scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-c...

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Autores principales: Clark, Stephen J., Argelaguet, Ricard, Kapourani, Chantriolnt-Andreas, Stubbs, Thomas M., Lee, Heather J., Alda-Catalinas, Celia, Krueger, Felix, Sanguinetti, Guido, Kelsey, Gavin, Marioni, John C., Stegle, Oliver, Reik, Wolf
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5823944/
https://www.ncbi.nlm.nih.gov/pubmed/29472610
http://dx.doi.org/10.1038/s41467-018-03149-4
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author Clark, Stephen J.
Argelaguet, Ricard
Kapourani, Chantriolnt-Andreas
Stubbs, Thomas M.
Lee, Heather J.
Alda-Catalinas, Celia
Krueger, Felix
Sanguinetti, Guido
Kelsey, Gavin
Marioni, John C.
Stegle, Oliver
Reik, Wolf
author_facet Clark, Stephen J.
Argelaguet, Ricard
Kapourani, Chantriolnt-Andreas
Stubbs, Thomas M.
Lee, Heather J.
Alda-Catalinas, Celia
Krueger, Felix
Sanguinetti, Guido
Kelsey, Gavin
Marioni, John C.
Stegle, Oliver
Reik, Wolf
author_sort Clark, Stephen J.
collection PubMed
description Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.
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spelling pubmed-58239442018-02-26 scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells Clark, Stephen J. Argelaguet, Ricard Kapourani, Chantriolnt-Andreas Stubbs, Thomas M. Lee, Heather J. Alda-Catalinas, Celia Krueger, Felix Sanguinetti, Guido Kelsey, Gavin Marioni, John C. Stegle, Oliver Reik, Wolf Nat Commun Article Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation. Nature Publishing Group UK 2018-02-22 /pmc/articles/PMC5823944/ /pubmed/29472610 http://dx.doi.org/10.1038/s41467-018-03149-4 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Clark, Stephen J.
Argelaguet, Ricard
Kapourani, Chantriolnt-Andreas
Stubbs, Thomas M.
Lee, Heather J.
Alda-Catalinas, Celia
Krueger, Felix
Sanguinetti, Guido
Kelsey, Gavin
Marioni, John C.
Stegle, Oliver
Reik, Wolf
scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells
title scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells
title_full scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells
title_fullStr scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells
title_full_unstemmed scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells
title_short scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells
title_sort scnmt-seq enables joint profiling of chromatin accessibility dna methylation and transcription in single cells
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5823944/
https://www.ncbi.nlm.nih.gov/pubmed/29472610
http://dx.doi.org/10.1038/s41467-018-03149-4
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