Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses DOI Creative Commons
Paweł Sega, Katarzyna Kruszka, Dawid Bielewicz

и другие.

Research Square (Research Square), Год журнала: 2020, Номер unknown

Опубликована: Сен. 30, 2020

Abstract Background: Small RNAs (sRNAs) are 20–30 nt regulatory elements which responsible for plant development regulation and participate in many stress responses. Insufficient inorganic phosphate (Pi) concentration triggers responses to balance the internal Pi level. Results: In this study, we describe Pi-starvation-responsive small transcriptome changes barley ( Hordeum vulgare L.) using N ext- G eneration S equencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) RNAs, (ii) degraded (iii) functional mRNAs. We find that differentially significantly expressed miRNAs (DEMs, p -value < 0.05) represented by 162 (44.88 % total RNAs) molecules shoot 138 (7.14 %) root; mainly various miR399 miR827 isomiRs. The remaining (i.e., those without perfect match reference sequences deposited miRBase) considered as other sRNAs (DESs, Bonferroni correction 0.05). roots, a more abundant diverse set 1796 unique sequences, 0.13 reads obtained under low-Pi) contributes compensation low-Pi than shoots 199 0.01 %). More 80 up-regulated both organs. Additionally, shoots, up-regulation is accompanied strong induction two nucleases (S1/P1 endonuclease 3’-5’ exonuclease). This suggests most may be generated upon endonucleolytic cleavage increase pool. Transcriptomic profiling Pi-starved identifies 98 genes (DEGs). A majority DEGs possess characteristic Pi-responsive cis -regulatory (P1BS and/or PHO element), located mostly proximal promoter regions. GO analysis shows discovered primarily alter defense, response, nutrient mobilization, or pathways involved gathering recycling phosphorus organic pools. Conclusions: Our results provide comprehensive demonstrate complex at RNA level maintain homeostasis indicate adapts Pi-starvation through elicitation degradation. Novel P-responsive were selected putative candidates overcome plants.

Язык: Английский

Co-transcriptional genome surveillance by HUSH is coupled to termination machinery DOI Creative Commons
Andrew Spencley,

Shiran Bar,

Tomek Swigut

и другие.

Molecular Cell, Год журнала: 2023, Номер 83(10), С. 1623 - 1639.e8

Опубликована: Май 1, 2023

The HUSH complex recognizes and silences foreign DNA such as viruses, transposons, transgenes without prior exposure to its targets. Here, we show that endogenous targets of the fall into two distinct classes based on presence or absence H3K9me3. These are further distinguished by their transposon content differential response loss HUSH. A de novo genomic rearrangement at Sox2 locus induces a switch from H3K9me3-independent H3K9me3-associated targeting, resulting in silencing. We demonstrate interacts with termination factor WDR82 and—via component MPP8—with nascent RNA. accumulates sites high RNAPII occupancy including long exons transcription manner dependent CPSF. Together, our results uncover functional diversity this vertebrate-specific exploits evolutionarily ancient machinery for co-transcriptional chromatin targeting genome surveillance.

Язык: Английский

Процитировано

29
The Evolutionary Significance of RNAi in the Fungal Kingdom DOI Open Access
Carlos Lax, Ghizlane Tahiri, J. Alberto Patiño-Medina

и другие.

International Journal of Molecular Sciences, Год журнала: 2020, Номер 21(24), С. 9348 - 9348

Опубликована: Дек. 8, 2020

RNA interference (RNAi) was discovered at the end of last millennium, changing way scientists understood regulation gene expression. Within following two decades, a variety different RNAi mechanisms were found in eukaryotes, reflecting evolutive diversity that entails. The essential silencing mechanism consists an RNase III enzyme called Dicer cleaves double-stranded (dsRNA) generating small interfering RNAs (siRNAs), hallmark RNAi. These siRNAs are loaded into RNA-induced complex (RISC) triggering cleavage complementary messenger by Argonaute protein, main component complex. Consequently, expression target genes is silenced. This has been thoroughly studied fungi due to their proximity animal phylum and conservation from lower higher eukaryotes. However, role even presence differ across fungal kingdom, as it evolved adapting particularities needs each species. Fungi have exploited regulate cell activities defense against exogenous potentially harmful DNA, genome integrity, development, drug tolerance, or virulence. pathway offered versatility through evolution, favoring enormous this kingdom comprises.

Язык: Английский

Процитировано

58
Prokaryotic Argonaute Proteins as a Tool for Biotechnology DOI Open Access
Ekaterina Kropocheva, Lidiya Lisitskaya, Aleksei Agapov

и другие.

Molecular Biology, Год журнала: 2022, Номер 56(6), С. 854 - 873

Опубликована: Авг. 30, 2022

Язык: Английский

Процитировано

28
Challenges and Opportunities Arising from Host–Botrytis cinerea Interactions to Outline Novel and Sustainable Control Strategies: The Key Role of RNA Interference DOI Open Access
Maria Spada, Claudio Pugliesi, Marco Fambrini

и другие.

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(12), С. 6798 - 6798

Опубликована: Июнь 20, 2024

The necrotrophic plant pathogenic fungus Botrytis cinerea (Pers., 1794), the causative agent of gray mold disease, causes significant losses in agricultural production. Control this fungal pathogen is quite difficult due to its wide host range and environmental persistence. Currently, management disease still mainly based on chemicals, which can have harmful effects not only environment human health but also because they favor development strains resistant fungicides. flexibility plasticity B. challenging defense mechanisms ability evolve strategies escape chemicals require new control for successful management. In review, some aspects host-pathogen interactions from novel sustainable could be developed (e.g., signaling pathways, molecules involved immune mechanisms, hormones, post-transcriptional gene silencing) were analyzed. New biotechnological tools use RNA interference (RNAi) are emerging crop protection scenario as versatile, sustainable, effective, environmentally friendly alternatives chemicals. RNAi-based fungicides expected approved soon, although will face several challenges before reaching market.

Язык: Английский

Процитировано

6
Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2 DOI Creative Commons
Akihito Fukudome, Jasleen Singh, Vibhor Mishra

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2021, Номер 118(51)

Опубликована: Дек. 13, 2021

Significance RDR2 is critical for siRNA-directed DNA methylation in Arabidopsis , functioning physical association with DNA-dependent Pol IV to synthesize the second strands of double-stranded siRNA precursors. Base-pairing between template strand transcribed by and nontemplate needed induce arrest IV/RDR2 transcriptional coupling, but how this occurs unknown. We report structure experimental evidence engages its RNA templates initiates transcription. ends RNAs displaced from RNA/DNA hybrids, suggesting a model which backtracking, accompanied reannealing, extrudes 3′ end transcript, allowing engagement second-strand synthesis RDR2.

Язык: Английский

Процитировано

34
Independent phenotypic plasticity axes define distinct obesity sub-types DOI Creative Commons
Chih-Hsiang Yang, Luca Fagnocchi, Stefanos Apostle

и другие.

Nature Metabolism, Год журнала: 2022, Номер 4(9), С. 1150 - 1165

Опубликована: Сен. 12, 2022

Studies in genetically 'identical' individuals indicate that as much 50% of complex trait variation cannot be traced to genetics or the environment. The mechanisms generate this 'unexplained' phenotypic (UPV) remain largely unknown. Here, we identify neuronatin (NNAT) a conserved factor buffers against UPV. We find Nnat deficiency isogenic mice triggers emergence bi-stable polyphenism, where littermates emerge into adulthood either 'normal' 'overgrown'. Mechanistically, is mediated by an insulin-dependent overgrowth arises from histone deacetylase (HDAC)-dependent β-cell hyperproliferation. A multi-dimensional analysis monozygotic twin discordance reveals existence two patterns human UPV, one which (Type B) phenocopies NNAT-buffered polyphenism identified mice. Specifically, Type-B co-twins exhibit coordinated increases fat and lean mass across body; decreased NNAT expression; increased HDAC-responsive gene signatures; clinical outcomes linked insulinemia. Critically, UPV signature stratifies both childhood adult cohorts four metabolic states, including phenotypically molecularly distinct types obesity.

Язык: Английский

Процитировано

26
Role of Argonaute proteins in RNAi pathway in Plutella xylostella: A review DOI

Muhammad Salman Hameed,

Yanliang Ren, Midori Tuda

и другие.

Gene, Год журнала: 2024, Номер 903, С. 148195 - 148195

Опубликована: Янв. 29, 2024

Язык: Английский

Процитировано

5
A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle DOI
Belete Kuraz Abebe, Jianfang Wang, Juntao Guo

и другие.

Gene, Год журнала: 2024, Номер 908, С. 148295 - 148295

Опубликована: Фев. 21, 2024

Язык: Английский

Процитировано

4
Representation of non-coding RNA-mediated regulation of gene expression using the Gene Ontology DOI Creative Commons
Giulia Antonazzo, Pascale Gaudet, Ruth C. Lovering

и другие.

RNA Biology, Год журнала: 2024, Номер 21(1), С. 36 - 48

Опубликована: Окт. 7, 2024

Regulatory non-coding RNAs (ncRNAs) are increasingly recognized as integral to the control of biological processes. This is often through targeted regulation mRNA expression, but this by no means only mechanism which regulatory ncRNAs act. The Gene Ontology (GO) has long been used for systematic annotation protein-coding and ncRNA gene function, rapid progress in understanding meant that ontology needed be revised accurately reflect current knowledge. Here, a effort revise GO terms described, focusing on microRNAs (miRNAs), (lncRNAs), small interfering (siRNAs) PIWI-interacting (piRNAs). paper provides guidance biocurators annotating ncRNA-mediated processes using serves background researchers wishing make use their studies they regulate.

Язык: Английский

Процитировано

4
The Role of Deregulated MicroRNAs in Immune Cells of Sjögren’s Disease DOI Creative Commons

Qimao Han,

Lijuan Gao,

Lu Chen

и другие.

International Journal of General Medicine, Год журнала: 2025, Номер Volume 18, С. 847 - 855

Опубликована: Фев. 1, 2025

The 2024 Nobel Prize in Physiology or Medicine, awarded for the discovery of microRNAs (miRNAs) as essential regulators gene expression, has spotlighted their pivotal roles disease processes, including autoimmune conditions such Sjögren's (SD). SD is a chronic marked by lymphocytic infiltration exocrine glands, resulting significant glandular dysfunction and diverse systemic effects. Recent research revealed that miRNAs play crucial pathogenesis, orchestrating immune cell activity, epithelial integrity, regulation inflammatory pathways. Dysregulation specific associated with exacerbated responses, damage, dysfunction, sustained inflammation, positioning these small RNA molecules central players progression. This review synthesizes current findings on SD, highlighting how certain contribute to dysregulation, chronicity. Additionally, we explore potential biomarkers reflecting both health, novel therapeutic targets. By consolidating recent advancements, aim offer comprehensive perspective involvement underscore miRNA-based strategies transform diagnosis, management, treatment SD.

Язык: Английский

Процитировано

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