Classification and experimental identification of plant long non-coding RNAs

Iqbal, Muneeza; Alam, Maheen; Lightfoot, David A.; Gurha, Priyatansh; Afzal, Ahmed J.

doi:10.1016/j.ygeno.2018.04.014

Cited by 98 publications

(69 citation statements)

References 132 publications

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“…Unlike Pol II transcripts, these lncRNAs are less characterized and possess some structural differences such as lack of poly-A tails (Zhou and Law, 2015). Identification of RNA Pol IV or PolV transcribed lncRNAs is particularly challenging due to their extremely low expression and instability (Rai et al, 2018). However, these transcripts are the major players driving RNA-mediated DNA methylation (RdDM).…”

Section: Biogenesis Of Lncrnasmentioning

confidence: 99%

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

2020

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Section: Biogenesis Of Lncrnasmentioning

confidence: 99%

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

2020

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“…Nevertheless, there are some plant lncRNAs whose regulatory functions have been studied extensively and are understood at a level of detail comparable to most proteins (Rai et al, 2018): COOLAIR in Brassicaceae has a crucial role in the vernalization process (Hawkes et al, 2016) and its transcription accelerates epigenetic silencing of the flowering locus C (FLC) (Rosa et al, 2016). The lncRNA HID1, a key component in promoting photomorphogenesis in response to different levels of red light (Wang et al, 2014).…”

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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“…A total of 14 loci did not have transcriptional evidence (Table S7, Supplementary File S2). Units 5S (34), 5.8S (8), two fragments from a large ribosomal subunit, five fragments from a small ribosomal subunit were identified, while two were indeterminate. Twenty-one high-confidence rRNA regions were identified in the pseudomolecule "Chromosome 0".…”

Section: Ribosomal Rnasmentioning

confidence: 99%

“…In plants, most studies usually identify a single class of ncRNAs, such as miRNAs or long non-coding RNAs [4][5][6][7][8]. Although several studies have identified miRNAs in plants [9][10][11], the identification has not always been performed in the most reliable way [12].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora

Lemos

Foncatti

Guyot

et al. 2020

ncRNA

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Coffea canephora grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of the C. canephora genome. This study aimed to provide a curated characterization of six ncRNA classes in the Coffea canephora genome. For this purpose, we employed a combination of similarity-based and structural-based computational approaches with stringent curation. Candidate ncRNA loci had expression evidence analyzed using sRNA-seq libraries. We identified 7455 ncRNA loci (6976 with transcriptional evidence) in the C. canephora genome. This comprised of total 115 snRNAs, 1031 snoRNAs, 92 miRNA precursors, 602 tRNAs, 72 rRNAs, and 5064 lncRNAs. For miRNAs, we identified 159 putative high-confidence targets. This study was the most extensive genomic catalog of curated ncRNAs in the Coffea genus. This data might help elaborating more robust hypotheses in future comparative genomic studies as well as gene regulation and genome dynamics, helping to understand the molecular basis of domestication, environmental adaptation, resistance to pests and diseases, and coffee productivity.

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Classification and experimental identification of plant long non-coding RNAs

Cited by 98 publications

References 132 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

Splicing conservation signals in plant long non-coding RNAs

Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora

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