miRNAs and lncRNAs in reproductive development

Li, Zhefeng; Zhang, Yuchan; Chen, Yue‐Qin

doi:10.1016/j.plantsci.2015.05.017

Cited by 32 publications

(22 citation statements)

References 55 publications

(69 reference statements)

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“…With development of high-throughput deep sequencing technology, a lot of noncoding RNAs such as microRNA and long noncoding RNAs were identified and confirmed as the crucial regulator for gene expression and biological function in many species [1][2][3]. As a rising star of noncoding RNA, circRNAs are widely exist in animal and plants and have a covalently closed continuous loop which derived from precursor mRNA backsplicing.…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of circular RNAs during the sea buckthorn fruit development

Zhang

Chen

et al. 2019

RNA Biology

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As a rising star of noncoding RNA, circular RNAs (circRNAs) have a covalently closed loop structure, which formed by 3ʹ-5ʹ ligation during splicing. A few circRNAs were identified and thought to be transcriptional noise due to cognitive defect over the past 40 years. Recently, with the development of high-throughput RNA sequencing techniques and specific algorithms for circRNA detection and quantification, plenty of potential circRNAs were identified in many species which play important roles in various biological processes. However, researches on circRNAs in fruit ripening process were lacking. Here, we totally identified 2616 circRNAs in sea buckthorn fruit development process, which uniformly distributed in sea buckthorn chromosome. Among them, 1721 (65.8%) circRNAs were arising from the exons of their host genes, 252 circRNAs were identified as the differentially expressed circRNAs (DEcircRNAs) between three different development stages, and 181 (71.8%) DEcircRNAs had sequence similarity with 235 identified circRNAs from five know plant species. Functional annotation revealed that host genes of DEcircRNAs were predicted to be involved in carotenoid biosynthesis, lipid synthesis and plant hormone signal transduction. Additionally, 53 DEcircRNAs were predicted as the corresponding nine miRNAs sponges in sea buckthorn. Divergent reverse-transcription PCR and RT-qPCR were used for validate the differential expression and back-splicing sites of six DEcircRNAs. These results revealed the role of circRNAs in sea buckthorn fruit ripening process and promoted the noncoding RNA researches in plants.

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Section: Introductionmentioning

confidence: 99%

Identification and characterization of circular RNAs during the sea buckthorn fruit development

Zhang

Chen

et al. 2019

RNA Biology

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“…In recent studies lncRNAs have been emerged as an important regulator of transcription and competing endogenous RNAs (ceRNAs) (48). lncRNAs are involved in the regulation of growth, differentiation, stress responses, developmental processes and chromatin modification (49–51). For example, cold induced long antisense intragenic RNA (COOLAIR) and cold assisted intronic noncoding RNA (COLDAIR) are the lncRNAs that are responsible for the suppression of Flowring Locus C (FLC) mediated transcription by chromatin modification which in turn regulate reproduction of plants (52,53).…”

Section: Resultsmentioning

confidence: 99%

Elucidating the functional role of predicted miRNAs in post-transcriptional gene regulation along with symbiosis inMedicago truncatula

Bahadur

Chowdhury

Basak

2018

Preprint

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27Non-coding RNAs (ncRNAs) are found to be important regulator of gene expression because 28 of their ability to modulate post-transcriptional processes. microRNAs are small ncRNAs 29 which inhibit translational and post-transcriptional processes whereas long ncRNAs are 30 found to regulate both transcriptional and post-transcriptional gene expression. Medicago 31 truncatula is a well-known model plant for studying legume biology and is also used as a 32 forage crop. In spite of its importance in nitrogen fixation and soil fertility improvement, 33 little information is available about Medicago ncRNAs that play important role in symbiosis. 34To understand the role of Medicago ncRNAs in symbiosis and regulation of transcription 35 factors, we have identified novel miRNAs and tried to establish an interaction model with 36 their targets. 149 novel miRNAs are predicted along with their 770 target proteins. We have 37 shown that 51 of these novel miRNAs are targeting 282 lncRNAs. We have analyzed the 38 interactions between miRNAs and their target mRNAs as well as their targets on lncRNAs. 39Role of Medicago miRNAs in the regulation of various transcription factors were also 40 elucidated. Knowledge gained from this study will have a positive impact on the nitrogen 41 fixing ability of this important model plant, which in turn will improve the soil fertility. 42 transcription factor 44 45 46 47 50 51 Functional RNA molecules, encoded by non-coding RNA genes, play important roles in 52 regulating the expression of various genes (1). MicroRNAs (miRNAs), first discovered in 53 Caenorhabditis elegans (lin-4) (2) are 20-24 nucleotides long, endogenous, small non-coding 54 ribonucleic acids that regulate gene expression post-transcriptionally in plants, animals and 55 viruses (3,4). miRNAs regulate gene expression in various ways including cleavage, 56 degradation and decaying of mRNA and nascent polypeptide, inhibition of translation by 57 forming miRNA-mRNA complex, ribosome drop-off resulting in premature termination, 58 sequestration of target mRNAs in P-bodies that are distinct foci consisting enzymes involved 59 in mRNA turnover (5), transcriptional inhibition by miRNA mediated chromatin 60 reorganization, inhibition of translation initiation by suppressing the cap recognition by 61 elF4E and 60S-40S joining (6-16). Plant miRNAs can repress translation by binding in a 62 near-perfect manner with target mRNAs (17) where animal miRNAs can recognize target 63 mRNAs through six to eight nucleotides long seed region of the 5'end of the mRNA (18). 64 Various miRNAs have been discovered in animals, plants and viruses with the help of 65 conventional experimental strategies along with bioinformatics tools (19,20). In spite of 66 present state-of-the art technologies including high throughput sequencing, identification of 67 miRNAs in various organisms is still complex and need proper blending of experimental 68 strategies and computational approaches to get more accurate results. miRNAs can be 69 identified by computat...

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“…In Cucumis melo, the insertion of transposable elements leads to DNA methylation of the WIP (WPP trp/pro/pro domain Interacting Proteins) promoter with the subsequent formation of female flowers (Martin et al 2009). Several microRNAs (miRNAs) also regulate sex determination and floral morphogenesis (reviewed in Li et al 2015). In Zea mays, for example, miRNA172 regulates the expression of the IDS1 (INDETERMINATE-SPIKLELET1) gene, whose differential expression determines differences in primordial initiation and thus regulates sex determination (Chuck et al 2007).…”

Section: Epigenetic Factors In Plant Sex Regulationmentioning

confidence: 99%