A simple ATAC-seq protocol for population epigenetics
| Type | Article | ||||||||
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| Date | 2020 | ||||||||
| Language | English | ||||||||
| Author(s) | de Carvalho Augusto Ronaldo 2, 15, Rey Oliver15, Cosseau Céline15, Chaparro Cristian15, Vidal-Dupiol Jeremie1, Allienne Jean-François15, Duval David15, Pinaud Silvain3, 15, Tönges Sina4, Andriantsoa Ranja4, Luquet Emilien5, Aubret Fabien6, 7, Dia Sow Mamadou8, David Patrice9, Thomson Vicki10, Joly Dominique11, Gomes Lima Mariana12, Federico Déborah13, Danchin Etienne13, Minoda Aki14, Grunau Christoph15 |
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| 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 |
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| 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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