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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}
}
Bourque, Guillaume; Burns, Kathleen H; Gehring, Mary; Gorbunova, Vera; Seluanov, Andrei; Hammell, Molly; Imbeault, Michaël; Izsvák, Zsuzsanna; Levin, Henry L; Macfarlan, Todd S; Mager, Dixie L; Feschotte, Cédric
Ten things you should know about transposable elements Journal Article
In: Genome Biology, vol. 19, no. 1, pp. 199, 2018, ISSN: 1474-760X.
Abstract | Links | BibTeX | Tags: Aicardi-Goutieres Syndrome, Endogenous Retroviruses (ERV), Human Endogenous Retroviruses (HERVs), Syncytin, transposable elements
@article{bourque_ten_2018,
title = {Ten things you should know about transposable elements},
author = {Guillaume Bourque and Kathleen H Burns and Mary Gehring and Vera Gorbunova and Andrei Seluanov and Molly Hammell and Michaël Imbeault and Zsuzsanna Izsvák and Henry L Levin and Todd S Macfarlan and Dixie L Mager and Cédric Feschotte},
url = {https://doi.org/10.1186/s13059-018-1577-z},
doi = {10.1186/s13059-018-1577-z},
issn = {1474-760X},
year = {2018},
date = {2018-01-01},
urldate = {2021-05-19},
journal = {Genome Biology},
volume = {19},
number = {1},
pages = {199},
abstract = {Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation. The rise of genomics and large-scale functional assays has shed new light on the multi-faceted activities of TEs and implies that they should no longer be marginalized. Here, we introduce the fundamental properties of TEs and their complex interactions with their cellular environment, which are crucial to understanding their impact and manifold consequences for organismal biology. While we draw examples primarily from mammalian systems, the core concepts outlined here are relevant to a broad range of organisms.},
keywords = {Aicardi-Goutieres Syndrome, Endogenous Retroviruses (ERV), Human Endogenous Retroviruses (HERVs), Syncytin, transposable elements},
pubstate = {published},
tppubtype = {article}
}
2017
Zhaohui Su, Guillaume Bourque
Retrotransposon-Derived Regulatory Regions and Transcripts in Stemness Journal Article
In: 2017.
Abstract | Links | BibTeX | Tags: Embryonic stem cells, ion, Long noncoding RNAs, transposable elements
@article{Su2017,
title = {Retrotransposon-Derived Regulatory Regions and Transcripts in Stemness},
author = {Zhaohui Su, Guillaume Bourque},
url = {https://link.springer.com/chapter/10.1007/978-3-319-48344-3_8#citeas},
doi = {DOI https://doi.org/10.1007/978-3-319-48344-3_8},
year = {2017},
date = {2017-01-04},
abstract = {Transposable elements (TEs) have contributed greatly to the regulatory landscape of many cell types, including to human embryonic stem cells. In this chapter we summarize recent studies that have shown that TE insertions have silenced nearby genes, introduced transcription factor-binding sites, as well as produced novel transcripts including those that are translated into viral particles and those that are functional as noncoding RNA. We focus on presenting results on human and other mammalian pluripotent stem cells because of their importance in studying human health and evolution. Finally we also discuss the applications, implications, and questions that are raised from this newfound knowledge.},
keywords = {Embryonic stem cells, ion, Long noncoding RNAs, transposable elements},
pubstate = {published},
tppubtype = {article}
}