A simple ATAC-seq protocol for population epigenetics

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

doi:10.12688/wellcomeopenres.15552.2

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A simple ATAC-seq protocol for population epigenetics

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A simple ATAC-seq protocol for population epigenetics

Ronaldo de Carvalho Augusto, Olivier REY, Céline Cosseau, Cristian Chaparro, Jeremie Vidal-Dupiol, Jean-François Allienne, David Duval, Silvain Pinaud, Sina Tönges, Ranja Andriantsoa, …

Wellcome Open Research, Vol.5

07/01/2021

DOI: https://doi.org/10.12688/wellcomeopenres.15552.2

PMCID: PMC7814285

Abstract

epigenetics

epigenomics

ATAC-seq

Daphnia pulex

Schistosoma mansoni

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.

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Title: A simple ATAC-seq protocol for population epigenetics
Creators - without role: Ronaldo de Carvalho Augusto - Université de Montpellier, Interactions Hôtes-Pathogènes Environnement - IHPE
Olivier REY - Université de Montpellier, Interactions Hôtes-Pathogènes Environnement - IHPE
Céline Cosseau - Université de Montpellier, Interactions Hôtes-Pathogènes Environnement - IHPE
Cristian Chaparro - Université de Montpellier, Interactions Hôtes-Pathogènes Environnement - IHPE
Jeremie Vidal-Dupiol - Université de Montpellier, Interactions Hôtes-Pathogènes Environnement - IHPE
Jean-François Allienne - Université de Montpellier, Interactions Hôtes-Pathogènes Environnement - IHPE
David Duval - Université de Montpellier, Interactions Hôtes-Pathogènes Environnement - IHPE
Silvain Pinaud - Université de Montpellier, Interactions Hôtes-Pathogènes Environnement - IHPE
Sina Tönges - German Cancer Research Center
Ranja Andriantsoa - German Cancer Research Center
Émilien Luquet - École Nationale des Travaux Publics de l'État
Fabien Aubret - Station d’Écologie Théorique et Expérimentale
Mamadou Dia Sow - Physiologie, Ecologie et Environnement
Patrice David - Université de Montpellier, Centre d'Ecologie Fonctionnelle et Evolutive - CEFE
Vicki Thomson - University of Adelaide
Dominique D. Joly - Université Paris-Sud
Mariana Gomes Lima - Fundação Oswaldo Cruz
Déborah Federico - Université de Toulouse
Etienne Danchin - Laboratoire Evolution et Diversite Biologique
Aki Minoda - RIKEN Center for Integrative Medical Sciences
Christoph Grunau - Université de Montpellier, Interactions Hôtes-Pathogènes Environnement - IHPE
Publication Details: Wellcome Open Research, Vol.5
Identifiers: 9940133609311
Academic Unit: Centre d'Ecologie Fonctionnelle et Evolutive - CEFE; Interactions Hôtes-Pathogènes Environnement - IHPE
Language: English
Resource Type: Journal article
Local Fields: hal-03145575