Regulatory activities of transposable elements: from conflicts to benefits

By Edward B. Chuong, Nels C. Elde, Cédric Feschotte. Nature reviews genetics, 2016

1,231 citations recorded by the source corpus.

Transposable elements (TEs) are a prolific source of tightly regulated, biochemically active non-coding elements, such as transcription factor-binding sites and non-coding RNAs. Many recent studies reinvigorate the idea that these elements are pervasively co-opted for the regulation of host genes. We argue that the inherent genetic properties of TEs and the conflicting relationships with their hosts facilitate their recruitment for regulatory functions in diverse genomes. We review recent findings supporting the long-standing hypothesis that the waves of TE invasions endured by organisms for eons have catalysed the evolution of gene-regulatory networks. We also discuss the challenges of dissecting and interpreting the phenotypic effect of regulatory activities encoded by TEs in health and disease.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/a6dd2bd298ba89fcd4c57fb22ffc69b86acd8324

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Citations in the corpus

KRAB zinc finger proteins (2017, background): “…changed this view, and it is increasingly recognized that some TEs are crucial components of transcriptional regulatory networks that play essential roles not only in the evolution but also the biology of most organisms (Garcia-Perez et al., 2016; Chuong et al., 2017; Thompson et al., 2016).”
Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution. (2019, background): “Most LINEs have acquired a vast number of mutations, some of which have created new functional elements, such as enhancers, promoters, or exons (Chuong et al., 2017).”
A complete Cannabis chromosome assembly and adaptive admixture for elevated cannabidiol (CBD) content (2018, methodology): “20 For all Illumina data we trimmed reads of adapter sequence with Trimmomatic (12), aligned them to the reference assembly with BWA MEM (13), sorted and compressed the alignments with Samtools (14), and marked duplicates with Picard tools (15).”
DNA methylation aging clocks: challenges and recommendations (2019, background): “Repetitive regions possess latent functionality [152, 153], however are robustly epigenetically repressed by DNA methylation [151, 154, 155].”