CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome

Abstract

The human genome contains millions of fragments from retrotransposons-highly repetitive DNA sequences that were once able to "copy and paste" themselves to other regions in the genome. However, the majority of retrotransposons have lost this capacity through acquisition of mutations or through endogenous silencing mechanisms. Without this imminent threat of transposition, retrotransposons have the potential to act as a major source of genomic innovation. Indeed, large numbers of retrotransposons have been found to be active in specific contexts: as gene regulatory elements and promoters for protein-coding genes or long noncoding RNAs, among others. In this review, we summarise recent findings about retrotransposons, with implications in gene expression regulation, the expansion of gene isoform diversity and the generation of long noncoding RNAs. We highlight key examples that demonstrate their role in cellular identity and their versatility as markers of cell states, and we discuss how their dysregulation may contribute to the formation of and possibly therapeutic response in human cancers.

Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes

“…Retrotransposon amplification threatens genome integrity through insertional mutations and chromosomal aberrations; consequently, defensive mechanisms evolved that suppress retrotransposons (for review, see Crichton et al 2014). Retrotransposons, however, can also provide functional gene parts, such as promoters, enhancers, exons, terminators, or splice junctions (for review, see de Souza et al 2013;Gerdes et al 2016;Göke and Ng 2016;Thompson et al 2016). Retrotransposons thus explore the space where their mutagenic potential coexists with other occasional contributions to gene expression.…”

Whole Genome Sequencing and Assembly of the Asian Honey BeeApis dorsata

“…First, there were 28 genes with Ty1/copia-like retrotransposon signatures. The "domestication" of transposable elements can lead to the emergence of species-specific genes by providing a source of biochemically active elements such as transcription factor-binding sites, and by generating genomic rearrangements [35][36][37][38], and the over-representation of transposable element-related signatures in the genome of A. dorsata, suggests that the evolution of "new" genes may have played a role in the behavioral diversification of A. dorsata from other honeybees.…”

The involvement of human endogenous retroviruses K (HERV-K) in aging processes via induction of inflammation

“…Long non-coding RNAs (lncRNAs) are key regulators of gene expression at the epigenetic level. A significant part of lncRNAs have promoters of retroviral origin (Göke and Ng, 2016). LncRNAs control DNA methylation through direct physical interactions between lncRNAs and DNA methyltransferases (DNMTs) [32], (Law & Jacobsen, 2010).…”