Transposable elements and the evolution of regulatory networks

By Cédric Feschotte. Nature reviews genetics, 2008

1,264 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/ec1af1861b5ac260bcfb592e54d4d348eb94b3e6

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Citations in the corpus

The rise of regulatory RNA (2014, background): “The raw material for evolution is gene duplication and transposition, the latter having the advantage of being able to mobilize functional cassettes in regulatory networks 302 , which appears to be the main driver of adaptive radiation 245,303 .”
Somatic retrotransposition alters the genetic landscape of the human brain (2011, background): “Apart from the obvious effects of exonic insertions, intronic events could act as subtle “transcriptional rheostats” 20 or as cis-regulatory elements 21 akin to the IAP insertion responsible for the viable yellow allele of Agouti in the mouse 22 .”
Endogenous viruses: insights into viral evolution and impact on host biology (2012, background): “Recently, several landmark studies have provided support to the four-decade-old hypothesis that mobile genetic elements had a pivotal role in the dispersion and turnover of transcription factor binding sites that coordinate gene regulatory networks in mammal”
Transposable elements have rewired the core regulatory network of human embryonic stem cells (2010, background): “We were interested in measuring whether this phenomenon was also a major contributing factor for the binding sites of OCT4, NANOG and CTCF in human embryonic stem cells because this could affect the regulation of neighboring gene”
The impact of retrotransposons on human genome evolution (2009, neutral): “Overall, it is striking that non-LTR retrotransposons seem to directly contribute a disproportionately small number of domesticated genes to genomes compared with other TEs (such as DNA transposons), despite the fact that they are the most numerous TEs in the human genom”
Epigenetically facilitated mutational assimilation: epigenetics as a hub within the inclusive evolutionary synthesis (2018, background): “When activated, TEs are important sources of genetic variation and genomic reorganization (Feschotte, 2008; Chenais et al., 2012; Stuart et al., 2017).”
Sequential regulatory activity prediction across chromosomes with convolutional neural networks (2017, background): “For example, processed consortium data discards multi-mapping read alignments, which leaves half the genome incompletely annotated, despite the substantial evidence that repetitive sequence is critical to gene regulation (Feschotte 2008) .”
Ever-changing landscapes: transcriptional enhancers in development and evolution (2016, background): “…throughout the genome via TE expansion, carrying with them cis-regulatory sequences that exploit the host trans environment for their transcription (Feschotte, 2008) and have the potential to acquire mutations that allow for their tissue-specific exaptation for host gene regulation (Bourque et…”
Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression (2012, positive): “The Impact of TEs and the piRNA Pathway on Gene Expression Many links have been made between TEs and the regulation of genes (Feschotte, 2008; Slotkin and Martienssen, 2007).”