一种用于群体表观遗传学的简单ATAC测序方案。

A simple ATAC-seq protocol for population epigenetics.

作者信息

Augusto Ronaldo de Carvalho, Rey Oliver, Cosseau Céline, Chaparro Cristian, Vidal-Dupiol Jérémie, 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

机构信息

Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France.

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.

出版信息

Wellcome Open Res. 2021 Jan 7;5:121. doi: 10.12688/wellcomeopenres.15552.2. eCollection 2020.

DOI:10.12688/wellcomeopenres.15552.2

PMID:33521328

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7814285/

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.

摘要

我们在此描述了一种用于群体表观基因组学研究的序列就绪文库生成及比对结果分析的方案。我们表明，该方案可用于监测群体在暴露于环境线索时染色质结构的变化。该方案是转座酶可及染色质高通量测序分析（ATAC-seq）的简化版本，可对可及的、推测为常染色质区域进行阳性显示。该方案操作简便，可用于小型个体，如水蚤和血吸虫，可能还适用于许多其他大小相当（约10,000个细胞）的生物样本，并且所需的分子生物学操作专业知识较少。