The Cis-Regulatory Impact of Transposable Elements on Gene Expression

Transposable Elements (TEs) can insert into genes or in their close vicinity without necessarily interrupting the protein functions that they encode. However, the proximity of a TE to an adjacent gene can lead to complex and biologically relevant changes to the transcriptional regulation of this gene. With many recent studies of genomes, epigenomes and transcriptomes from various organisms, the field is now appreciating the diversity of TE landscapes and how TEs contribute to shaping the diversity of transcripts among individuals, during development or in response to the environment. This Collection aims at exploring the various facets by which TEs can impact the expression of genes beyond the simple disruption of their protein-coding capacity, through compilation of new and original results on species across the tree of life, including cultivated organisms and natural populations. The Collection aims to gather research articles providing original results on the biological effects of TE insertions on nearby genes, genome-wide or for specific loci, addressing notably the following themes: TE dynamics and their contribution as gene promoters, enhancers or silencers TE contribution to the rewiring of gene regulatory networks Impact of silencing pathways impairment on TE chromatin and collateral effect on transcriptional regulation of adjacent genes New TE insertions (through natural or engineered movement) and dissection of their effect on adjacent gene transcription Characterization of TE-binding transcription factors and impact of their genetic mutation on gene transcriptional modification Bioinformatics, biostatistics and molecular biology methodologies to assess the effect of TEs on nearby gene transcriptional regulation