Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots

PLANT PHYSIOLOGY, Journal Year: 2023, Volume and Issue: 193(3), P. 1933 - 1953

Published: June 22, 2023

Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in plant genomes. While some lincRNAs characterized as important regulators different biological processes, little is known about the transcriptional regulation for most lincRNAs. Through integration 8 annotation resources, we defined 6,599 high-confidence lincRNA loci Arabidopsis (Arabidopsis thaliana). For belonging to evolutionary age categories, major differences sequence and chromatin features, well level conservation purifying selection acting during evolution. Spatiotemporal gene expression profiles combined with transcription factor (TF) immunoprecipitation (ChIP) data were used construct a TF-lincRNA regulatory network containing 2,659 15,686 interactions. We found that properties characterizing expression, conservation, differ between plants animals. Experimental validation confirmed role 3 TFs, KANADI 1, MYB DOMAIN PROTEIN 44, PHYTOCHROME INTERACTING FACTOR 4, key controlling root-specific demonstrating predictive power our network. Furthermore, 58 lincRNAs, regulated by these showing strong root cell type-specific or accessibility, which are linked genome-wide association studies genetic associations related system development growth. The multilevel characterization covering state information, promoter immunoprecipitation-based TF binding, all detectable across 769 samples, permits rapidly defining context relevance through networks.

Language: Английский

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Transposon-triggered epigenetic chromatin dynamics modulate EFR-related pathogen response

Nature Structural & Molecular Biology, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 27, 2024

Infectious diseases drive wild plant evolution and impact crop yield. Plants, like animals, sense biotic threats through pattern recognition receptors (PRRs). Overly robust immune responses can harm plants; thus, understanding the tuning of defense response mechanisms is crucial for developing pathogen-resistant crops. In this study, we found that an inverted-repeat transposon (EFR-associated IR, Ea-IR) located between loci encoding PRRs ELONGATION FACTOR-TU RECEPTOR (EFR) myosin XI-k (XI-k) in Arabidopsis affects chromatin organization, promoting formation a repressive loop. Upon pathogen infection, changes around EFR correlate with increased transcription. Pathogen-induced opening causes RNA polymerase II readthrough, producing longer, Ea-IR-containing transcript, processed by Dicer-like enzymes into small RNAs, which reset to state attenuating after infection. accessions lacking Ea-IR have higher basal levels resistance pathogens. We show scenario transposon, organization gene expression interact fine-tune responses, during both course infection evolution. Here, authors next receptor (EFR)-encoding controls response.

Language: Английский

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Genetic and epigenetic control of the plant metabolome

PROTEOMICS, Journal Year: 2023, Volume and Issue: 23(13-14)

Published: Feb. 14, 2023

Plant metabolites are mainly produced through chemical reactions catalysed by enzymes encoded in the genome. Mutations enzyme-encoding or transcription factor-encoding genes can alter metabolome changing enzyme's catalytic activity abundance, respectively. Insertion of transposable elements into non-coding regions has also been reported to affect and ultimately metabolite content. In addition genetic mutations, transgenerational epigenetic variations have found metabolic content controlling metabolism-related genes. However, majority cases so far, which mechanisms associated with metabolism, non-transgenerational, triggered developmental signals environmental stress. Although, accumulating research provided evidence strong control metabolome, largely untouched. Here, we provide a review metabolism focus on epigenetics. We discuss both non-transgenerational marks regulating as well prospects field where intricate interactions between genetics epigenetics involved.

Language: Английский

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The MVPs (masterful versatile players): Chromatin factors as pivotal mediators between 3D genome organization and the response to environment

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 81, P. 102599 - 102599

Published: July 10, 2024

In recent years, the study of genome dynamics has become a prominent research field due to its influence on understanding control gene expression. The 3D organization unveiled multiple mechanisms in orchestrating chromosome folding. Growing evidence reveals that these are not only important for organization, but play pivotal role enabling plants adapt environmental stimuli. this review, we provide an overview current knowledge concerning epigenetic factors and regulatory elements driving their responses external We discuss most findings, previous evidence, explore implications future research.

Language: Английский

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Noncoding RNA-Mediated Regulation of DNA Methylation: Insights into Plant Epigenetic Mechanisms

Journal of Plant Growth Regulation, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 25, 2024

Language: Английский

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