A stable tRNA-like molecule is generated from the long noncoding RNA <i>GUT15</i> in <i>Arabidopsis</i>

Plewka, Patrycja; Thompson, Agnieszka; Szymański, Maciej; Nuc, Przemysław; Knop, Katarzyna; Rasinska, Agnieszka; Bialkowska, Aleksandra; Szweykowska-Kulińska, Zofia; Karłowski, Wojciech M.; Jarmołowski, Artur

doi:10.1080/15476286.2018.1445404

Cited by 7 publications

(9 citation statements)

References 49 publications

(60 reference statements)

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“…It was noteworthy that some targets of A. membranaceus MIR156 were homologues of Arabidopsis GUT15 ( AtGUT15 , AT2G18440), a long noncoding RNA [42].…”

Section: Resultsmentioning

confidence: 99%

Identification of miRNAs and Their Response to Cold Stress in Astragalus Membranaceus

Abla

Sun

et al. 2019

Biomolecules

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Astragalus membranaceus is an important medicinal plant widely cultivated in East Asia. MicroRNAs (miRNAs) are endogenous regulatory molecules that play essential roles in plant growth, development, and the response to environmental stresses. Cold is one of the key environmental factors affecting the yield and quality of A. membranaceus, and miRNAs may mediate the gene regulation network under cold stress in A. membranaceus. To identify miRNAs and reveal their functions in cold stress response in A. membranaceus, small RNA sequencing was conducted followed by bioinformatics analysis, and quantitative real time PCR (qRT-PCR) analysis was performed to profile the expression of miRNAs under cold stress. A total of 168 conserved miRNAs belonging to 34 families and 14 putative non-conserved miRNAs were identified. Many miRNA targets were predicted and these targets were involved in diversified regulatory and metabolic pathways. By using qRT-PCR, 27 miRNAs were found to be responsive to cold stress, including 4 cold stress-induced and 17 cold-repressed conserved miRNAs, and 6 cold-induced non-conserved miRNAs. These cold-responsive miRNAs probably mediate the response to cold stress by regulating development, hormone signaling, defense, redox homeostasis, and secondary metabolism in A. membranaceus. These cold-corresponsive miRNAs may be used as the candidate genes in further molecular breeding for improving cold tolerance of A. membranaceus.

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“…It was noteworthy that some targets of A. membranaceus MIR156 were homologues of Arabidopsis GUT15 ( AtGUT15 , AT2G18440), a long noncoding RNA [42].…”

Section: Resultsmentioning

confidence: 99%

Identification of miRNAs and Their Response to Cold Stress in Astragalus Membranaceus

Abla

Sun

et al. 2019

Biomolecules

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“…5B, Additional File 3). LncRNAs containing structural RNA sequences have been previously identified in other organisms including humans (sno-lncRNAs) and plants (lncRNA containing a tRNA-like molecule) [28][29][30]. We also identified examples where more than one structural RNA sequence was contained within a single lncRNA.…”

Section: Some Lncrnas Contain Structural Rna Sequencesmentioning

confidence: 90%

A manually curated annotation characterises genomic features of P. falciparum lncRNAs

Hoshizaki

Adjalley

Thathy

et al. 2022

Preprint

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Background: Important regulation occurs at the level of transcription in Plasmodium falciparum and growing evidence suggests that these apicomplexan parasites have complex regulatory networks. Recent studies implicate long noncoding RNAs (lncRNAs) as transcriptional regulators in P. falciparum. However, due to limited research and the lack of necessary experimental tools, our understanding of their role in the malaria-causing parasite remains largely unelucidated. In this work, we address one of these limitations, the lack of an updated and improved lncRNA annotation in P. falciparum. Results: We generated long-read RNA sequencing data and integrated information extracted and curated from multiple sources to manually annotate lncRNAs. We identified 1522 novel lncRNAs and validated and refined 847 existing annotations. Utilising the collated datasets, we generated evidence-based ranking scores for each annotation and characterised the distinct genomic contexts and features of P. falciparum lncRNAs. Certain features indicated subsets with potential biological significance such as 25 lncRNAs containing multiple introns, 335 lncRNAs lacking mutations in piggyBac mutagenic studies and lncRNAs associated with specific biologic processes including two new types of lncRNAs found proximal to var genes. Conclusions: The insights and the annotation presented in this study will serve as valuable tools for researchers seeking to understand the role of lncRNAs in parasite biology through both bioinformatics and experimental approaches.

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“…It was later found that the stability of the transcript is more tissue specific [94]. The primitive arabidopsis GUT15 transcript serves as a precursor for two stable RNAs, one of which is a TLS [92]. This TLS is CCA modified and has an inhibitory effect on the slicing of its host intron [92].…”

Section: Tlss In Noncoding Rnasmentioning

confidence: 99%

“…The primitive arabidopsis GUT15 transcript serves as a precursor for two stable RNAs, one of which is a TLS [92]. This TLS is CCA modified and has an inhibitory effect on the slicing of its host intron [92]. Canonical tRNAs that are encoded within introns, however, have no similar effect [92], suggesting that this may be a function independent of tRNA similarity.…”

Section: Tlss In Noncoding Rnasmentioning

confidence: 99%

tRNA‐like structures and their functions

Wang

2021

The FEBS Journal

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HIV-1: Human immunodeficiency virus type 1 IFNA5: Interferon-alpha 5 IRES: Internal ribosome entry site MALAT1: Metastasis-associated lung adenocarcinoma transcript 1 mascRNA: MALAT1-associated small cytoplasmic RNA NeRNV: Nemesia ring necrosis virus PTS: Phloem transport signals sgRNA: Small guide RNA ssRNA: Single strand RNA SLC: Stem-loop C TLS: tRNA-like structures tRNA: Transfer RNA tRF: tRNA-derived fragments, TYMV: Turnip yellow mosiaic virus TMV: Tobacco mosaic virus Y4RNAfr: Fragment of Y4-RNA

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A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis

Cited by 7 publications

References 49 publications

Identification of miRNAs and Their Response to Cold Stress in Astragalus Membranaceus

Identification of miRNAs and Their Response to Cold Stress in Astragalus Membranaceus

A manually curated annotation characterises genomic features of P. falciparum lncRNAs

tRNA‐like structures and their functions

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