plant miRNAs are also found in flax and these may play important roles in growth and development of flax.

Expression-based functional investigation of the organ-specific microRNAs in Arabidopsis

MicroRNAs (miRNAs) play a pivotal role in plant development. The expression patterns of the miRNA genes significantly influence their regulatory activities. By utilizing small RNA (sRNA) high-throughput sequencing (HTS) data, the miRNA expression patterns were investigated in four organs (flowers, leaves, roots and seedlings) of Arabidopsis. Based on a set of criteria, dozens of organ-specific miRNAs were discovered. A dominant portion of the organ-specific miRNAs identified from the ARGONAUTE 4-enriched sRNA HTS libraries were highly expressed in flowers. Additionally, the expression of the precursors of the organ-specific miRNAs was analyzed. Degradome sequencing data-based approach was employed to identify the targets of the organ-specific miRNAs. The miRNA–target interactions were used for network construction. Subnetwork analysis unraveled some novel regulatory cascades, such as the feedback regulation mediated by miR161, the potential self-regulation of the genes miR172, miR396, miR398 and miR860, and the miR863-guided cleavage of the SERRATE transcript. Our bioinformatics survey expanded the organ-specific miRNA–target list in Arabidopsis, and could deepen the biological view of the miRNA expression and their regulatory roles.

Identification and characterization of miRNAs and their potential targets in flax

MicroRNAs (miRNAs) are small non-protein coding regulatory RNAs released after the cleavage of a primary transcript. A computational homology search of expressed sequence tags (ESTs) available in public databases allowed the identification of 20 conserved miRNAs belonging to 13 different families in flax (Linum usitatissimum). Most of the miRNAs were 21 nucleotides-long and carried a uracil at the 5' end. They originated from precursor transcripts that vary greatly in length. A single precursor containing 2 different stem-loop structures, each one carrying a member of the miR398 family, was identified for the first time in plants. qRT-PCR analyses of 4 selected miRNAs indicated that all were differentially expressed in flax tissues. The 20 miRNAs could potentially regulate 112 different targets including genes involved in cell wall metabolism. Analyses of pri-miRNA and potential gene expression profiles in a publically available microarray data set allowed the identification of a number of highly opposite pri-miRNA/target gene profiles potentially involved in regulating plantacyanin levels, F-box mediated signalling processes, protein metabolism and ion homeostasis, as well as 6 unknown processes.

Genetic and genomic approaches for R-gene mediated disease resistance in tomato: retrospects and prospects

Tomato (Solanum lycopersicum) is one of the world's most important vegetable crops. Managing the health of this crop can be particularly challenging; crop resistance may be overcome by new pathogen races while new pathogens have been introduced by global agricultural markets. Tomato is extensively used as a model plant for resistance studies and much has been attained through both genetic and biotechnological approaches. In this paper, we illustrate genomic methods currently employed to preserve resistant germplasm and to facilitate the study and transfer of resistance genes, and we describe the genomic organization of R-genes. Patterns of gene activation during disease resistance response, identified through functional approaches, are depicted. We also describe the opportunities offered by the use of new genomic technologies, including high-throughput DNA sequencing, large-scale expression data production and the comparative hybridization technique, whilst reporting multifaceted approaches to achieve genetic tomato disease control. Future strategies combining the huge amount of genomic and genetic data will be able to accelerate development of novel resistance varieties sustainably on a worldwide basis. Such strategies are discussed in the context of the latest insights obtained in this field.

Characterization and evolution of microRNA genes derived from repetitive elements and duplication events in plants

MicroRNAs (miRNAs) are a major class of small non-coding RNAs that act as negative regulators at the post-transcriptional level in animals and plants. In this study, all known miRNAs in four plant species (Arabidopsis thaliana, Populus trichocarpa, Oryza sativa and Sorghum bicolor) have been analyzed, using a combination of computational and comparative genomic approaches, to systematically identify and characterize the miRNAs that were derived from repetitive elements and duplication events. The study provides a complete mapping, at the genome scale, of all the miRNAs found on repetitive elements in the four test plant species. Significant differences between repetitive element-related miRNAs and non-repeat-derived miRNAs were observed for many characteristics, including their location in protein-coding and intergenic regions in genomes, their conservation in plant species, sequence length of their hairpin precursors, base composition of their hairpin precursors and the minimum free energy of their hairpin structures. Further analysis showed that a considerable number of miRNA families in the four test plant species arose from either tandem duplication events, segmental duplication events or a combination of the two. However, comparative analysis suggested that the contribution made by these two duplication events differed greatly between the perennial tree species tested and the other three annual species. The expansion of miRNA families in A. thaliana, O. sativa and S. bicolor are more likely to occur as a result of tandem duplication events than from segmental duplications. In contrast, genomic segmental duplications contributed significantly more to the expansion of miRNA families in P. trichocarpa than did tandem duplication events. Taken together, this study has successfully characterized miRNAs derived from repetitive elements and duplication events at the genome scale and provides comprehensive knowledge and deeper insight into the origins and evolution of miRNAs in plants.