Functions of long non-coding RNAs in plants: a riddle to explore

Singh, Pankaj Kumar; Ganguli, Sayak; Pal, Amita

doi:10.1007/s13237-018-0249-4

Cited by 5 publications

(3 citation statements)

References 77 publications

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“…Although identifying conserved lncRNA sequences has proven challenging, studies of plant and animal transcriptomes have suggested better sequence conservation at lncRNA promotor sites of vertebrates than the sequence conservation at lncRNA transcripts, particular gene structures and locations around protein-coding genes (Kutter et al, 2012;Johnsson et al, 2014;Nitsche et al, 2015;Deng et al, 2018;Singh et al, 2018), as well as at the structural and functional levels (Kashi et al, 2016). Such positional information and gene structure characteristics such as splice sites will reveal lncRNA genes in other organisms and guide researchers toward more accurate lncRNA identification; however, this approach requires highquality reference genomes and transcriptomes.…”

Section: Drawbacks In Lncrna Identification and Target Predictionmentioning

confidence: 99%

Long Non-coding RNA in Plants in the Era of Reference Sequences

2020

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Section: Drawbacks In Lncrna Identification and Target Predictionmentioning

confidence: 99%

Long Non-coding RNA in Plants in the Era of Reference Sequences

2020

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“…Included in the group of infrastructural ncRNA are rRNA, tRNA, small nuclear RNA (snRNA), and small nucleolar RNA (snoRNA). Meanwhile, in the group of regulatory ncRNA, several types have been distinguished as micro RNA (miRNA), PIWI-interacting RNA (piRNA; animals only), small interfering RNA (siRNA), promoter-associated RNA (PAR), enhancer RNA (eRNA), and long non-coding RNA [ 1 , 2 , 3 , 4 ]. The regulatory ncRNA groups differ in the lengths of their molecules, transcript origin, and biogenesis pathway components.…”

Section: Plant Mirnas What We Are Dealing With?mentioning

confidence: 99%

Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis

Wójcik

2020

IJMS

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During early plant embryogenesis, some of the most fundamental decisions on fate and identity are taken making it a fascinating process to study. It is no surprise that higher plant embryogenesis was intensively analysed during the last century, while somatic embryogenesis is probably the most studied regeneration model. Encoded by the MIRNA, short, single-stranded, non-coding miRNAs, are commonly present in all Eukaryotic genomes and are involved in the regulation of the gene expression during the essential developmental processes such as plant morphogenesis, hormone signaling, and developmental phase transition. During the last few years dedicated to miRNAs, analytical methods and tools have been developed, which have afforded new opportunities in functional analyses of plant miRNAs, including (i) databases for in silico analysis; (ii) miRNAs detection and expression approaches; (iii) reporter and sensor lines for a spatio-temporal analysis of the miRNA-target interactions; (iv) in situ hybridisation protocols; (v) artificial miRNAs; (vi) MIM and STTM lines to inhibit miRNA activity, and (vii) the target genes resistant to miRNA. Here, we attempted to summarise the toolbox for functional analysis of miRNAs during plant embryogenesis. In addition to characterising the described tools/methods, examples of the applications have been presented.

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“…Getting advantage of the high-throughput RNA-seq data, the involvement of lncRNAs has already been demonstrated in diverse and fundamental BPs (Shafiq et al, 2016;Singh et al, 2018). Similarly, several studies have explicated the lncRNA-mediated gene regulation in different plant-pathogen interactions (Li et al, 2018c,d;Yu et al, 2020;Zhang et al, 2020;Summanwar et al, 2021); however, only a few studies have investigated their regulatory roles in response to nematode invasion (Li et al, 2018a,b;Muthusamy et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Identification of the Complex Interplay Between Nematode-Related lncRNAs and Their Target Genes in Glycine max L.

Khoei

Karimi²,

Karamian

et al. 2021

Front. Plant Sci.

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Soybean (Glycine max) is a major plant protein source and oilseed crop. However, plant-parasitic nematodes (PPNs) affect its annual yield. In the current study, in order to better understand the regulation of defense mechanism against PPNs in soybean, we investigated the role of long non-coding RNAs (lncRNAs) in response to two nematode species, Heterodera glycines (SCN: soybean cyst nematode) and Rotylenchulus reniformis (reniform). To this end, two publicly available RNA-seq data sets (SCN data set and RAD: reniform-associated data set) were employed to discover the lncRNAome profile of soybean under SCN and reniform infection, respectively. Upon identification of unannotated transcripts in these data sets, a seven-step pipeline was utilized to sieve these transcripts, which ended up in 384 and 283 potential lncRNAs in SCN data set and RAD, respectively. These transcripts were then used to predict cis and trans nematode-related targets in soybean genome. Computational prediction of target genes function, some of which were also among differentially expressed genes, revealed the involvement of putative nematode-responsive genes as well as enrichment of multiple stress responses in both data sets. Finally, 15 and six lncRNAs were proposed to be involved in microRNA-mediated regulation of gene expression in soybean in response to SNC and reniform infection, respectively. Collectively, this study provides a novel insight into the signaling and regulatory network of soybean-pathogen interactions and opens a new window for further research.

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Functions of long non-coding RNAs in plants: a riddle to explore

Cited by 5 publications

References 77 publications

Long Non-coding RNA in Plants in the Era of Reference Sequences

Long Non-coding RNA in Plants in the Era of Reference Sequences

Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis

Identification of the Complex Interplay Between Nematode-Related lncRNAs and Their Target Genes in Glycine max L.

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