Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells
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Date
2023
Authors
Wong, Y.Y.
Harbison, J.E.
Hope, C.M.
Gundsambuu, B.
Brown, K.A.
Wong, S.W.
Brown, C.Y.
Couper, J.J.
Breen, J.
Liu, N.
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Journal article
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Scientific Reports, 2023; 13(1):5506-1-5506-15
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Ying Y. Wong, Jessica E. Harbison, Christopher M. Hope, BatjargalGundsambuu, KatherineA. Brown, SoonW. Wong, CherylY Brown, Jennifer J. Couper, Jimmy Breen, Ning Liu, Stephen M. Pederson, Maren Köhne, Kathrin Klee, Joachim Schultze, Marc Beyer, Timothy Sadlon, Simon C. Barry
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Abstract
Epigenetic features such as DNA accessibility dictate transcriptional regulation in a cell type- and cell state- specific manner, and mapping this in health vs. disease in clinically relevant material is opening the door to new mechanistic insights and new targets for therapy. Assay for Transposase Accessible Chromatin Sequencing (ATAC-seq) allows chromatin accessibility profiling from low cell input, making it tractable on rare cell populations, such as regulatory T (Treg) cells. However, little is known about the compatibility of the assay with cryopreserved rare cell populations. Here we demonstrate the robustness of an ATAC-seq protocol comparing primary Treg cells recovered from fresh or cryopreserved PBMC samples, in the steady state and in response to stimulation. We extend this method to explore the feasibility of conducting simultaneous quantitation of chromatin accessibility and transcriptome from a single aliquot of 50,000 cryopreserved Treg cells. Profiling of chromatin accessibility and gene expression in parallel within the same pool of cells controls for cellular heterogeneity and is particularly beneficial when constrained by limited input material. Overall, we observed a high correlation of accessibility patterns and transcription factor dynamics between fresh and cryopreserved samples. Furthermore, highly similar transcriptomic profiles were obtained from whole cells and from the supernatants recovered from ATAC-seq reactions. We highlight the feasibility of applying these techniques to profile the epigenomic landscape of cells recovered from cryopreservation biorepositories.
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© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.