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'Jumping genes' help plants adapt to extreme temperature and pathogens

'Jumping genes' help plants adapt to extreme temperature and pathogens
Epigenetic regulation of TE-ATTS. a Representative genome loci showing Epi-ATE-G isoform production with TE-ATTS events. Tracks (from top to bottom): ChIP-seq data for RNA Pol II phosphorylated at Ser5/Ser2 in CTD repeats (bins per million); ChIP-seq data for IBM2 and EDM2 localization (bins per million); Col-0 ChIP-seq of H3K9me2 (reads per million); methylation levels of Col-0 in CG, CHG, and CHH contexts (0–100%); poly(A) sites obtained from the PlantAPA database; DRS read alignments of Col-0 and indicated mutants; TE and transcript annotations of AtRTD3 and DRS-AtRTD3 in this study and the orientation of genes and TEs. b Metaplots for ChIP-seq signals of Pol II (Ser2P), IBM2, EDM2, and H3K9me2 over TEs with ATTS (isoform switching with q < 0.05 detected at least once among mutants; Supplementary Data 5; n = 223) or randomly selected TEs (n = 223). c Changes in Pol II (Ser2P) ChIP-seq signals in TEs with ATTS (n = 223) between the wild-type and mutants. The centerline represents the median. The borders of the boxplots are the first and third quartiles (Q1 and Q3). Whiskers represent data range, bounded to 1.5 * (Q3-Q1). Credit: Nature Communications (2023). DOI: 10.1038/s41467-023-38954-z

Jumping genes, or transposons, are sections of DNA that can copy themselves and jump between different parts of the genome, and might help plants adapt to stressful, changing conditions, according to a study published in Nature Communications on June 5, 2023.

Using a cutting-edge sequencing technique, researchers from the Okinawa Institute of Science and Technology (OIST) and the Center for Sustainable Resource Science, RIKEN found that Arabidopsis thaliana, a plant used as a model for scientific research, expresses thousands of hybrids between regular and . The plant alters the expression of these hybrid genes in response to such as excessive heat, or pathogens. These findings could contribute to the development of new crops that can better cope with stressful environments.

Regulation of gene expression (in other words, how a cell controls which genes are active) is vital for the correct functioning of all living things. When genes are expressed, genetic instructions are converted from DNA into RNA transcripts, ensuring useful products like proteins are made at the right time and in the right place.

Typically, plants and animals also use to suppress the activity of transposons, says Dr. Jeremy Berthelier, lead author of the study and post-doctoral researcher in the Plant Epigenetics Unit. "Transposons can be damaging, as these sections of DNA can insert themselves into genes and cause harmful mutations."

However, in this new study, the scientists found that Arabidopsis thaliana expresses thousands of RNA transcripts that are hybrids of regular genes and transposons. These hybrid RNA molecules, called gene-transposon transcripts, occur when transposons jump near or within a gene, and are then expressed together.

'Jumping genes' help plants adapt to extreme temperature and pathogens
From left to right: Professor Hidetoshi Saze, Dr. Leonardo Furci, Dr. Jeremy Berthelier and Munissa Sadykova. Credit: Okinawa Institute of Science and Technology

The researchers identified these transcripts using a cutting-edge method called Direct RNA Sequencing that can read long RNA sequences. They then used a computational tool they developed, called ParasiTE, to classify the gene-transposon transcripts, based on the effect that the transposon had on the gene.

The researchers then conducted a systematic study of how environmental stresses affect gene-transposon transcripts. They found that a transposon called ONSEN, caused a change in expression of its associated gene, GER5, in response to excessive heat.

Another finding relates to a gene called RPP4, which produces a protein that helps A. thaliana fight against pathogen infections. The researchers found that suppressing expression of the gene-transposon transcripts of the RPP4 gene affects the plant's resistance to pathogens.

Gene-transposon transcripts can therefore help plant adapt to environmental stresses and changing environmental conditions.

"The broader implications of the study are that transposons can regulate their associated genes in a sophisticated way, by changing their DNA sequence and modulating their expression and stability. This may be very important for plant life, and their response to changing environmental conditions, such as or to pathogens," says Dr. Berthelier.

The study could also prove to be useful for developing resilient crops. Professor Hidetoshi Saze, senior author of the study and head of the Plant Epigenetic Unit at OIST, says, "We can now study other plants that are important crop species. We could find even more genes which have -dependent regulation and target these genes for editing, to make more productive crops for cultivation."

More information: Jérémy Berthelier et al, Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana, Nature Communications (2023). DOI: 10.1038/s41467-023-38954-z

Journal information: Nature Communications

Citation: 'Jumping genes' help plants adapt to extreme temperature and pathogens (2023, June 15) retrieved 15 April 2024 from
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