Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?

Lannes, Romain; Rizzon, Carène; Lerat, Emmanuelle

doi:10.3390/genes10030249

Cited by 8 publications

(8 citation statements)

References 82 publications

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“…In many previous reports, influence of transposable elements on the development of epigenetic regulatory networks has been documented. For example, as learned from the analysis of evolution of duplicated genes in human DNA, the key factor influencing the regulatory epigenetic landscape is the presence of transposable elements [43].…”

Section: Discussionmentioning

confidence: 99%

H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks

Igolkina

Zinkevich

Карандашева

et al. 2019

Cells

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Background: Transposons are selfish genetic elements that self-reproduce in host DNA. They were active during evolutionary history and now occupy almost half of mammalian genomes. Close insertions of transposons reshaped structure and regulation of many genes considerably. Co-evolution of transposons and host DNA frequently results in the formation of new regulatory regions. Previously we published a concept that the proportion of functional features held by transposons positively correlates with the rate of regulatory evolution of the respective genes. Methods: We ranked human genes and molecular pathways according to their regulatory evolution rates based on high throughput genome-wide data on five histone modifications (H3K4me3, H3K9ac, H3K27ac, H3K27me3, H3K9me3) linked with transposons for five human cell lines. Results: Based on the total of approximately 1.5 million histone tags, we ranked regulatory evolution rates for 25075 human genes and 3121 molecular pathways and identified groups of molecular processes that showed signs of either fast or slow regulatory evolution. However, histone tags showed different regulatory patterns and formed two distinct clusters: promoter/active chromatin tags (H3K4me3, H3K9ac, H3K27ac) vs. heterochromatin tags (H3K27me3, H3K9me3). Conclusion: In humans, transposon-linked histone marks evolved in a coordinated way depending on their functional roles.

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Section: Discussionmentioning

confidence: 99%

H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks

Igolkina

Zinkevich

Карандашева

et al. 2019

Cells

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“…Growing evidence suggests that epigenetic mechanisms are involved in the regulation of duplicated gene transcription [ 57 , 58 , 59 , 60 , 61 ]. TEs have been found to affect the epigenetic status of duplicate genes [ 62 ], however, how TE-derived ACRs function in the regulation of duplicated genes in rice remains unclear. To answer this question, we chose ATAC-seq data from the stamen and pistil (SP) for analyses because it has the most ACRs among the six tissues.…”

Section: Resultsmentioning

confidence: 99%

Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (Oryza Sativa)

Zhang

2022

IJMS

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Growing evidence indicates that transposons or transposable elements (TEs)-derived accessible chromatin regions (ACRs) play essential roles in multiple biological processes by interacting with trans-acting factors. However, the function of TE-derived ACRs in the regulation of gene expression in the rice genome has not been well characterized. In this study, we examined the chromatin dynamics in six types of rice tissues and found that ~8% of ACRs were derived from TEs and exhibited distinct levels of accessibility and conservation as compared to those without TEs. TEs exhibited a TE subtype-dependent impact on ACR formation, which can be mediated by changes in the underlying DNA methylation levels. Moreover, we found that tissue-specific TE-derived ACRs might function in the tissue development through the modulation of nearby gene expression. Interestingly, many genes in domestication sweeps were found to overlap with TE-derived ACRs, suggesting their potential functions in the rice domestication. In addition, we found that the expression divergence of 1070 duplicate gene pairs were associated with TE-derived ACRs and had distinct distributions of TEs and ACRs around the transcription start sites (TSSs), which may experience different selection pressures. Thus, our study provides some insights into the biological implications of TE-derived ACRs in the rice genome. Our results imply that these ACRs are likely involved in the regulation of tissue development, rice domestication and functional divergence of duplicated genes.

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“…Moreover, the relationship between TEs and epigenetic control is two-way, and if DNA hypomethylation is a cause of TE activation, the presence of TEs in a genomic region is also a cause of chromatin hypermethylation. Thus, epigenetic modification of TE regulatory sequences can impact the expression of neighboring genes [ 25 , 26 , 27 ].…”

Section: Te Insertion and Its Consequences On The Genome And Gene Exp...mentioning

confidence: 99%

Transposable Elements and Human Diseases: Mechanisms and Implication in the Response to Environmental Pollutants

Chénais

2022

IJMS

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Transposable elements (TEs) are recognized as major players in genome plasticity and evolution. The high abundance of TEs in the human genome, especially the Alu and Long Interspersed Nuclear Element-1 (LINE-1) repeats, makes them responsible for the molecular origin of several diseases. This involves several molecular mechanisms that are presented in this review: insertional mutation, DNA recombination and chromosomal rearrangements, modification of gene expression, as well as alteration of epigenetic regulations. This literature review also presents some of the more recent and/or more classical examples of human diseases in which TEs are involved. Whether through insertion of LINE-1 or Alu elements that cause chromosomal rearrangements, or through epigenetic modifications, TEs are widely implicated in the origin of human cancers. Many other human diseases can have a molecular origin in TE-mediated chromosomal recombination or alteration of gene structure and/or expression. These diseases are very diverse and include hemoglobinopathies, metabolic and neurological diseases, and common diseases. Moreover, TEs can also have an impact on aging. Finally, the exposure of individuals to stresses and environmental contaminants seems to have a non-negligible impact on the epigenetic derepression and mobility of TEs, which can lead to the development of diseases. Thus, improving our knowledge of TEs may lead to new potential diagnostic markers of diseases.

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Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?

Cited by 8 publications

References 82 publications

H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks

H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks

Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (Oryza Sativa)

Transposable Elements and Human Diseases: Mechanisms and Implication in the Response to Environmental Pollutants

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