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Approches in silico de l'impact des éléments transposables sur la régulation de l'expression des gènes.

Abstract : Plant genomes are populated by different types of repetitive elements including transposable elements (TEs) and simple sequence repeats (SSRs) that can have a strong impact on genome size and dynamic as well as on the regulation of gene transcription. At least two-thirds of the tomato genome is composed of repeats. While their bulk impact on genome organization has been largely revealed by whole genome assembly, their influence on tomato biology and phenotype remains largely unaddressed. More specifically, the effects and roles of DNA repeats on the maturation of fleshy fruit, which is a complex process of key agro-economic interest, still needs to be investigated comprehensively and tomato is arguably an excellent model for such study. We have performed a comprehensive annotation of the tomato repeatome to explore its potential impact on tomato genome composition and gene transcription. Our results show that the tomato genome can be fractioned into three compartments with different gene and repeat density, each compartment presenting contrasting repeat and gene composition, repeat-gene associations and different gene transcriptional levels. In the context of fruit ripening, we found that repeats are present in the majority of differentially methylated regions (DMRs) and thousands of repeat associated DMRs are found in the proximity of genes, including hundreds that are differentially regulated during this process. Furthermore, we found that repeats are also present in the proximity of DNA binding sites of the key ripening protein RIN. We also observed that some repeat families are present at unexpected high frequency in the proximity of genes that are differentially expressed during tomato ripening. Given the link between these different entities, we wondered whether it was possible that some transposable elements of the tomato genome were selected during evolution for their impact on the genome. To address this question, we have developed a series of analyzes to try to detect in silico such elements. A total of 36 transposable elements families were found to present empirical properties of selection, and some are associated with particular gene functions. More refined analyzes of the sequences could then potentially make it possible to discover motifs of interest, in particular for the transcriptional regulation of genes.
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  • HAL Id : tel-02516180, version 1


Ophélie Jouffroy. Approches in silico de l'impact des éléments transposables sur la régulation de l'expression des gènes.. Biologie moléculaire. Université Paris Saclay (COmUE), 2018. Français. ⟨NNT : 2018SACLA044⟩. ⟨tel-02516180⟩



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