MicroRNAs in plants

Ehrenreich, Ian M.; Purugganan, Michael D.

doi:10.4161/psb.3.10.5914

Cited by 13 publications

(6 citation statements)

References 19 publications

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“…But, miRNA targets in primate-specific genes have no obvious signal of selection for site accessibility and translation efficiency (Figures 5 and 6). These are consistent with the observations made by previous works [1], [17], [18], [51]. They had suggested purifying selection was smaller in younger miRNA targets than that in conserved miRNA targets.…”

Section: Discussionsupporting

confidence: 93%

Biological Basis of miRNA Action when Their Targets Are Located in Human Protein Coding Region

Wang

Zhai

et al. 2013

PLoS ONE

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Recent analyses have revealed many functional microRNA (miRNA) targets in mammalian protein coding regions. But, the mechanisms that ensure miRNA function when their target sites are located in protein coding regions of mammalian mRNA transcripts are largely unknown. In this paper, we investigate some potential biological factors, such as target site accessibility and local translation efficiency. We computationally analyze these two factors using experimentally identified miRNA targets in human protein coding region. We find site accessibility is significantly increased in miRNA target region to facilitate miRNA binding. At the mean time, local translation efficiency is also selectively decreased near miRNA target region. GC-poor codons are preferred in the flank region of miRNA target sites to ease the access of miRNA targets. Within-genome analysis shows substantial variations of site accessibility and local translation efficiency among different miRNA targets in the genome. Further analyses suggest target gene’s GC content and conservation level could explain some of the differences in site accessibility. On the other hand, target gene’s functional importance and conservation level can affect local translation efficiency near miRNA target region. We hence propose both site accessibility and local translation efficiency are important in miRNA action when miRNA target sites are located in mammalian protein coding regions.

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Section: Discussionsupporting

confidence: 93%

Biological Basis of miRNA Action when Their Targets Are Located in Human Protein Coding Region

Wang

Zhai

et al. 2013

PLoS ONE

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“…microRNAs (miRNAs) are 21–24 nucleotide-long primary endogenous small RNAs that regulate gene expression at the translational level [ 1 , 2 ], including DNA elimination, mRNA cleavage, deadenylation and translational repression [ 3 ]. Generally, the miRNAs initially identified in plants, which have been found in many organisms, may serve as key signature molecules that regulate transcription factors and other genes in flowering plant development [ 4 , 5 ], such as flowering time, floral organ patterning and ovule development [ 6 , 7 ]. Based on their extensive integration within genetic networks, the mechanism for miRNA biogenesis in plants has been well investigated in Arabidopsis thaliana [ 8 – 10 ].…”

Section: Introductionmentioning

confidence: 99%

Identification of MicroRNAs and their Targets Associated with Embryo Abortion during Chrysanthemum Cross Breeding via High-Throughput Sequencing

et al. 2015

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BackgroundMicroRNAs (miRNAs) are important regulators in plant development. They post-transcriptionally regulate gene expression during various biological and metabolic processes by binding to the 3’-untranslated region of target mRNAs to facilitate mRNA degradation or inhibit translation. Chrysanthemum (Chrysanthemum morifolium) is one of the most important ornamental flowers with increasing demand each year. However, embryo abortion is the main reason for chrysanthemum cross breeding failure. To date, there have been no experiments examining the expression of miRNAs associated with chrysanthemum embryo development. Therefore, we sequenced three small RNA libraries to identify miRNAs and their functions. Our results will provide molecular insights into chrysanthemum embryo abortion.ResultsThree small RNA libraries were built from normal chrysanthemum ovules at 12 days after pollination (DAP), and normal and abnormal chrysanthemum ovules at 18 DAP. We validated 228 miRNAs with significant changes in expression frequency during embryonic development. Comparative profiling revealed that 69 miRNAs exhibited significant differential expression between normal and abnormal embryos at 18 DAP. In addition, a total of 1037 miRNA target genes were predicted, and their annotations were defined by transcriptome data. Target genes associated with metabolic pathways were most highly represented according to the annotation. Moreover, 52 predicted target genes were identified to be associated with embryonic development, including 31 transcription factors and 21 additional genes. Gene ontology (GO) annotation also revealed that high-ranking miRNA target genes related to cellular processes and metabolic processes were involved in transcription regulation and the embryo developmental process.ConclusionsThe present study generated three miRNA libraries and gained information on miRNAs and their targets in the chrysanthemum embryo. These results enrich the growing database of new miRNAs and lay the foundation for the further understanding of miRNA biological function in the regulation of chrysanthemum embryo abortion.

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“…The importance of miRNAs has been realized owing to their wide occurrence in all kinds of organisms and their important biological function in regulation of gene expression [11] – [12] . Increasing evidence shows that the length of 20–24 nt miRNAs plays a crucial role in developmental and physiological processes, including developmental timing, tissue-specific development, and stem cell maintenance and differentiation [13] – [14] . Plant organogenesis and somatic embryogenesis are the most important strategies for in vitro plant regeneration [15] .…”

Section: Introductionmentioning

confidence: 99%

Analysis of miRNAs and Their Targets during Adventitious Shoot Organogenesis of Acacia crassicarpa

Liu

Hou

et al. 2014

PLoS ONE

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Organogenesis is an important process for plant regeneration by tissue or cell mass differentiation to regenerate a complete plant. MicroRNAs (miRNAs) play an essential role in regulating plant development by mediating target genes at transcriptional and post-transcriptional levels, but the diversity of miRNAs and their potential roles in organogenesis of Acacia crassicarpa have rarely been investigated. In this study, approximately 10 million sequence reads were obtained from a small RNA library, from which 189 conserved miRNAs from 57 miRNA families, and 7 novel miRNAs from 5 families, were identified from A. crassicarpa organogenetic tissues. Target prediction for these miRNAs yielded 237 potentially unique genes, of which 207 received target Gene Ontology annotations. On the basis of a bioinformatic analysis, one novel and 13 conserved miRNAs were selected to investigate their possible roles in A. crassicarpa organogenesis by qRT-PCR. The stage-specific expression patterns of the miRNAs provided information on their possible regulatory functions, including shoot bud formation, modulated function after transfer of the culture to light, and regulatory roles during induction of organogenesis. This study is the first to investigate miRNAs associated with A. crassicarpa organogenesis. The results provide a foundation for further characterization of miRNA expression profiles and roles in the regulation of diverse physiological pathways during adventitious shoot organogenesis of A. crassicarpa.

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MicroRNAs in plants

Cited by 13 publications

References 19 publications

Biological Basis of miRNA Action when Their Targets Are Located in Human Protein Coding Region

Biological Basis of miRNA Action when Their Targets Are Located in Human Protein Coding Region

Identification of MicroRNAs and their Targets Associated with Embryo Abortion during Chrysanthemum Cross Breeding via High-Throughput Sequencing

Analysis of miRNAs and Their Targets during Adventitious Shoot Organogenesis of Acacia crassicarpa

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