Ewing, Adam D; Smits, Nathan; Sanchez-Luque, Francisco J; Faivre, Jamila; Brennan, Paul M; Richardson, Sandra R; Cheetham, Seth W; Faulkner, Geoffrey J Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling (Journal Article) Molecular Cell, 2020, ISSN: 1097-2765. (Abstract | Links | BibTeX | Altmetric) @article{ewing_nanopore_2020,
title = {Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling},
author = {Adam D Ewing and Nathan Smits and Francisco J Sanchez-Luque and Jamila Faivre and Paul M Brennan and Sandra R Richardson and Seth W Cheetham and Geoffrey J Faulkner},
url = {http://www.sciencedirect.com/science/article/pii/S1097276520307310},
doi = {10.1016/j.molcel.2020.10.024},
issn = {1097-2765},
year = {2020},
date = {2020-01-01},
urldate = {2020-11-30},
journal = {Molecular Cell},
abstract = {Transposable elements (TEs) drive genome evolution and are a notable source of pathogenesis, including cancer. While CpG methylation regulates TE activity, the locus-specific methylation landscape of mobile human TEs has to date proven largely inaccessible. Here, we apply new computational tools and long-read nanopore sequencing to directly infer CpG methylation of novel and extant TE insertions in hippocampus, heart, and liver, as well as paired tumor and non-tumor liver. As opposed to an indiscriminate stochastic process, we find pronounced demethylation of young long interspersed element 1 (LINE-1) retrotransposons in cancer, often distinct to the adjacent genome and other TEs. SINE-VNTR-Alu (SVA) retrotransposons, including their internal tandem repeat-associated CpG island, are near-universally methylated. We encounter allele-specific TE methylation and demethylation of aberrantly expressed young LINE-1s in normal tissues. Finally, we recover the complete sequences of tumor-specific LINE-1 insertions and their retrotransposition hallmarks, demonstrating how long-read sequencing can simultaneously survey the epigenome and detect somatic TE mobilization.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Transposable elements (TEs) drive genome evolution and are a notable source of pathogenesis, including cancer. While CpG methylation regulates TE activity, the locus-specific methylation landscape of mobile human TEs has to date proven largely inaccessible. Here, we apply new computational tools and long-read nanopore sequencing to directly infer CpG methylation of novel and extant TE insertions in hippocampus, heart, and liver, as well as paired tumor and non-tumor liver. As opposed to an indiscriminate stochastic process, we find pronounced demethylation of young long interspersed element 1 (LINE-1) retrotransposons in cancer, often distinct to the adjacent genome and other TEs. SINE-VNTR-Alu (SVA) retrotransposons, including their internal tandem repeat-associated CpG island, are near-universally methylated. We encounter allele-specific TE methylation and demethylation of aberrantly expressed young LINE-1s in normal tissues. Finally, we recover the complete sequences of tumor-specific LINE-1 insertions and their retrotransposition hallmarks, demonstrating how long-read sequencing can simultaneously survey the epigenome and detect somatic TE mobilization. |
Beaton, Ainsley; Lood, Cédric; Cunningham-Oakes, Edward; MacFadyen, Alison; Mullins, Alex J; Bestawy, Walid El; Botelho, João; Chevalier, Sylvie; Coleman, Shannon; Dalzell, Chloe; Dolan, Stephen K; Faccenda, Alberto; Ghequire, Maarten G K; Higgins, Steven; Kutschera, Alexander; Murray, Jordan; Redway, Martha; Salih, Talal; da Silva, Ana C; Smith, Brian A; Smits, Nathan; Thomson, Ryan; Woodcock, Stuart; Welch, Martin; Cornelis, Pierre; Lavigne, Rob; van Noort, Vera; Tucker, Nicholas P Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies (Journal Article) FEMS Microbiol Lett, 365 (9), 2018, ISSN: 0378-1097. (Abstract | Links | BibTeX | Altmetric) @article{beaton_community-led_2018,
title = {Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies},
author = {Ainsley Beaton and C\'{e}dric Lood and Edward Cunningham-Oakes and Alison MacFadyen and Alex J Mullins and Walid El Bestawy and Jo\~{a}o Botelho and Sylvie Chevalier and Shannon Coleman and Chloe Dalzell and Stephen K Dolan and Alberto Faccenda and Maarten G K Ghequire and Steven Higgins and Alexander Kutschera and Jordan Murray and Martha Redway and Talal Salih and Ana C da Silva and Brian A Smith and Nathan Smits and Ryan Thomson and Stuart Woodcock and Martin Welch and Pierre Cornelis and Rob Lavigne and Vera van Noort and Nicholas P Tucker},
url = {https://academic.oup.com/femsle/article/365/9/fny069/4951603},
doi = {10.1093/femsle/fny069},
issn = {0378-1097},
year = {2018},
date = {2018-05-01},
urldate = {2019-06-26},
journal = {FEMS Microbiol Lett},
volume = {365},
number = {9},
abstract = {Here, we present the high-quality draft genome of Pseudomonas baetica, a bacterial pathogen that has been demonstrated to cause disease in fish cultivated in aq},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Here, we present the high-quality draft genome of Pseudomonas baetica, a bacterial pathogen that has been demonstrated to cause disease in fish cultivated in aq |
Nathan Smits started his studies in 2013 at the University of Antwerp in Belgium. He obtained his Bachelor of Science in Bioscience engineering in 2016, and continued his studies at the KU Leuven in Belgium. He completed his Master’s thesis on “Nanopore-based sequencing and its application in the analysis of pathogenic Pseudomonas strains” in the Laboratory of Gene technology at the KU Leuven, which allowed him to acquire hands-on experience with the Oxford Nanopore Technologies’ sequencing platform and the subsequent data processing. He graduated in 2018 as a Master of Science in Bioscience engineering with a major in cellular and gene technology and a minor in bioinformatics. Nathan joined the Faulkner lab in 2019 as a Research Assistant for Dr. Seth Cheetham and focusses on L1 mobilization and regulation in cancer. 
