Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs

The Plant Cell, Journal Year: 2023, Volume and Issue: 35(6), P. 1762 - 1786

Published: Feb. 4, 2023

Abstract Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to variety regulatory processes. Functionally characterized lncRNAs play critical roles plants, ranging from regulating flowering controlling lateral root formation. However, findings the past decade have revealed thousands present plant transcriptomes, characterization has lagged far behind identification. In this setting, distinguishing function noise is challenging. community been at forefront discovery lncRNA biology, providing many functional mechanistic insights increased our understanding gene class. review, we examine key discoveries made biology over two half decades. We describe how pregenomics era informed efforts identify functionally characterize subsequent provide an overview archetypes into which fit speculate on new avenues research may uncover yet more archetypes. Finally, review discusses challenges facing field some exciting molecular computational approaches help inform comparative analyses.

Language: Английский

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From environmental responses to adaptation: the roles of plant lncRNAs

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(1), P. 232 - 244

Published: Jan. 21, 2024

Abstract As sessile organisms, plants are continuously exposed to heterogeneous and changing environments constantly need adapt their growth strategies. They have evolved complex mechanisms recognize various stress factors, activate appropriate signaling pathways, respond accordingly by reprogramming the expression of multiple genes at transcriptional, post-transcriptional, even epigenome levels tolerate stressful conditions such as drought, high temperature, nutrient deficiency, pathogenic interactions. Apart from protein-coding genes, long non-coding RNAs (lncRNAs) emerged key players in plant adaptation environmental stresses. transcripts larger than 200 nucleotides without potential. Still, they appear regulate a wide range processes, including epigenetic modifications chromatin reorganization, well transcriptional post-transcriptional modulation gene expression, allowing LncRNAs can positively or negatively modulate responses, affecting processes hormone signaling, temperature tolerance, deficiency adaptation. Moreover, also seem play role memory, wherein prior exposure mild enhances ability subsequent conditions. In this review, we summarize contribution lncRNAs biotic abiotic stresses, memory. The evolutionary conservation is discussed provides insights into future research directions field.

Language: Английский

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Emerging mechanistic insights into the regulation of specialized metabolism in plants

Nature Plants, Journal Year: 2022, Volume and Issue: 9(1), P. 22 - 30

Published: Dec. 23, 2022

Language: Английский

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The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants

Genome biology, Journal Year: 2022, Volume and Issue: 23(1)

Published: Aug. 29, 2022

Abstract Background RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP ( APOLO ), are emerging as important regulators of three-dimensional chromatin conformation and gene transcriptional activity. Results Here, we show that in addition to PRC1-component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), interacts with methylcytosine-binding protein VARIANT IN METHYLATION (VIM1), a conserved homolog mammalian DNA methylation regulator UBIQUITIN-LIKE CONTAINING PHD AND RING FINGER DOMAINS (UHRF1). The -VIM1-LHP1 complex directly regulates transcription auxin biosynthesis YUCCA2 by dynamically determining H3K27me3 deposition over its promoter during plant thermomorphogenic response. Strikingly, demonstrate UHRF1 Protein Associated Transcript UPAT direct interactor humans, can be recognized VIM1 LHP1 cells, despite lack sequence homology between . In addition, increased levels or hamper binding globally alter transcriptome similar manner. Conclusions Collectively, our results uncover new mechanism which coordinates Polycomb action through interaction VIM1, indicates evolutionary unrelated lncRNAs potentially structures may exert functions interacting partners.

Language: Английский

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Predicted roles of long non-coding RNAs in abiotic stress tolerance responses of plants

Molecular Horticulture, Journal Year: 2024, Volume and Issue: 4(1)

Published: May 15, 2024

Abstract The plant genome exhibits a significant amount of transcriptional activity, with most the resulting transcripts lacking protein-coding potential. Non-coding RNAs play pivotal role in development and regulatory processes plants. Long non-coding (lncRNAs), which exceed 200 nucleotides, may enhancing resilience to various abiotic stresses, such as excessive heat, drought, cold, salinity. In addition, exogenous application chemicals, abscisic acid salicylic acid, can augment defense responses against stress. While how lncRNAs stress tolerance is relatively well-studied model plants, this review provides comprehensive overview current understanding function horticultural crop It also delves into potential chemical priming plants order acquire tolerance, although many limitations exist proving lncRNA functionality under conditions.

Language: Английский

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Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations

Non-Coding RNA, Journal Year: 2021, Volume and Issue: 7(1), P. 12 - 12

Published: Feb. 17, 2021

The first reference to the “C-value paradox” reported an apparent imbalance between organismal genome size and morphological complexity. Since then, next-generation sequencing has revolutionized genomic research revealed that eukaryotic transcriptomes contain a large fraction of non-protein-coding components. Eukaryotic genomes are pervasively transcribed noncoding regions give rise plethora RNAs with undeniable biological functions. Among them, long (lncRNAs) seem represent new layer gene expression regulation, participating in wide range molecular mechanisms at transcriptional post-transcriptional levels. In addition their role epigenetic plant lncRNAs have been associated degradation complementary RNAs, regulation alternative splicing, protein sub-cellular localization, promotion translation post-translational modifications. this review, we report integrate numerous complex through which transcripts regulate plants.

Language: Английский

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When junk DNA turns functional: transposon-derived non-coding RNAs in plants

Journal of Experimental Botany, Journal Year: 2021, Volume and Issue: 72(11), P. 4132 - 4143

Published: Feb. 12, 2021

Transposable elements (TEs) are major contributors to genome complexity in eukaryotes. TE mobilization may cause instability, although it can also drive diversity throughout evolution. transposition influence the transcriptional activity of neighboring genes by modulating epigenomic profile region or altering relative position regulatory elements. Notably, TEs have emerged last few years as an important source functional long and small non-coding RNAs. A plethora RNAs derived from been linked trans regulation gene at post-transcriptional levels. Furthermore, TE-derived shown modulate expression interacting with protein partners, sequestering active RNAs, forming duplexes DNA other RNA molecules. In this review, we summarize our current knowledge mechanistic paradigms discuss their role plant development

Language: Английский

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LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis

The EMBO Journal, Journal Year: 2023, Volume and Issue: 42(11)

Published: April 13, 2023

Abstract How the noncoding genome affects cellular functions is a key biological question. A particular challenge to distinguish effects of DNA elements from long RNAs (lncRNAs) that coincide at same loci. Here, we identified flowering‐associated intergenic lncRNA ( FLAIL ) in Arabidopsis through early flowering flail mutants. Expression RNA different chromosomal location combination with strand‐specific knockdown characterized as trans‐acting molecule. directly binds differentially expressed target genes control via RNA–DNA interactions conserved sequence motifs. interacts protein and components spliceosome affect mRNA expression co‐transcriptional alternative splicing (AS) linked chromatin regulation. In absence , defects direct gene LACCASE 8 (LAC8) correlated reduced expression. Double mutant analyses support model where ‐mediated LAC8 promotes its represses flowering. Our study suggests lncRNAs accessory regulate AS impact organismal development.

Language: Английский

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The long non-coding RNA DANA2 positively regulates drought tolerance by recruiting ERF84 to promote JMJ29-mediated histone demethylation

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(8), P. 1339 - 1353

Published: Aug. 1, 2023

Language: Английский

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LncRNA DANA1 promotes drought tolerance and histone deacetylation of drought responsive genes in Arabidopsis

EMBO Reports, Journal Year: 2024, Volume and Issue: 25(2), P. 796 - 812

Published: Jan. 2, 2024

Abstract Although many long noncoding RNAs have been discovered in plants, little is known about their biological function and mode of action. Here we show that the drought-induced intergenic RNA DANA1 interacts with L1p/L10e family member protein -INTERACTING PROTEIN 1 (DIP1) cell nucleus Arabidopsis, both DIP1 promote plant drought resistance. increase histone deacetylase HDA9 binding to CYP707A1 CYP707A2 loci. further PWWP3, a PEAT complex associates has activity. Mutation enhances acetylation expression resulting impaired tolerance, agreement dip1 pwwp3 mutant phenotypes. Our results demonstrate positive regulator response works jointly novel chromatin-related factor on epigenetic reprogramming transcriptome during drought.

Language: Английский

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