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 |