Rewiring of chromatin state and gene expression by transposable elements

Abstract

Transposable elements form a major fraction of the genome in various eukaryotic species. Although deleterious effects of transpositions within the genome have been reported, recent findings suggest that transposable elements can function as novel regulatory elements to fine‐tune gene expression. Transposable elements can impact the chromatin state through processes such as heterochromatin formation, enhancer–promoter interactions, and chromatin boundary formation, mainly because of the functions of chromatin‐based pathways that regulate the expression of transposable elements via DNA methylation and repressive histone modification. Therefore, transposable elements can rewire the chromatin state and gene expression depending on their insertions. Here, we review the findings that reveal the role of transposable elements as modifiers of the chromatin state and gene expression as well as the molecular mechanisms capable of inducing these changes.

Copy number variation introduced by a massive mobile element underpins global thermal adaptation in a fungal wheat pathogen

“…Surprisingly, the Swordfish element resides within a highly conserved region across sister species and neighbors the gene VeltB , which is a key regulator of reproduction, metabolism and growth processes in fungi 102 . The strong epigenetic repression across the entire Swordfish element is consistent with the strong repression of TE activity immediately adjacent to a transcriptionally open and conserved region of the chromosome 152 . We hypothesize that this Starship likely inserted itself at this locus after the emergence of the species, followed by a complex set of duplications and transposition events facilitated by high TE activity in the region.…”

R-loop landscape in mature human sperm: Regulatory and evolutionary implications

“…TEs constitute a major part of primate genomes, and thus, intronic sequences. With the likely detrimental effect of insertional mutagenesis into exonic sequences, reduced evolutionary constraints hold for introns, although TEs shape the function of their corresponding introns by triggering differential splicing, premature stop codons and maintaining an open chromatin state ( Cordaux and Batzer, 2009 ; Zhang et al, 2011 ; Ohtani and Iwasaki, 2021 ). Therefore, in particular larger TEs such as composite retroposons, for example, SVAs, and LINEs are more likely to be conserved in introns and intergenic regions as compared to TE insertions in coding sequences.…”

A butterfly pan-genome reveals a large amount of structural variation underlies the evolution of chromatin accessibility

“…In several studies, TEs have been correlated to evolutionary changes in chromatin state, gene expression, and adaptive evolution at a genome-wide scale (Bourque et al 2018; Diehl et al 2020; Ohtani and Iwasaki 2021; Liu et al 2019). The TE family composition of TEs that associated with open ATAC-seq peaks was markedly different between the three Heliconius species (Figure S4).…”

“…Another TE insertion has been linked to the silencing of a cortex regulatory region and may be responsible for the yellow band on the hindwing in geographic variants of Heliconius melpomene butterflies (Livraghi et al 2021). In several studies, TEs have been correlated to evolutionary changes in chromatin state, gene expression, and adaptive evolution at a genome-wide scale (Bourque et al 2018;Diehl et al 2020;Ohtani and Iwasaki 2021;Liu et al 2019). The TE family composition of TEs that associated with open ATAC-seq peaks was markedly different between the three Heliconius species (Figure S4).…”