Mechanisms of epigenetic regulation of transcription by lncRNAs in plants DOI
Benjamin J.-M. Tremblay, Julia I. Qüesta

IUBMB Life, Journal Year: 2022, Volume and Issue: 75(5), P. 427 - 439

Published: Oct. 12, 2022

Long noncoding RNAs (lncRNAs) are an ubiquitous feature of eukaryotic genomes and in recent decades have been shown to be highly abundant varied. Many prominent examples described as having essential roles regulating the expression genes different developmental environmental contexts. As a result, much work has done on elucidating mechanisms by which they modulate protein coding genes. In this review, we focus those characterized plants. We specifically examine common epigenetic that regulate gene at level transcription. regard, lncRNAs plants primarily associated with controlling chromatin environment modifications, RNA POLYMERASE II (RNAPII) processivity efficiency transcription, mediating formation transcriptionally activating repressive loops. discuss open questions plant lncRNA regulation opportunities for future study functionally significant yet-unknown mechanisms.

Language: Английский

LncRNAs: the art of being influential without protein DOI Creative Commons
Lorena Ramírez Gonzales, Suze Blom, Rossana Henriques

et al.

Trends in Plant Science, Journal Year: 2024, Volume and Issue: 29(7), P. 770 - 785

Published: Feb. 16, 2024

The plant long noncoding (lnc)RNA field is on the brink of transitioning from large-scale identification lncRNAs to their functional characterization. Due cross-kingdom conservation interaction types and molecular functions, there much be learned mammalian lncRNA research. Here, we discuss different processes involving regulation chromatin splicing. Furthermore, interactome, which includes proteins, other RNAs, DNA. We explore how functionalities could reflected in similar pathways plants hypothesize that several breakthroughs research lead discovery novel functions. Expanding our knowledge biological role multiple applications paves way for future agricultural applications.

Language: Английский

Citations

17
Rock, scissors, paper: How RNA structure informs function DOI Creative Commons
Sarah M. Assmann, Hong‐Li Chou, Philip C. Bevilacqua

et al.

The Plant Cell, Journal Year: 2023, Volume and Issue: 35(6), P. 1671 - 1707

Published: Feb. 7, 2023

RNA can fold back on itself to adopt a wide range of structures. These from relatively simple hairpins intricate 3D folds and be accompanied by regulatory interactions with both metabolites macromolecules. The last 50 yr have witnessed elucidation an astonishing array structures including transfer RNAs, ribozymes, riboswitches, the ribosome, spliceosome, most recently entire structuromes. advances in structural biology deepened insight into fundamental biological processes gene editing, transcription, translation, structure-based detection response temperature other environmental signals. discoveries reveal that static, like rock; it catalytic functions cutting bonds, scissors; myriad functional shapes, paper. We relate these extraordinary structure plant way life. trace plant-specific discovery ribozymes alternative splicing, organellar ribosomes, thermometers, whole-transcriptome structuromes pan-structuromes, conclude plants special set confer unique types regulation. finish consideration future directions for structure-function field.

Language: Английский

Citations

27
From environmental responses to adaptation: the roles of plant lncRNAs DOI Creative Commons
Soledad Traubenik, Céline Charon, Thomas Blein

et al.

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

Citations

16
The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants DOI Creative Commons
Camille Fonouni‐Farde, Aurélie Christ, Thomas Blein

et al.

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

Citations

30
Epigenetics and plant hormone dynamics - a functional and methodological perspective DOI Creative Commons
Jiří Rudolf,

Lucia Tomovicova,

Klára Panzarová

et al.

Journal of Experimental Botany, Journal Year: 2024, Volume and Issue: 75(17), P. 5267 - 5294

Published: Feb. 19, 2024

Abstract Plant hormones, pivotal regulators of plant growth, development, and response to environmental cues, have recently emerged as central modulators epigenetic processes governing gene expression phenotypic plasticity. This review addresses the complex interplay between hormones mechanisms, highlighting diverse methodologies that been harnessed decipher these intricate relationships. We present a comprehensive overview understand how phytohormones orchestrate modifications, shaping adaptation survival strategies. Conversely, we explore ensure hormonal balance regulate signalling pathways key hormones. Furthermore, our investigation includes search for novel genes are regulated by under control processes. Our offers contemporary epigenetic–plant hormone crosstalk, emphasizing its significance in potential agronomical applications.

Language: Английский

Citations

7
Temperature regulation of auxin-related gene expression and its implications for plant growth DOI
Luciana Bianchimano, María Belén De Luca, María Belén Borniego

et al.

Journal of Experimental Botany, Journal Year: 2023, Volume and Issue: 74(22), P. 7015 - 7033

Published: July 9, 2023

Abstract Twenty-five years ago, a seminal paper demonstrated that warm temperatures increase auxin levels to promote hypocotyl growth in Arabidopsis thaliana. Here we highlight recent advances auxin-mediated thermomorphogenesis and identify unanswered questions. In the warmth, PHYTOCHROME INTERACTING FACTOR 4 (PIF4) PIF7 bind YUCCA8 gene promoter and, concert with histone modifications, enhance its expression synthesis cotyledons. Once transported hypocotyl, promotes cell elongation. The meta-analysis of auxin-related genes seedlings exposed ranging from cold hot shows complex patterns response. Changes only partially account for these responses. many SMALL AUXIN UP RNA (SAUR) reaches maximum decreasing towards both temperature extremes correlation rate growth. Warm primary root growth, response requires auxin, hormone tip but impacts on division expansion are not clear. A deeper understanding control plant architecture is necessary face challenge global warming.

Language: Английский

Citations

14
Epiallelic variation of non-coding RNA genes and their phenotypic consequences DOI Creative Commons
Jie Liu, Xuehua Zhong

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 14, 2024

Epigenetic variations contribute greatly to the phenotypic plasticity and diversity. Current functional studies on epialleles have predominantly focused protein-coding genes, leaving of non-coding RNA (ncRNA) genes largely understudied. Here, we uncover abundant DNA methylation ncRNA their significant correlations with plant adaptation among 1001 natural Arabidopsis accessions. Through genome-wide association study (GWAS), identify large numbers QTL (methylQTL) that are independent known methyltransferases enriched in specific chromatin states. Proximal methylQTL closely located a larger effect than distal methylQTL. We ectopically tether methyltransferase MQ1v miR157a by CRISPR-dCas9 show de novo establishment accompanied decreased abundance early flowering. These findings provide important insights into genetic basis epigenetic highlight contribution phenotypes

Language: Английский

Citations

6
The plant noncoding transcriptome: a versatile environmental sensor DOI
Uciel Chorostecki, Nicolás G. Bologna, Federico Ariel

et al.

The EMBO Journal, Journal Year: 2023, Volume and Issue: 42(20)

Published: Sept. 21, 2023

Language: Английский

Citations

13
Rose long noncoding RNA lncWD83 promotes flowering by modulating ubiquitination of the floral repressor RcMYC2L DOI Creative Commons
Yeqing Chen, Jun Lu, Wang Weinan

et al.

PLANT PHYSIOLOGY, Journal Year: 2023, Volume and Issue: 193(4), P. 2573 - 2591

Published: Sept. 19, 2023

Long noncoding RNAs (lncRNAs) play important roles in various signaling pathways vascular plants. However, the crosstalk between lncRNAs and E3 ubiquitin ligases has been barely reported. In this study, we demonstrate that lncRNA lncWD83 from rose (Rosa chinensis) 'Old blush' activates flowering by modulating ubiquitination of floral repressor MYC2 LIKE (RcMYC2L). Flowering was substantially delayed virus-induced gene silencing lncWD83. an vitro pull-down assay, associated with PLANT U-BOX PROTEIN 11 (PUB11), a U-box-containing ligase. Seedlings knocked down RcPUB11 transcripts phenocopied later-flowering phenotype lncWD83-silenced seedlings. RcMYC2L physically interacted ubiquitinated RcPUB11-dependent manner vitro. Accordingly, fully reversed resulting knockdown. Furthermore, bound to G-box-related motifs FLOWERING LOCUS T (RcFT) promoter repressed its transcription. alleviated repression RcFT expression via proteasomal degradation RcMYC2L, enhanced associating RcPUB11. Therefore, promotes These findings reveal distinct regulatory mechanism for facilitating ubiquitin-mediated proteolysis regulate flowering.

Language: Английский

Citations

10
From molecular basics to agronomic benefits: Insights into noncoding RNA‐mediated gene regulation in plants DOI Open Access
Yuqiu Wang, Xing Wang Deng, Danmeng Zhu

et al.

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 64(12), P. 2290 - 2308

Published: Dec. 1, 2022

Abstract The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, have evolved various subtle regulatory mechanisms for altering gene expression. N c oding RNA s (ncRNAs) constitute major portion the transcriptomes eukaryotes. Various ncRNAs been recognized as important regulators expression genes involved in essential biological processes throughout whole life cycles plants. In this review, we summarize current understanding biogenesis and contributions mall n ucle o lar (snoRNA)‐ l ong (lncRNA)‐mediated regulation plant environmental responses. Many appear be associated with increased yield, quality disease resistance species cultivars. These may potentially used genetic resources improving agronomic traits molecular breeding. challenges ncRNA biology possibilities make use these valuable future are discussed review.

Language: Английский

Citations

15