IMPLICON : an ultra-deep sequencing method to uncover DNA methylation at imprinted regions

Detalhes bibliográficos
Autor(a) principal: Klobučar, Tajda
Data de Publicação: 2020
Outros Autores: Kreibich, Elisa, Krueger, Felix, Arez, Maria, Pólvora-Brandão, Duarte, von Meyenn, Ferdinand, da Rocha, Simão T., Eckersley-Maslin, Melanie
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10451/48571
Resumo: © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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spelling IMPLICON : an ultra-deep sequencing method to uncover DNA methylation at imprinted regions© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.Genomic imprinting is an epigenetic phenomenon leading to parental allele-specific expression. Dosage of imprinted genes is crucial for normal development and its dysregulation accounts for several human disorders. This unusual expression pattern is mostly dictated by differences in DNA methylation between parental alleles at specific regulatory elements known as imprinting control regions (ICRs). Although several approaches can be used for methylation inspection, we lack an easy and cost-effective method to simultaneously measure DNA methylation at multiple imprinted regions. Here, we present IMPLICON, a high-throughput method measuring DNA methylation levels at imprinted regions with base-pair resolution and over 1000-fold coverage. We adapted amplicon bisulfite-sequencing protocols to design IMPLICON for ICRs in adult tissues of inbred mice, validating it in hybrid mice from reciprocal crosses for which we could discriminate methylation profiles in the two parental alleles. Lastly, we developed a human version of IMPLICON and detected imprinting errors in embryonic and induced pluripotent stem cells. We also provide rules and guidelines to adapt this method for investigating the DNA methylation landscape of any set of genomic regions. In summary, IMPLICON is a rapid, cost-effective and scalable method, which could become the gold standard in both imprinting research and diagnostics.Babraham Institute Translational Advisory Group award (to M.E.-M. and F.v.M.); M.E.-M. is supported by a BBSRC Discovery Fellowship [BB/T009713/1]; EMBO Fellowship [ALTF938-2014]; Marie Sklodowska-Curie Individual Fellowship; Work in S.T.d.R.’s team at iMM JLA was supported by Fundação para a Ciência e Tecnologia (FCT) Ministério da Ciência, Tecnologia e Ensino Superior (MCTES), Portugal [PTDC/BEX‐BCM/2612/2014, PTDC/BIA‐MOL/29320/2017 IC&DT]; S.T.d.R. has a CEECUIND/01234/207 assistant research contract from FCT/MCTES; T.K.’s work was supported by Erasmus+ and University Foundation of eng. Lenarčič Milan at the University of Ljubljana. Funding for open access charge: accounts payable, Babraham Institute.Oxford University PressRepositório da Universidade de LisboaKlobučar, TajdaKreibich, ElisaKrueger, FelixArez, MariaPólvora-Brandão, Duartevon Meyenn, Ferdinandda Rocha, Simão T.Eckersley-Maslin, Melanie2021-06-15T11:22:36Z20202020-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/48571engNucleic Acids Res. 2020 Sep 18;48(16):e92.0305-104810.1093/nar/gkaa5671362-4962info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-08T16:51:55Zoai:repositorio.ul.pt:10451/48571Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T22:00:22.821436Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv IMPLICON : an ultra-deep sequencing method to uncover DNA methylation at imprinted regions
title IMPLICON : an ultra-deep sequencing method to uncover DNA methylation at imprinted regions
spellingShingle IMPLICON : an ultra-deep sequencing method to uncover DNA methylation at imprinted regions
Klobučar, Tajda
title_short IMPLICON : an ultra-deep sequencing method to uncover DNA methylation at imprinted regions
title_full IMPLICON : an ultra-deep sequencing method to uncover DNA methylation at imprinted regions
title_fullStr IMPLICON : an ultra-deep sequencing method to uncover DNA methylation at imprinted regions
title_full_unstemmed IMPLICON : an ultra-deep sequencing method to uncover DNA methylation at imprinted regions
title_sort IMPLICON : an ultra-deep sequencing method to uncover DNA methylation at imprinted regions
author Klobučar, Tajda
author_facet Klobučar, Tajda
Kreibich, Elisa
Krueger, Felix
Arez, Maria
Pólvora-Brandão, Duarte
von Meyenn, Ferdinand
da Rocha, Simão T.
Eckersley-Maslin, Melanie
author_role author
author2 Kreibich, Elisa
Krueger, Felix
Arez, Maria
Pólvora-Brandão, Duarte
von Meyenn, Ferdinand
da Rocha, Simão T.
Eckersley-Maslin, Melanie
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Klobučar, Tajda
Kreibich, Elisa
Krueger, Felix
Arez, Maria
Pólvora-Brandão, Duarte
von Meyenn, Ferdinand
da Rocha, Simão T.
Eckersley-Maslin, Melanie
description © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020-01-01T00:00:00Z
2021-06-15T11:22:36Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10451/48571
url http://hdl.handle.net/10451/48571
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Nucleic Acids Res. 2020 Sep 18;48(16):e92.
0305-1048
10.1093/nar/gkaa567
1362-4962
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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