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https://www.readbyqxmd.com/read/28550151/evolutionary-footprints-reveal-insights-into-plant-microrna-biogenesis
#1
Uciel Chorostecki, Belen Moro, Arantxa L M Rojas, Juan M Debernardi, Arnaldo L Schapire, Cedric Notredame, Javier Palatnik
MicroRNAs (miRNAs) are endogenous small RNAs that recognize target sequences by base complementarity and play a role in the regulation of target gene expression. They are processed from longer precursor molecules that harbor a fold-back structure. Plant miRNA precursors are quite variable in size and shape, and are recognized by the processing machinery in different ways. However, ancient miRNAs and their binding sites in target genes are conserved during evolution. Here, we designed a strategy to systematically analyze MIRNAs from different species generating a graphical representation of the conservation of the primary sequence and secondary structure...
May 26, 2017: Plant Cell
https://www.readbyqxmd.com/read/28536099/repression-of-mir156-by-mir159-regulates-the-timing-of-the-juvenile-to-adult-transition-in-arabidopsis
#2
Changkui Guo, Yunmin Xu, Min Shi, Yongmin Lai, Xi Wu, Huasen Wang, Zhujun Zhu, R Scott Poethig, Gang Wu
Temporally-regulated miRNAs have been identified as master regulators of developmental timing in both animals and plants. In plants, vegetative development is regulated by a temporal decrease in miR156 level, but how this decreased expression is initiated and then maintained during shoot development remains elusive. Here we show that miR159 is required for the correct timing of vegetative development in Arabidopsis thaliana. Loss of miR159 increases miR156 level throughout shoot development and delays vegetative development, whereas overexpression of miR159 slightly accelerated vegetative development...
May 23, 2017: Plant Cell
https://www.readbyqxmd.com/read/28534166/in-silico-identification-and-validation-of-potential-micrornas-in-kinnow-mandarin-citrus-reticulata-blanco
#3
Prashant Mohanpuria, Naveen Duhan, Navraj Kaur Sarao, Manvir Kaur, Mandip Kaur
MicroRNAs (miRNAs) are a large family of 19-25 nucleotides, regulatory, non-coding RNA molecules that control gene expression by cleaving or inhibiting the translation of target gene transcripts in animals and plants. Despite the important functions of miRNAs related to regulation of plant growth and development processes, metabolism, and abiotic and biotic stresses, little is known about the disease-related miRNA. Here, we present a new pipeline for miRNA analysis using expressed sequence tags (ESTs)-based bioinformatics approach in Kinnow mandarin, a commercially important citrus fruit crop...
May 22, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28530244/retraction-circulating-plant-mirnas-can-regulate-human-gene-expression-in-vitro
#4
Chiara Pastrello, Mike Tsay, Rosanne McQuaid, Mark Abovsky, Elisa Pasini, Elize Shirdel, Marc Angeli, Tomas Tokar, Joseph Jamnik, Max Kotlyar, Andrea Jurisicova, Joanne Kotsopoulos, Ahmed El-Sohemy, Igor Jurisica
This corrects the article DOI: 10.1038/srep32773.
May 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28529980/the-evolutionary-origin-of-plant-and-animal-micrornas
#5
Yehu Moran, Maayan Agron, Daniela Praher, Ulrich Technau
microRNAs (miRNAs) are a unique class of short endogenous RNAs that became known in the last few decades as major players in gene regulation at the post-transcriptional level. Their regulatory roles make miRNAs crucial for normal development and physiology in several distinct groups of eukaryotes including plants and animals. The common notion in the field is that miRNAs have evolved independently in those distinct lineages, but recent evidence from non-bilaterian metazoans, plants, as well as various algae raise the possibility that already the last common ancestor of these lineages might have employed a miRNA pathway for post-transcriptional regulation...
February 21, 2017: Nat Ecol Evol
https://www.readbyqxmd.com/read/28529519/genome-wide-identification-of-sorghum-bicolor-laccases-reveals-potential-targets-for-lignin-modification
#6
Jinhui Wang, Juanjuan Feng, Weitao Jia, Pengxiang Fan, Hexigeduleng Bao, Shizhong Li, Yinxin Li
Laccase is a key enzyme in plant lignin biosynthesis as it catalyzes the final step of monolignols polymerization. Sweet sorghum [Sorghum bicolor (L.) Moench] is considered as an ideal feedstock for ethanol production, but lignin greatly limits the production efficiency. No comprehensive analysis on laccase has ever been conducted in S. bicolor, although it appears as the most promising target for engineering lignocellulosic feedstock. The aim of our work is to systematically characterize S. bicolor laccase gene family and to identify the lignin-specific candidates...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28526728/genetic-subtraction-profiling-identifies-candidate-mirnas-involved-in-rice-female-gametophyte-abortion
#7
Liyu Yang, Ya Wu, Wenliang Wang, Bigang Mao, Bingran Zhao, Jianbo Wang
Female gametophyte is an important participant in sexual reproduction of plants. The molecular mechanism of its development has received much attention in recent years. As important regulators of gene expression, miRNAs have been certified to play a significant role in many biological processes of plants including sexual reproduction. In this study, to investigate the potential regulatory effects of miRNAs on rice female gametophytes abortion, we used the high-throughput sequencing method to compare the miRNA transcriptome in ovules of a high frequency female-sterile line (fsv1) and a rice wild-type line (Gui 99) during ovule development...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28521946/genomics-of-the-asian-rice-gall-midge-and-its-interactions-with-rice
#8
REVIEW
Deepak Kumar Sinha, Isha Atray, Ruchi Agarrwal, Jagadish Sanmallappa Bentur, Suresh Nair
Understanding virulence and manipulative strategies of gall formers will reveal new facets of plant defense and insect counter defense. Among the gall midges, the Asian rice gall midge (AGM) has emerged as a model for studies on plant-insect interactions. Data from several genomics, transcriptomics and metabolomics studies have revealed diverse strategies adopted by AGM to successfully invade the host while overcoming its defense. Adaptive skills of AGM transcend from its genomic and transcriptomic make-up...
February 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28515146/transcriptome-of-wheat-inflorescence-development-from-spikelet-initiation-to-floral-patterning
#9
Nan Feng, Gaoyuan Song, Jiantao Guan, Kai Chen, Meiling Jia, Dehua Huang, Jiajie Wu, Lichao Zhang, Xiuying Kong, Shuaifeng Geng, Jun Liu, Aili Li, Long Mao
Early reproductive development in cereals is crucial for final grain number per spike, and hence the yield potential of the crop. To date, however, no systematic analyses of gene expression profiles during this important process have been conducted for common wheat (Triticum aestivum). Here, we studied the transcriptome profiles at four stages of early wheat reproductive development, from spikelet initiation to floral organ differentiation. K-means clustering and stage-specific transcript identification detected dynamically expressed homoeologs of important transcription regulators in spikelet and floral meristems that may be involved in spikelet initiation, floret meristem specification, and floral organ patterning, as inferred from their homologs in model plants...
May 17, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28515145/target-rna-secondary-structure-is-a-major-determinant-of-mir159-efficacy
#10
Zihui Zheng, Marlene Reichel, Ira Deveson, Gigi Wong, Junyan Li, Anthony A Millar
In plants, microRNA (miRNA)-target complementarity has long been considered the predominant factor determining the silencing outcome of the miRNA-target interaction, although the efficacy of such interactions have rarely been appraised in plants. Here, we perform in planta silencing efficacy assays on seven Arabidopsis MYB genes, all of which contain conserved miR159-binding sites of analogous complementarity. These genes were found to be differentially silenced by miR159; MYB81, MYB97, MYB101, MYB104 and DUO1 were all poorly silenced, whereas MYB33 and MYB65 were strongly silenced...
May 17, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28512179/cooperative-regulatory-functions-of-mir858-and-myb83-during-cyst-nematode-parasitism
#11
Sarbottam Piya, Christina Kihm, J Hollis Rice, Thomas J Baum, Tarek Hewezi
microRNAs (miRNAs) recently have been established as key regulators of transcriptome reprogramming that defines cell function and identity. Nevertheless, the molecular functions of the greatest number of miRNA genes remain to be determined. Here, we report cooperative regulatory functions of miR858 and its MYB83 transcription factor target gene in transcriptome reprogramming during Heterodera cyst nematode parasitism of Arabidopsis. Gene expression analyses and promoter-GUS fusion assays documented a role of miR858 in post-transcriptional regulation of MYB83 in the Heterodera schachtii-induced feeding sites, the syncytia...
May 16, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28507539/new-insight-into-inter-kingdom-communication-horizontal-transfer-of-mobile-small-rnas
#12
REVIEW
Geyu Zhou, Yu Zhou, Xi Chen
Small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs), are conventionally regarded as critical molecular regulators of various intracellular processes. However, recent accumulating evidence indicates that sRNAs can be transferred within cells and tissues and even across species. In plants, nematodes and microbes, these mobile sRNAs can mediate inter-kingdom communication, environmental sensing, gene expression regulation, host-parasite defense and many other biological functions...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28501625/circular-rnas-roll-into-the-regulatory-network-of-plants
#13
Quan-Feng Li, Yu-Chan Zhang, Yue-Qin Chen, Yang Yu
As a novel class of endogenous non-coding RNAs, circular RNAs (circRNAs) have become a new research hotspot in recent years. The wide distribution of circRNAs in different plant species has been proven. Furthermore, circRNAs show significant tissue-specific expression patterns in plant development and are responsive to a variety of biotic and abiotic stresses, indicating that circRNAs might have important biological functions in plant development. Here, we summarize the current knowledge of plant circRNAs in recent years and discuss views and perspectives on the possible regulatory roles of plant circRNAs, including the function of miRNA sponges, regulating the expression of their parental genes or linear mRNAs, translating into peptides or proteins and responses to different stresses...
May 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28500720/casting-away-the-shadows-elucidating-the-role-of-light-mediated-posttranscriptional-control-in-plants
#14
REVIEW
Carlos E Hernando, Carolina Garcia, Julieta L Mateos
Light signals trigger precise changes in gene expression networks that activate distinctive developmental programs in plants. The transcriptome is shaped at different stages, both by the regulation of gene expression and also by posttranscriptional mechanisms that alter the sequence or abundance of the transcripts generated. Posttranscriptional mechanisms have attracted much interest in recent years with the advent of high-throughput technologies and bioinformatics tools. One such posttranscriptional process, alternative splicing, increases proteome diversity without increasing gene number by changing the function of individual proteins, while another, miRNA-mediated gene silencing, fine-tunes the amount of mRNA produced...
May 2017: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/28499866/identification-and-characterization-of-novel-lncrnas-in-arabidopsis-thaliana
#15
Zhaogeng Lu, Xiao Xia, Bei Jiang, Kaibiao Ma, Likui Zhu, Li Wang, Biao Jin
Long noncoding RNAs (lncRNAs) are important regulators of various biological processes, but few studies have identified lncRNAs in plants; genome-wide discovery of novel lncRNAs is thus required. We used deep strand-specific sequencing (ssRNA-seq) to obtain approximately 62 million reads from all developmental stages of Arabidopsis thaliana and identified 156 novel lncRNAs that we classified according to their localization. These novel identified lncRNAs showed low expression levels and sequence conservation...
May 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28499417/genome-wide-characterization-and-expression-analyses-of-superoxide-dismutase-sod-genes-in-gossypium-hirsutum
#16
Wei Wang, Xiaopei Zhang, Fenni Deng, Rui Yuan, Fafu Shen
BACKGROUND: Superoxide dismutases (SODs) are a key antioxidant enzyme family, which have been implicated in protecting plants against the toxic effects of reactive oxygen species. Despite current studies have shown that the gene family are involved in plant growth and developmental processes and biotic and abiotic stress responses, little is known about its functional role in upland cotton. RESULTS: In the present study, we comprehensively analyzed the characteristics of the SOD gene family in upland cotton (Gossypium hirsutum)...
May 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28494025/sequencing-of-small-rnas-of-the-fern-pleopeltis-minima-polypodiaceae-offers-insight-into-the-evolution-of-the-microrna-repertoire-in-land-plants
#17
Florencia Berruezo, Flávio S J de Souza, Pablo I Picca, Sergio I Nemirovsky, Leandro Martínez Tosar, Mercedes Rivero, Alejandro N Mentaberry, Alicia M Zelada
MicroRNAs (miRNAs) are short, single stranded RNA molecules that regulate the stability and translation of messenger RNAs in diverse eukaryotic groups. Several miRNA genes are of ancient origin and have been maintained in the genomes of animal and plant taxa for hundreds of millions of years, playing key roles in development and physiology. In the last decade, genome and small RNA (sRNA) sequencing of several plant species have helped unveil the evolutionary history of land plants. Among these, the fern group (monilophytes) occupies a key phylogenetic position, as it represents the closest extant cousin taxon of seed plants, i...
2017: PloS One
https://www.readbyqxmd.com/read/28490318/integrated-mrna-and-microrna-transcriptome-variations-in-the-multi-tepal-mutant-provide-insights-into-the-floral-patterning-of-the-orchid-cymbidium-goeringii
#18
Fengxi Yang, Genfa Zhu, Zhen Wang, Hailin Liu, Qingquan Xu, Dan Huang, Chaoyi Zhao
BACKGROUND: Cymbidium goeringii is a very famous traditional orchid plant in China, which is well known for its spectacular and diverse flower morphology. In particular, the multi-tepal mutants have considerable ecological and cultural value. However, the current understanding of the molecular mechanisms of floral patterning and multi-tepal development is limited. In this study, we performed expression profiling of both microRNA (miRNA) and mRNA from wild-type and typical multi-tepal-mutant flowers of C...
May 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28488082/genome-wide-identification-of-cucumber-green-mottle-mosaic-virus-responsive-micrornas-in-watermelon
#19
Yuyan Sun, Xiaowei Niu, Min Fan
Cucumber green mottle mosaic virus (CGMMV) is a damaging pathogen that attacks crop plants belonging to the family Cucurbitaceae. Little is known about the regulatory role of microRNAs (miRNAs) in response to CGMMV infection. To identify CGMMV-responsive miRNAs, two sRNA libraries from mock-inoculated and CGMMV-infected watermelon leaves were constructed and sequenced using Solexa sequencing technology. In total, 471 previously known and 1,809 novel miRNAs were obtained, of which 377 known and 246 novel miRNAs were found to be differentially expressed during CGMMV infection...
May 9, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28481299/integrative-rna-and-mirna-profile-analysis-reveals-a-likely-role-of-br-and-auxin-signaling-in-branch-angle-regulation-of-b-napus
#20
Hongtao Cheng, Mengyu Hao, Wenxiang Wang, Desheng Mei, Rachel Wells, Jia Liu, Hui Wang, Shifei Sang, Min Tang, Rijin Zhou, Wen Chu, Li Fu, Qiong Hu
Oilseed rape (Brassica napus L.) is the second largest oilseed crop worldwide and one of the most important oil crops in China. As a component of plant architecture, branch angle plays an important role in yield performance, especially under high-density planting conditions. However, the mechanisms underlying the regulation of branch angle are still largely not understood. Two oilseed rape lines with significantly different branch angles were used to conduct RNA- and miRNA-profiling at two developmental stages, identifying differential expression of a large number of genes involved in auxin- and brassinosteroid (BR)-related pathways...
May 8, 2017: International Journal of Molecular Sciences
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