TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

Lerat, Emmanuelle; Fablet, Marie; Modolo, Laurent; Lopez-Maestre, Hélène; Vieira, Cristina

doi:10.1093/nar/gkw953

Cited by 98 publications

(123 citation statements)

References 66 publications

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“…Several recent studies have shown that using both uniquely mapped reads and multimapped reads to quantify TEs might introduce biases in expression (Lerat et al 2017;Jin et 22 al. 2015;Criscione et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Atlas of transcriptionally active transposable elements in human adult tissues

Bogu

Reverter

Martí‐Renom

et al. 2019

Preprint

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Approximately half of the human genome consists of mobile repetitive DNA sequences known as transposable elements (TEs). They are usually silenced by epigenetic mechanisms, but a few are known to escape silencing at embryonic stages, affecting early human development by regulating nearby protein-coding genes. To investigate transcriptional activity in human adult tissues we systematically investigate the expression landscape of about 4.2 million non-coding TEs in 8,051 RNA-Seq datasets from up to 49 adult tissues and 540 individuals. We show that approximately 79,558 individual TEs (2%).belonging to 856 subfamilies escape epigenetic silencing in adult tissues and become transcriptionally active, often in a very tissue-specific manner. Supporting a role for TEs in the regulation of expression of nearby genes, we found the expression of TEs often correlated with the expression of nearby genes, and significantly stronger when the TEs include eQTLs for the genes. We identified thousands of tissue-elevated, sex-associated TEs in the breast, ethnicity-associated in the skin and age-associated in the tibial artery, where we found a potential implication of two TE subfamilies in atherosclerosis. Our results suggest a functional role of TEs in the regulation of gene expression, support their implication in human phenotypes, and also serve as a comprehensive resource of transcriptionally active TEs in human adult tissues.

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Section: Discussionmentioning

confidence: 99%

Atlas of transcriptionally active transposable elements in human adult tissues

Bogu

Reverter

Martí‐Renom

et al. 2019

Preprint

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“…Disentangling epigenetic from genetic variability is becoming easier but remains a very challenging problem, in particular if TEs are accounted for. We envision studies that do a better job of quantifying genome size, the percentage of the genome made up of TEs and the total number of small TE variations (Goubert et al, ; Lerat, Fablet, Modolo, Lopez‐Maestre, & Vieira, ). This could be done by simulating genomes with different TE amounts and using software like dnaPipeTE (Goubert et al, ) for which no reference genome is needed.…”

Section: Discussionmentioning

confidence: 99%

Biological invasion: The influence of the hidden side of the (epi)genome

et al. 2019

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Understanding the mechanisms underlying biological invasions and rapid adaptation to global change remains a fundamental challenge, particularly in small populations lacking in genetic variation. Two understudied mechanisms that could facilitate adaptive evolution and adaptive plasticity are the increased genetic variation due to transposable elements (TEs), and associated or independent modification of gene expression through epigenetic changes. Here, we focus on the potential role of these genetic and non‐genetic mechanisms for facilitating invasion success. Because novel or stressful environments are known to induce both epigenetic changes and TE activity, these mechanisms may play an underappreciated role in generating phenotypic and genetic variation for selection to act on. We review how these mechanisms operate, the evidence for how they respond to novel or stressful environments, and how these mechanisms can contribute to the success of biological invasions by facilitating adaptive evolution and phenotypic plasticity. Because genetic and phenotypic variations due to TEs and epigenetic changes are often well regulated or “hidden” in the native environment, the independent and combined contribution of these mechanisms may only become important when populations colonize novel environments. A focus on the mechanisms that generate and control the expression of this variation in new environments may provide insights into biological invasions that would otherwise not be obvious. Global changes and human activities impact on ecosystems and allow new opportunities for biological invasions. Invasive species succeed by adapting rapidly to new environments. The degree to which rapid responses to environmental change could be mediated by the epigenome—the regulatory system that integrates how environmental and genomic variation jointly shape phenotypic variation—requires greater attention if we want to understand the mechanisms by which populations successfully colonize and adapt to new environments. A free Plain Language Summary can be found within the Supporting Information of this article.

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“…Genes with q-values lower than 0.05 and log2FC above 0.5 were considered as differentially expressed. TE differential expression was analyzed using TETOOLs (Lerat et al , 2016).…”

Section: Methodsmentioning

confidence: 99%

Mild drought induces phenotypic and DNA methylation plasticity but no transgenerational effects in Arabidopsis

Dooren¹,

Silveira²,

Gilbault³

et al. 2018

Preprint

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SummaryWhether environmentally induced changes in phenotypes can be heritable is a topic with revived interest, in part because of observations in plants that heritable trait variation can occur without DNA sequence mutations. This other system of inheritance, called transgenerational epigenetics, typically involves differences in DNA methylation that are stable across multiple generations. However, it remains unknown if such a system responds to environmental changes and if it could therefore provide a rapid way for plants to generate adaptive heritable phenotypic variation. Here, we used a well-controlled phenotyping platform and whole-genome bisulfite sequencing to investigate potential heritable effects of mild drought applied over two successive generations in Arabidopsis thaliana. Plastic phenotypic responses were observed in plants exposed to drought. After an intervening generation without stress, descendants of stressed and non-stressed plants were phenotypically indistinguishable, except for very few trait-based parental effects, and irrespective of whether they were grown in control conditions or under water deficit. Moreover, while mild drought induced changes to the DNA methylome of exposed plants, DNA methylation variants were not inherited. These findings add to the growing body of evidence indicating that transgenerational epigenetics is not a common response of plants to environmental changes.

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TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

Cited by 98 publications

References 66 publications

Atlas of transcriptionally active transposable elements in human adult tissues

Atlas of transcriptionally active transposable elements in human adult tissues

Biological invasion: The influence of the hidden side of the (epi)genome

Mild drought induces phenotypic and DNA methylation plasticity but no transgenerational effects in Arabidopsis

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