Crossroads between transposons and gene regulation

Abstract

Transposons are mobile genetic elements that have made a large contribution to genome evolution in a largely species-specific manner. A wide variety of different transposons have invaded genomes throughout evolution, acting in a first instance as ‘selfish’ elements, whose success was determined by their ability to self-replicate and expand within the host genome. However, their coevolution with the host has created many crossroads between transposons and the regulation of host gene expression. Transposons are an abundant source of transcriptional modulatory elements, such as gene promoters and enhancers, splicing and termination sites, and regulatory non-coding RNAs. Moreover, transposons have driven the evolution of host defence mechanisms that have been repurposed for gene regulation. However, dissecting the potential functional roles of transposons remains challenging owing to their evolutionary path, as well as their repetitive nature, which requires the development of specialized analytical tools. In this special issue, we present a collection of articles that lay out current paradigms in the field and discuss a vision for future research. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

Evolutionary Pathways and Trajectories in Antibiotic Resistance

“…In any case, it remains true that the same type of MGE tends to be associated with the same type of host (945). Historical coexistence with MGEs has likely contributed to speciation (or at least with the gene regulatory mechanisms that impose "styles of life") in a particular ancient host (946). It is not surprising that mobility and maintenance should be more effective within particular speciesPlasmid stabilization is likely to occur in a bacterial host, mediated by different mechanisms, such as mutations in a replication protein gene, acquisition by the resistance plasmid of a transposon from a co-residing plasmid encoding a putative TA system, and a previous mutation in the host's global transcriptional regulation genes (551).…”

Evolutionary Pathways and Trajectories in Antibiotic Resistance

“…In any case, it remains true that the same type of MGE tends to be associated with the same type of host (945). Historical coexistence with MGEs has likely contributed to speciation (or at least with the gene regulatory mechanisms that impose "styles of life") in a particular ancient host (946). It is not surprising that mobility and maintenance should be more effective within particular speciesPlasmid stabilization is likely to occur in a bacterial Integrons are extremely ancient groups of elements with low basic diversity (only three main classes associated with broad bacterial taxons but with many variants) and widespread chromosomal elements.…”

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

“…Although the genome-wide distribution patterns of SVs and TEs seems to resemble that of SNPs, we next wanted to investigate the functional and adaptive significance of lineage-specific intergenic SVs. TEs, for example, have been suggested to be important genomic material for cis -regulatory element evolution (Branco and Chuong 2020; Pontis et al 2019; Fueyo et al 2022). To test this, we studied the genomic distribution of potential cis -regulatory elements (CREs) using Assays for Transposase-Accessible Chromatin using sequencing (ATAC-seq) (Buenrostro et al 2013).…”