Plant Epigenomics

Furci, Leonardo; Berthelier, Jérémy; Juez, Oscar; Miryeganeh, Matin; Saze, Hidetoshi

doi:10.1016/b978-0-323-91909-8.00007-4

Cited by 3 publications

(4 citation statements)

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“…Next, we investigated the potential impact of TE indels located within or close to genes. For instance, de novo TE insertions can drive change in the host phenotype by affecting genes [ 35 , 36 , 41 ]. In TisoArg, 37 TE indels were located within or close (±1,000 bp) to 57 genes.…”

Section: Resultsmentioning

confidence: 99%

“…TEs are known to be major actors in the genome evolution of organisms and can give rise to new phenotypes by impacting gene expression or function [ 35 , 36 , 41 ]. Because potential autonomous TEs were characterized in T .…”

Section: Discussionmentioning

confidence: 99%

“…In eukaryotes, TEs are commonly grouped into two classes according to their mechanism of mobility: class I retrotransposons move by a copy-paste mechanism via RNA intermediaries; class II DNA transposons move by cut-paste mechanisms [ 34 ]. Although TE indels are mostly harmful or neutral to the host, they can also participate in the rise of evolved phenotypic traits [ 35 , 36 ]. For plant crops, TEs have been found to promote various domesticated traits [ 35 , 37 , 38 ].…”

Section: Introductionmentioning

confidence: 99%

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Phenotype stability and dynamics of transposable elements in a strain of the microalga Tisochrysis lutea with improved lipid traits

et al. 2023

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Microalgal domestication is an expanding research field that aims to multiply and accelerate the potential of microalgae for various biotechnological purposes. We investigated the stability of improved lipid traits and genetic changes of a domesticated strain of the haptophyte Tisochrysis lutea, TisoS2M2, previously obtained by a mutation-selection improvement program. After 7 years of maintenance, TisoS2M2 still displayed improved lipid traits compared with the native strain, demonstrating that a mutation-selection improvement program is suitable for obtaining a domesticated strain with stable, improved phenotype over time. We identified specific genetic variations between the native and domesticated strains and focused on the dynamics of transposable elements (TEs). DNA transposons mainly caused specific TE indels of the domesticated strain TisoS2M2, and some specific TE indels may have impacted genes associated to the neutral lipid pathway. We revealed transposition events for TEs in T. lutea and discussed on the potential role of the improvement program on their activity.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phenotype stability and dynamics of transposable elements in a strain of the microalga Tisochrysis lutea with improved lipid traits

et al. 2023

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“…Transposable elements (TEs) are major components of eukaryotic genomes, influencing the organization of chromosome structure and expansion of genome size 1,2 . TEs can insert into intragenic regions of gene units, including promoter, 5’/3’-untranslated regions (UTRs), exons, and introns, impacting both genetic and epigenetic regulation of gene transcription and transcriptome diversity 3 . For example, TEs can act as regulatory elements of nearby genes in response to environmental stresses 4–6 .…”

Section: Introductionmentioning

confidence: 99%

Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana

Berthelier

Furci

Asai

et al. 2022

Preprint

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Transposable elements (TEs) are accumulated in both intergenic and intragenic regions in plant genomes. Intragenic TEs often act as regulatory elements of associated genes, and are also co-transcribed with genes, generating chimeric TE-gene transcripts. Despite its potential impacts on mRNA regulation and gene function, the prevalence and transcriptional regulation of TE-gene transcripts remain elusive. By the long-read Direct RNA Sequencing (DRS) and a dedicated bioinformatic pipeline ParasiTE, we investigated transcription and RNA processing of TE-gene transcripts in Arabidopsis thaliana. We identified that thousands of Arabidopsis gene loci generate TE-gene transcripts, where in many loci TEs are associated with alternative Transcription Start Sites (ATSS) or Transcription Termination Sites (ATTS). Epigenetic state of intragenic TE affects PolII elongation and usage of alternative polyA signals in TE sequences, regulating alternative TE-gene isoform production. Co-transcription and inclusion of TE-derived sequence into gene transcripts impacts regulation of RNA stability and environmental responses in some loci. Our study provides novel insights into TE-gene interaction that contributes to mRNA regulation and transcriptome diversity in plants.

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Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana

et al. 2023

Self Cite

View full text Add to dashboard Cite

Transposable elements (TEs) are accumulated in both intergenic and intragenic regions in plant genomes. Intragenic TEs often act as regulatory elements of associated genes and are also co-transcribed with genes, generating chimeric TE-gene transcripts. Despite the potential impact on mRNA regulation and gene function, the prevalence and transcriptional regulation of TE-gene transcripts are poorly understood. By long-read direct RNA sequencing and a dedicated bioinformatics pipeline, ParasiTE, we investigated the transcription and RNA processing of TE-gene transcripts in Arabidopsis thaliana. We identified a global production of TE-gene transcripts in thousands of A. thaliana gene loci, with TE sequences often being associated with alternative transcription start sites or transcription termination sites. The epigenetic state of intragenic TEs affects RNAPII elongation and usage of alternative poly(A) signals within TE sequences, regulating alternative TE-gene isoform production. Co-transcription and inclusion of TE-derived sequences into gene transcripts impact regulation of RNA stability and environmental responses of some loci. Our study provides insights into TE-gene interactions that contributes to mRNA regulation, transcriptome diversity, and environmental responses in plants.

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Plant Epigenomics

Cited by 3 publications

References 284 publications

Phenotype stability and dynamics of transposable elements in a strain of the microalga Tisochrysis lutea with improved lipid traits

Phenotype stability and dynamics of transposable elements in a strain of the microalga Tisochrysis lutea with improved lipid traits

Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana

Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana

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