Alternative silencing states of transposable elements in Arabidopsis associated with H3K27me3

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 20, 2025

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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Towards an unbiased characterization of genetic polymorphism

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 30, 2024

Our view of genetic polymorphism is shaped by methods that provide a limited and reference-biased picture. Long-read sequencing technologies, which are starting to nearly complete genome sequences for population samples, should solve the problem—except characterizing making sense non-SNP variation difficult even with perfect sequence data. Here, we analyze 27 genomes Arabidopsis thaliana in an attempt address these issues, illustrate what can be learned analyzing whole-genome data unbiased manner. Estimated sizes range from 135 155 Mb, differences almost entirely due centromeric rDNA repeats. The completely assembled chromosome arms comprise roughly 120 Mb all accessions, but full structural variants, many caused insertions transposable elements (TEs) subsequent partial deletions such insertions. Even only pan-genome coordinate system includes resulting ends up being 40% larger than size any one genome. analysis reveals incompletely annotated mobile-ome: our ability predict actually moving poor, detect several novel TE families. In contrast this, genic portion, or “gene-ome”, highly conserved. By annotating each using accession-specific transcriptome data, find 13% genes segregating most transcriptionally silenced. Finally, show short-read previously massively underestimated kinds, including SNPs—mostly regions where short reads could not mapped reliably, also were incorrectly. We demonstrate SNP-calling errors biased choice reference genome, RNA-seq BS-seq results strongly affected mapping rather assayed individual. conclusion, while pose tremendous analytical challenges, they will ultimately revolutionize understanding evolution.

Language: Английский

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Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen

Mobile DNA, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 15, 2023

The genome of the obligate biotrophic phytopathogenic barley powdery mildew fungus Blumeria hordei is inflated due to highly abundant and possibly active transposable elements (TEs). In absence otherwise common repeat-induced point mutation transposon defense mechanism, noncoding RNAs could be key for regulating activity TEs coding genes during pathogenic life cycle.We performed time-course whole-transcriptome shotgun sequencing (RNA-seq) total RNA derived from infected leaf epidermis at various stages fungal pathogenesis observed significant transcript accumulation time point-dependent regulation in B. hordei. Using a manually curated consensus database 344 TEs, we discovered phased small mapping 104 transposons, suggesting that interference contributes significantly their regulation. Further, identified 5,127 long (lncRNAs) genome-wide hordei, which 823 originated antisense strand TE. Co-expression network analysis lncRNAs, throughout asexual cycle points extensive positive negative co-regulation subsets genes.Our work suggests similar mammals plants, lncRNAs support dynamic modulation levels, including pivotal host infection. may transcriptional diversity plasticity amid loss fungi give rise novel regulatory virulence peptides, thus representing drivers rapid evolutionary adaptation promote pathogenicity overcome defense.

Language: Английский

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LTR retrotransposon-derived novel lncRNA2 enhances cold tolerance in Moso bamboo by modulating antioxidant activity and photosynthetic efficiency

PeerJ, Journal Year: 2025, Volume and Issue: 13, P. e19056 - e19056

Published: Feb. 26, 2025

In Moso bamboo, the mechanism of long terminal repeat (LTR) retrotransposon-derived non-coding RNA (TElncRNA) in response to cold stress remains unclear. this study, several Pe-TElncRNAs were identified from bamboo transcriptome data. qRT-PCR analysis showed that expression a novel Pe-TElncRNA2 seedlings reached its highest level at 8 hours treatment 4 °C and was significantly higher stems compared leaves, roots, buds. Furthermore, cellular localization revealed cytoplasm than nucleus. overexpression protoplasts positively regulated FZR2 , NOT3 ABCG44 AGD6 genes. Further validation lncRNA Arabidopsis thaliana enhanced antioxidant activities, as evidenced by increased superoxide dismutase (SOD) activity proline content, well maximum photochemical efficiency PS II dark-adapted leaves ( F v / m ), transgenic plants wild-type controls. Conversely, malondialdehyde (MDA) lipid peroxidation marker (a oxidative stress), reduced plants. Notably, levels both genes upregulated after two days treatment. These findings elucidate critical role LTR lncRNAs mediating responses bamboo.

Language: Английский

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Naturally occurring variation in gene-associated transposable elements impacts gene expression and phenotypic diversity in woodland strawberry

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: April 22, 2025

Transposable elements (TEs) constitute a major portion of plant genomes and play key roles in shaping genome architecture, regulating gene expression, driving evolution. In this study, we generated comprehensive curated TE library for the woodland strawberry (Fragaria vesca) by integrating two bioinformatic pipelines (EDTA DeepTE). Our annotation revealed that TEs account approximately 37% F. vesca genome. Analysis TE-derived inverted repeats (IRs) miniature inverted-repeat transposable (MITEs) demonstrated their association with 24-nt small interfering RNA (siRNA) production differential DNA methylation patterns across tissues, suggesting role epigenetic regulation particularly during fruit ripening. This MITE-mediated regulatory mechanism was confirmed evaluating expression chromatin organization at FvH4_7g18570, which encodes alcohol acyl transferase (FvAAT1). Three MITEs located upstream or downstream FvAAT1 coding sequence were shown to influence epigenetically expression. Furthermore, analyzed 210 re-sequenced accessions from European germplasm collection identify annotate insertion deletion polymorphisms. A principal component analysis (PCA) based on these polymorphisms subpopulation structures reflect geographic origins. genome-wide study (GWAS) uncovered significant associations between specific economically important traits, including aroma-related volatile compounds size. Among them, hAT MITE near FvH4_2g00610 correlated increased levels γ-decalactone, desirable aroma compound strawberries. These findings underscore functional significance as contributors phenotypic diversity through novel functions. By into population-genomic studies, work provides valuable insights development quality traits. It also highlights potential harnessing TE-mediated variation breeding initiatives editing strategies improve quality.

Language: Английский

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Dynamics of DNA methylation and its impact on plant embryogenesis

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 81, P. 102593 - 102593

Published: June 27, 2024

Flowering plants exhibit unique DNA methylation dynamics during development. Particular attention can be focused on seed development and the embryo, which represents starting point of sporophytic life cycle. A build-up CHH is now recognized as highly characteristic embryo This process thought to occur in order silence potentially harmful transposable element expression, though roles promoting dormancy dessication tolerance have also been revealed. Recent studies show that increased embryos inhabits both novel loci, unmethylated elsewhere plant, well shared exhibiting more dense methylation. The role cis-regulatory gene regulation less established compared mammals, here we discuss potential dynamic expression.

Language: Английский

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Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome

Plants, Journal Year: 2025, Volume and Issue: 14(8), P. 1160 - 1160

Published: April 8, 2025

Transposon is the main component of eukaryotic genome, and more plant genome data show that transposons are diverse in regulating structure, variation, function evolution, with different transposition mechanisms genome. Hybridization polyploidy play an important role promoting speciation recent studies have shown usually accompanied by expansion transposons, which affect size structure polyploid plants. Transposons can insert into genes intergenic regions, resulting great differences overall closely related species, it also capture gene segments to increase copy number genes. In addition, influence epigenetic modification state regulate expression gene, while phenotype, biological abiotic stress response regulated transposons. Overall, especially adaptation evolution.

Language: Английский

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Harnessing transposable elements for plant functional genomics and genome engineering

Trends in Plant Science, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Transposable elements (TEs) constitute a large portion of many plant genomes and play important roles in regulating gene expression driving genome evolution crop domestication. Despite advances understanding the functions mechanisms TEs, comprehensive review their integrated knowledge cutting-edge biotechnological applications TEs is still needed. We provide thorough overview that connects discoveries, mechanisms, technologies associated with TEs. discuss identification function driven by functional genomics, epigenetic regulation utilization active genomics engineering. In summary, expanding application will be beneficial to breeding synthetic biology future.

Language: Английский

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Comprehensive genome annotation of the model ciliate Tetrahymena thermophila by in-depth epigenetic and transcriptomic profiling

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 9, 2024

The ciliate Tetrahymena thermophila is a well-established unicellular model eukaryote, contributing significantly to foundational biological discoveries. Despite its acknowledged importance, current studies on biology face challenges due gene annotation inaccuracy, particularly the notable absence of untranslated regions (UTRs). To comprehensively annotate macronuclear genome, we collected extensive transcriptomic data spanning various cell stages. ascertain transcript orientation and transcription start/end sites, incorporated epigenetic marks displaying enrichment towards 5' end bodies, including H3 lysine 4 tri-methylation (H3K4me3), histone variant H2A.Z, nucleosome positioning N6-methyldeoxyadenine (6mA). Cap-seq was subsequently applied validate accuracy identified start sites. Additionally, integrated Nanopore direct RNA sequencing (DRS), strand-specific (RNA-seq) assay for transposase-accessible chromatin with high-throughput (ATAC-seq) data. Using newly developed bioinformatic pipeline, coupled manual curation experimental validation, our work yielded substantial improvements models, addition 2,481 new genes, updates 23,936 existing incorporation 8,339 alternatively spliced isoforms. Furthermore, novel UTR information annotated 26,687 high-confidence genes. Intriguingly, 20% protein-coding genes were have natural antisense transcripts characterized by high diversity in alternative splicing, thus offering insights into understanding transcriptional regulation. Our will enhance utility as robust genetic toolkit advancing research, provides promising framework genome other eukaryotes.

Language: Английский

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