A simple ATAC-seq protocol for population epigenetics

Christoph Grunau; Ronaldo de Carvalho Augusto; Oliver Rey; Céline Cosseau; Cristian Chaparro; Jérémie Vidal-Dupiol; Jean François Allienne; David Duval; Silvain Pinaud; Sina Tönges; Ranja Andriantsoa; Emilien Luquet; Fabien Aubret; Mamadou Dia Sow; Patrice David; Vicki Thomson; Dominique Joly; Mariana Gomes Lima; Déborah Federico; Etienne Danchin; Aki Minoda

doi:10.12688/wellcomeopenres.15552.2

A simple ATAC-seq protocol for population epigenetics

Christoph Grunau, Ronaldo de Carvalho Augusto, Oliver Rey, Céline Cosseau, Cristian Chaparro, Jérémie Vidal-Dupiol, Jean François Allienne, David Duval, Silvain Pinaud, Sina Tönges, Ranja Andriantsoa, Emilien Luquet, Fabien Aubret, Mamadou Dia Sow, Patrice David, Vicki Thomson, Dominique Joly, Mariana Gomes Lima, Déborah Federico, Etienne DanchinAki Minoda

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Abstract

We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.

Original language	English
Article number	121
Pages (from-to)	1-24
Number of pages	24
Journal	Wellcome Open Research
Volume	5
DOIs	https://doi.org/10.12688/wellcomeopenres.15552.2
Publication status	Published - 7 Jan 2021
Externally published	Yes

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10.12688/wellcomeopenres.15552.2Licence: CC BY

ArticleFinal published version, 3.77 MBLicence: CC BY

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Grunau, C., Augusto, R. D. C., Rey, O., Cosseau, C., Chaparro, C., Vidal-Dupiol, J., Allienne, J. F., Duval, D., Pinaud, S., Tönges, S., Andriantsoa, R., Luquet, E., Aubret, F., Dia Sow, M., David, P., Thomson, V., Joly, D., Gomes Lima, M., Federico, D., ... Minoda, A. (2021). A simple ATAC-seq protocol for population epigenetics. Wellcome Open Research, 5, 1-24. [121]. https://doi.org/10.12688/wellcomeopenres.15552.2

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title = "A simple ATAC-seq protocol for population epigenetics",

abstract = "We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.",

keywords = "ATAC-seq, Daphnia pulex, Epigenetics, Epigenomics, Schistosoma mansoni",

author = "Christoph Grunau and Augusto, {Ronaldo de Carvalho} and Oliver Rey and C{\'e}line Cosseau and Cristian Chaparro and J{\'e}r{\'e}mie Vidal-Dupiol and Allienne, {Jean Fran{\c c}ois} and David Duval and Silvain Pinaud and Sina T{\"o}nges and Ranja Andriantsoa and Emilien Luquet and Fabien Aubret and {Dia Sow}, Mamadou and Patrice David and Vicki Thomson and Dominique Joly and {Gomes Lima}, Mariana and D{\'e}borah Federico and Etienne Danchin and Aki Minoda",

note = "Funding Information: We thank J.F. Allienne at the Bio-environment platform (University Perpignan Via Domitia) for support in NGS library preparation and sequencing, and the Environmental Epigenomics platform for support with ATAC-Seq procedure. This study is set within the framework of the {"}Laboratoires d'Excellences (LABEX){"} TULIP (ANR-10-LABX-41). Publisher Copyright: {\textcopyright} 2021 Augusto RdC et al.",

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doi = "10.12688/wellcomeopenres.15552.2",

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Grunau, C, Augusto, RDC, Rey, O, Cosseau, C, Chaparro, C, Vidal-Dupiol, J, Allienne, JF, Duval, D, Pinaud, S, Tönges, S, Andriantsoa, R, Luquet, E, Aubret, F, Dia Sow, M, David, P, Thomson, V, Joly, D, Gomes Lima, M, Federico, D, Danchin, E & Minoda, A 2021, 'A simple ATAC-seq protocol for population epigenetics', Wellcome Open Research, vol. 5, 121, pp. 1-24. https://doi.org/10.12688/wellcomeopenres.15552.2

TY - JOUR

T1 - A simple ATAC-seq protocol for population epigenetics

AU - Grunau, Christoph

AU - Augusto, Ronaldo de Carvalho

AU - Rey, Oliver

AU - Cosseau, Céline

AU - Chaparro, Cristian

AU - Vidal-Dupiol, Jérémie

AU - Allienne, Jean François

AU - Duval, David

AU - Pinaud, Silvain

AU - Tönges, Sina

AU - Andriantsoa, Ranja

AU - Luquet, Emilien

AU - Aubret, Fabien

AU - Dia Sow, Mamadou

AU - David, Patrice

AU - Thomson, Vicki

AU - Joly, Dominique

AU - Gomes Lima, Mariana

AU - Federico, Déborah

AU - Danchin, Etienne

AU - Minoda, Aki

N1 - Funding Information: We thank J.F. Allienne at the Bio-environment platform (University Perpignan Via Domitia) for support in NGS library preparation and sequencing, and the Environmental Epigenomics platform for support with ATAC-Seq procedure. This study is set within the framework of the "Laboratoires d'Excellences (LABEX)" TULIP (ANR-10-LABX-41). Publisher Copyright: © 2021 Augusto RdC et al.

PY - 2021/1/7

Y1 - 2021/1/7

N2 - We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.

AB - We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.

KW - ATAC-seq

KW - Daphnia pulex

KW - Epigenetics

KW - Epigenomics

KW - Schistosoma mansoni

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U2 - 10.12688/wellcomeopenres.15552.2

DO - 10.12688/wellcomeopenres.15552.2

M3 - Article

AN - SCOPUS:85100736430

SN - 2398-502X

VL - 5

SP - 1

EP - 24

JO - Wellcome Open Research

JF - Wellcome Open Research

M1 - 121

ER -

A simple ATAC-seq protocol for population epigenetics

Abstract

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