A simple ATAC-seq protocol for population epigenetics

Type Article
Date 2020
Language English
Author(s) de Carvalho Augusto RonaldoORCID2, 15, Rey Oliver15, Cosseau Céline15, Chaparro CristianORCID15, Vidal-Dupiol Jeremie1, Allienne Jean-François15, Duval David15, Pinaud Silvain3, 15, Tönges Sina4, Andriantsoa Ranja4, Luquet EmilienORCID5, Aubret Fabien6, 7, Dia Sow MamadouORCID8, David Patrice9, Thomson VickiORCID10, Joly Dominique11, Gomes Lima Mariana12, Federico Déborah13, Danchin Etienne13, Minoda Aki14, Grunau ChristophORCID15
Affiliation(s) 1 : Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
2 : LBMC, Laboratoire de Biologie et Modélisation de la Cellule Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1210, Lyon, 69007, France
3 : Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
4 : Division of Epigenetics, DKFZ ZMBH Alliance, German Cancer Research Center, Heidelberg, 69120, Germany
5 : Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, F-69622, France
6 : CNRS,Station d'Ecologie Théorique et Expérimentale, Université Paul Sabatier, Moulis, 09200, France
7 : School of Molecular and Life Sciences, Curtin University, Bentley, Australia
8 : LBLGC, INRA, Université d’Orléans, Orléans, France
9 : Univ Montpellier, CNRS, CEFE, F-34293, Montpellier, France
10 : School of Biological Sciences, University of Adelaide, Adelaide, 5005, Australia
11 : Laboratoire Evolution, Génomes Comportement, Ecologie, CNRS Université Paris Sud UMR 9191, Gif sur Yvette, 91198, France
12 : Laboratório de Malacologia, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, RJ, Brazil
13 : Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse; CNRS, Toulouse, 31062, France
14 : RIKEN Center for Integrative Medical Sciences, Epigenome Technology Exploration Unit, Tsurumi, Kanagawa, 230-0045, Japan
15 : Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
Source Wellcome Open Research (2398-502X) (F1000 Research Ltd), 2020 , Vol. 5 , P. 121 (24p.)
DOI 10.12688/wellcomeopenres.15552.2
Keyword(s) epigenetics, epigenomics, ATAC-seq, Daphnia pulex, Schistosoma mansoni
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.

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de Carvalho Augusto Ronaldo, Rey Oliver, Cosseau Céline, Chaparro Cristian, Vidal-Dupiol Jeremie, Allienne Jean-François, Duval David, Pinaud Silvain, Tönges Sina, Andriantsoa Ranja, Luquet Emilien, Aubret Fabien, Dia Sow Mamadou, David Patrice, Thomson Vicki, Joly Dominique, Gomes Lima Mariana, Federico Déborah, Danchin Etienne, Minoda Aki, Grunau Christoph (2020). A simple ATAC-seq protocol for population epigenetics. Wellcome Open Research, 5, 121 (24p.). Publisher's official version : https://doi.org/10.12688/wellcomeopenres.15552.2 , Open Access version : https://archimer.ifremer.fr/doc/00681/79353/