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2018
Venuto, David; Bourque, Guillaume
Identifying co-opted transposable elements using comparative epigenomics Journal Article
In: Development, Growth & Differentiation, vol. 60, no. 1, pp. 53-62, 2018.
Abstract | Links | BibTeX | Tags: comparative epigenomics, epigenetics, functional genome, genomics, transposable elements
@article{https://doi.org/10.1111/dgd.12423,
title = {Identifying co-opted transposable elements using comparative epigenomics},
author = {David Venuto and Guillaume Bourque},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/dgd.12423},
doi = {https://doi.org/10.1111/dgd.12423},
year = {2018},
date = {2018-01-01},
journal = {Development, Growth & Differentiation},
volume = {60},
number = {1},
pages = {53-62},
abstract = {The human genome gives rise to different epigenomic landscapes that define each cell type and can be deregulated in disease. Recent efforts by ENCODE, the NIH Roadmap and the International Human Epigenome Consortium (IHEC) have made significant advances towards assembling reference epigenomic maps of various tissues. Notably, these projects have found that approximately 80% of human DNA was biochemically active in at least one epigenomic assay while only approximately 10% of the sequence displayed signs of purifying selection. Given that transposable elements (TEs) make up at least 50% of the human genome and can be actively transcribed or act as regulatory elements either for their own purposes or be co-opted for the benefit of their host; we are interested in exploring their overall contribution to the “functional” genome. Traditional methods used to identify functional DNA have relied on comparative genomics, conservation analysis and low throughput validation assays. To discover co-opted TEs, and distinguish them from noisy genomic elements, we argue that comparative epigenomic methods will also be important.},
keywords = {comparative epigenomics, epigenetics, functional genome, genomics, transposable elements},
pubstate = {published},
tppubtype = {article}
}
The human genome gives rise to different epigenomic landscapes that define each cell type and can be deregulated in disease. Recent efforts by ENCODE, the NIH Roadmap and the International Human Epigenome Consortium (IHEC) have made significant advances towards assembling reference epigenomic maps of various tissues. Notably, these projects have found that approximately 80% of human DNA was biochemically active in at least one epigenomic assay while only approximately 10% of the sequence displayed signs of purifying selection. Given that transposable elements (TEs) make up at least 50% of the human genome and can be actively transcribed or act as regulatory elements either for their own purposes or be co-opted for the benefit of their host; we are interested in exploring their overall contribution to the “functional” genome. Traditional methods used to identify functional DNA have relied on comparative genomics, conservation analysis and low throughput validation assays. To discover co-opted TEs, and distinguish them from noisy genomic elements, we argue that comparative epigenomic methods will also be important.