A photoregulatory mechanism of the circadian clock in Arabidopsis

Nature Plants, Год журнала: 2021, Номер 7(10), С. 1397 - 1408

Опубликована: Окт. 14, 2021

Язык: Английский

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Importance of pre-mRNA splicing and its study tools in plants

Advanced Biotechnology, Год журнала: 2024, Номер 2(1)

Опубликована: Фев. 8, 2024

Alternative splicing (AS) significantly enriches the diversity of transcriptomes and proteomes, playing a pivotal role in physiology development eukaryotic organisms. With continuous advancement high-throughput sequencing technologies, an increasing number novel transcript isoforms, along with factors related to their associated functions, are being unveiled. In this review, we succinctly summarize compare different mechanisms across prokaryotes eukaryotes. Furthermore, provide extensive overview recent progress various studies on AS covering developmental stages diverse plant species response abiotic stresses. Additionally, discuss modern techniques for studying functions quantification transcripts, as well protein products. By integrating genetic studies, quantitative methods, omics techniques, can discover isoforms functional factors, thereby enhancing our understanding roles modes species.

Язык: Английский

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ASpli: integrative analysis of splicing landscapes through RNA-Seq assays

Bioinformatics, Год журнала: 2021, Номер 37(17), С. 2609 - 2616

Опубликована: Фев. 27, 2021

Genome-wide analysis of alternative splicing has been a very active field research since the early days next generation sequencing technologies. Since then, ever-growing data availability and development increasingly sophisticated methods have uncovered complexity general repertoire. A large number methodologies exist, each them presenting its own strengths weaknesses. For instance, exclusively relying on junction information do not take advantage majority reads produced in an RNA-seq assay, isoform reconstruction might detect novel intron retention events, some solutions can only handle canonical many existing perform pairwise comparisons.In this contribution, we present ASpli, computational suite implemented R statistical language, that allows identification changes both, annotated alternative-splicing events deal with simple, multi-factor or paired experimental designs. Our integrative workflow, considers same GLM model applied to different sets junctions, computation complementary signals. Analyzing simulated real data, found consolidation these signals resulted robust proxy occurrence alterations. While junctions allowed us uncover as well non-annotated read coverage notably increased recall capabilities at competitive performance when compared against other state-of-the-art algorithms.ASpli is freely available from Bioconductor project site https://doi.org/doi:10.18129/B9.bioc.ASpli.Supplementary are Bioinformatics online.

Язык: Английский

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ABA Mediates Plant Development and Abiotic Stress via Alternative Splicing

International Journal of Molecular Sciences, Год журнала: 2022, Номер 23(7), С. 3796 - 3796

Опубликована: Март 30, 2022

Alternative splicing (AS) exists in eukaryotes to increase the complexity and adaptability of systems under biophysiological conditions by increasing transcriptional protein diversity. As a classic hormone, abscisic acid (ABA) can effectively control plant growth, improve stress resistance, promote dormancy. At level, ABA helps plants respond outside world regulating transcription factors through signal transduction pathways regulate gene expression. However, at post-transcriptional mechanism which biological processes mediating alternative is not well understood. Therefore, this paper briefly introduces ABA-induced role AS response environment its own growth.

Язык: Английский

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The lncRNA MARS modulates the epigenetic reprogramming of the marneral cluster in response to ABA

Molecular Plant, Год журнала: 2022, Номер 15(5), С. 840 - 856

Опубликована: Фев. 9, 2022

Язык: Английский

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Superoxide is promoted by sucrose and affects amplitude of circadian rhythms in the evening

Proceedings of the National Academy of Sciences, Год журнала: 2021, Номер 118(10)

Опубликована: Март 4, 2021

Significance Distinguishing the effects of light and sugars in photoautotrophic cells is challenging. The circadian system a regulatory network that integrates metabolic signals controls rhythmic physiology growth. Our experimental approach has defined light-independent, sugar-regulated transcriptome Arabidopsis revealed reactive oxygen species (ROS) as prominent feature. ROS are byproducts photosynthetic metabolism oscillate with rhythms but have not previously been demonstrated inputs to plant oscillator. data suggest role for superoxide sugar signal which acts evening affects gene expression

Язык: Английский

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Circadian Clock Components Offer Targets for Crop Domestication and Improvement

Genes, Год журнала: 2021, Номер 12(3), С. 374 - 374

Опубликована: Март 6, 2021

During plant domestication and improvement, farmers select for alleles present in wild species that improve performance new selective environments associated with cultivation use. The selected become enriched other depleted elite cultivars. One important aspect of crop improvement is expansion the geographic area suitable cultivation; this frequently includes growth at higher or lower latitudes, requiring to adapt novel photoperiodic environments. Many crops exhibit control flowering altered sensitivity commonly required optimal latitudes. Alleles a number circadian clock genes have been their effects on multiple crops. coordinates many additional aspects growth, metabolism physiology, including responses abiotic biotic stresses. these clock-regulated processes contribute performance. Examples selection function tomato demonstrate domestication, phasing delayed respect light-dark cycle period lengthened; modified increased chlorophyll content long days. These data suggest an attractive target during breeding improvement.

Язык: Английский

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Time of the day prioritizes the pool of translating mRNAs in response to heat stress

The Plant Cell, Год журнала: 2021, Номер 33(7), С. 2164 - 2182

Опубликована: Апрель 16, 2021

Abstract The circadian clock helps organisms to anticipate and coordinate gene regulatory responses changes in environmental stimuli. Under growth limiting temperatures, the time of day modulates accumulation polyadenylated mRNAs. In response heat stress, plants will conserve energy selectively translate How and/or regulates mRNAs bound by ribosomes stress is unknown. In-depth analysis Arabidopsis thaliana translating found that gates approximately one-third circadian-regulated heat-responsive translatome. Specifically, interact prioritize pool cue be translated. For a subset mRNAs, we observed stronger gated during day, preferentially before peak expression. We propose previously overlooked transcription factors (TFs) as nodes show plays role temperature for select TFs. When was removed, redefined priorities translation recovered within 1 h, though slower recovery abiotic regulators. Through hierarchical network connections between genes prioritized TFs, our work provides framework target key underlying tolerance throughout day.

Язык: Английский

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OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security

Plants, Год журнала: 2021, Номер 10(7), С. 1423 - 1423

Опубликована: Июль 12, 2021

The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to Green Revolution, which significantly increased yields ensures food security, despite population explosion. However, new challenges such as rapid climate change, deteriorating soil, accumulation pollutants require much faster responses more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing efficiency agriculture are undoubtedly associated with inclusion strategy knowledge obtained using high-throughput technologies tools future ensure design plant genomes predict desired phenotype. This article provides an overview current state research these areas, well study soil microbiomes, prospective use their potential a field microbiome engineering. In terms genomic phenomic predictions, we also propose integrated approach combines high-density genotyping phenotyping techniques, can improve prediction accuracy quantitative traits species.

Язык: Английский

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COLD REGULATED GENE 27 and 28 antagonize the transcriptional activity of the RVE8/LNK1/LNK2 circadian complex

PLANT PHYSIOLOGY, Год журнала: 2023, Номер 192(3), С. 2436 - 2456

Опубликована: Апрель 5, 2023

Abstract Many molecular and physiological processes in plants occur at a specific time of day. These daily rhythms are coordinated part by the circadian clock, timekeeper that uses daylength temperature to maintain ∼24 h various clock-regulated phenotypes. The MYB-like transcription factor REVEILLE 8 (RVE8) interacts with its transcriptional coactivators NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED 1 (LNK1) LNK2 promote expression evening-phased clock genes cold tolerance factors. While genetic approaches have commonly been used discover connections within between elements other pathways, here, we affinity purification coupled mass spectrometry (APMS) identify time-of-day–specific protein interactors RVE8-LNK1/LNK2 complex Arabidopsis (Arabidopsis thaliana). Among RVE8/LNK1/LNK2 were COLD-REGULATED GENE 27 (COR27) COR28, which coprecipitated an evening-specific manner. In addition COR27 found enrichment temperature-related led us establish previously uncharacterized role for LNK1 entrainment clock. We established RVE8, LNK1, either or COR28 form tripartite yeast (Saccharomyces cerevisiae) effect this interaction planta serves antagonize activation RVE8 target genes, potentially through mediating degradation evening. Together, these results illustrate how proteomic approach can be interactions. Discovery RVE8-LNK-COR indicates unknown regulatory mechanism signaling pathways.

Язык: Английский

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