Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species

Zhang, Jinfang; Wei, Lijuan; Jiang, Jun; Mason, Annaliese S.; Li, Haojie; Cui, Cheng; Chai, Linna; Zheng, Beibei; Zhu, Yongqing; Xia, Qing; Jiang, Long; Fu, Donghui

doi:10.1038/s41598-018-23334-1

Cited by 34 publications

(32 citation statements)

References 70 publications

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“…Competing endogenous RNAs (ceRNAs) acts as "sponges" for miRNAs. In plants, ceRNAs are a large class of lncRNAs (Yuan et al, 2017;Paschoal et al, 2018) and form extensive regulatory networks (Meng et al, 2018;Zhang et al, 2018). The paradigmatic examples in A. thaliana is IPS1, which sequesters miR399 (Franco-Zorrilla et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Splicing conservation signals in plant long non-coding RNAs

Corona-Gómez

Garcia-Lopez

Stadler

2019

Preprint

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AbstractLong non-coding RNAs (lncRNAs) have recently emerged as prominent regulators of gene expression in eukaryotes. LncRNAs often drive the modification and maintenance of gene activation or gene silencing states via chromatin conformation rearrangements. In plants, lncRNAs have been shown to participate in gene regulation, and are essential to processes such as vernalization and photomorphogenesis. Despite their prominent functions only over a dozen lncRNAs have been experimentally and functionally characterized.Similar to its animal counterparts, the rates of sequence divergence are much higher in plant lncRNAs than in protein coding mRNAs, making it difficult to identify lncRNA conservation using traditional sequence comparison methods. Beyond this, little is known about the evolutionary patterns of lncRNAs in plants. Here, we characterized the splicing conservation of lncRNAs in Brassicaceae. We generated a whole-genome alignment of 16 Brassica species and used it to identify synthenic lncRNA orthologues. Using a scoring system trained on transcriptomes from A. thaliana and B. oleracea, we identified splice sites across the whole alignment and measured their conservation. Our analysis revealed that 17.9% (112/627) of all intergenic lncRNAs display splicing conservation in at least one exon, an estimate that is substantially higher to previous estimates of lncRNA conservation in this group. Our findings agree with similar studies in vertebrates, demonstrating that splicing conservation can be evidence of stabilizing selection. We provide conclusive evidence for the existence of evolutionary deeply conserved lncRNAs in plants and describe a generally applicable computational workflow to identify functional lncRNAs in plants.

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Section: Introductionmentioning

confidence: 99%

Splicing conservation signals in plant long non-coding RNAs

Corona-Gómez

Garcia-Lopez

Stadler

2019

Preprint

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“…Bioinformatic analysis revealed that PSG10P can promote the expression of IL1RAP by sponging miR‐19a‐3p. Many studies have been performed on the interactions among RNA molecules, such as interactions between lncRNA‐miRNA and miRNA‐mRNA . Here, we focused on the interaction between PSG10P‐miR‐19a‐3p and miR‐19a‐3p‐ IL1RAP .…”

Section: Introductionmentioning

confidence: 99%

“…Many studies have been performed on the interactions among RNA molecules, such as interactions between lncRNA-miRNA and miRNA-mRNA. 24,25 Here, we focused on the interaction between PSG10P-miR-19a-3p and miR-19a-3p-IL1RAP. In addition, we hypothesized that the PSG10P/ miR-19a-3p/IL1RAP network regulates the growth and invasion of trophoblastic cells under hypoxia.…”

Section: Introductionmentioning

confidence: 99%

Potential regulatory network in the PSG10P/miR‐19a‐3p/IL1RAP pathway is possibly involved in preeclampsia pathogenesis

Wang

Xue

2018

J Cellular Molecular Medi

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Preeclampsia (PE), a pregnancy‐specific disorder, is a leading cause of perinatal maternal‐fetal mortality and morbidity. Impaired cell migration and invasion of trophoblastic cells and an imbalanced systemic maternal inflammatory response have been proposed as potential mechanisms of PE pathogenesis. Comparative analysis between PE placentas and normal placentas profiled differentially expressed miRNAs, lncRNAs, and mRNAs, including miR‐19a‐3p (miRNA), PSG10P (lncRNA), and IL1RAP (mRNA). This study was conducted to investigate their potential roles in PE pathogenesis. The expression of miR‐19a‐3p, PSG10P, and IL1RAP was examined in PE and normal placentas using RT‐qPCR. An in vitro experiment was performed in human trophoblast HET8/SVneo and TEV‐1 cells cultured in normoxic and hypoxic conditions. MiR‐19a‐3p targets were identified using Targetscan, miRanda, and PicTar analysis as well as luciferase reporter assays. The mouse model of PE was conducted using sFlt‐1 for in vivo tests. Lower levels of miR‐19a‐3p, but higher levels of PSG10P and IL1RAP were observed in PE placentas and the trophoblast cells in hypoxia. Luciferase reporter assays confirmed that PSG10P and IL1RAP were both direct targets of miR‐19a‐3p. Exposure to hypoxia inhibited cell viability, migration, and invasion of HET8/SVneo and TEV‐1 cells. Knocking out PSG10P and IL1RAP or overexpressing miR‐19a‐3p rescued the inhibition caused by hypoxia. In vivo experiments showed that IL1RAP promoted the expression of caspase‐3, a key apoptosis enzyme, but inhibited MMP9, which is responsible for degrading the extracellular matrix, suggesting a significant role of IL1RAP in cell proliferation, migration, and invasion. miR‐19a‐3p, PSG10P, and IL1RAP were all found to be involved in PE pathogenesis. With a common targeting region in their sequences, a regulatory network in the PSG10P/miR‐19a‐3p/IL1RAP pathway may contribute to PE pathogenesis during pregnancy.

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“…The pre-miRNA were checked for the ability of folding into an appropriate hairpin secondary structure and mature miRNA should be placed in one arm of the hairpin structure ( Here, (A+U) content of pre-miRNA were found between the range of 55% to 61%, which was also observed in the other higher plants miRNAs [109,110,111]. Five conserved miRNA families (miR1536, miR9567-3p, miR4391, miR11300 and miR8689) were found in the jute genome which were also reported in the different plant families [112,113,114,115] and the predictive putative miRNAs were entitled as cca-miR1536, cca-miR9567-3p, cca-miR4391, cca-miR11300, and cca-miR8689. Multiple sequence alignment and comparative nucleotide composition studies exhibited that the putative miRNAs of jute were highly conserved in the other organisms which supported the evolutionary convergent relationships among the higher plant species [116,117,118].…”

Section: Discussionmentioning

confidence: 55%

In silicoIdentification and Functional Characterization of Conserved miRNAs in Fibre Biogenesis CropCorchorus capsularis

Hasan

Ahmed

et al. 2020

Preprint

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Corchorus capsularis, commonly known as jute occupies the leading position in the production of natural fibre and fibre based products alongside lower environmental threat. Nowadays, the study of lignin biosynthesis pathways with other molecular basis of fibres formation are being more focused for its economic perspective. Small noncoding ~21 to 24 nt nucleotides long microRNAs play significant roles in regulating the gene expression as well as different functions in cellular growth and development. Here, the study adopted a comprehensive in silico approach to identify and characterize the conserved miRNAs in the genome of C. capsularis including specific gene targets involved in the crucial cellular process. Expressed Sequence Tags (ESTs) based homology search of 3350 known miRNAs of dicotyledons were allowed against 763 nonredundant ESTs of jute genome resulted in the prediction of 5 potential miRNA candidates belonging five different miRNA families (miR1536, miR9567-3p, miR4391, miR11300, and miR8689). The putative miRNAs were 18 nucleotide length, within a range of -0.49 to -1.56 MFEI values and 55% to 61% of (A+U) content of their correspondence pre-miRNAs. A total of 1052 gene targets of putative miRNAs were identified and their functions were extensively analyzed. Most of the gene targets were involved in plant growth, cell cycle regulation, organelle synthesis, developmental process and environmental responses. The five gene targets, namely, NAC Domain Containing Protein, WRKY DNA binding protein, 3-dehydroquinate synthase, Sadenosyl-L-Met-dependent methyl transferase and Vascular-related NAC-Domain were found to be involved in the lignin biosynthesis, phenylpropanoid pathways and secondary wall formation which could play significant roles in the overall fibre biogenesis. The characterization of conserved miRNAs and their functional annotation of specific gene targets might enhance the more miRNA discovery, strengthening the complete understanding of miRNAs association in the cellular basis of lignin biosynthesis towards the production of high standard jute products.

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Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species

Cited by 34 publications

References 70 publications

Splicing conservation signals in plant long non-coding RNAs

Splicing conservation signals in plant long non-coding RNAs

Potential regulatory network in the PSG10P/miR‐19a‐3p/IL1RAP pathway is possibly involved in preeclampsia pathogenesis

In silicoIdentification and Functional Characterization of Conserved miRNAs in Fibre Biogenesis CropCorchorus capsularis

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