Emerging Approaches to Profile Accessible Chromatin from Ffpe Sections

Vishnu Udayakumar Sunita Kumary; Bryan J Venters; Karthikeyan Raman; Sagnik Sen; Pierre-Olivier Estève; Martis W Cowles; Michael-Christopher Keogh; Sriharsa Pradhan

doi:10.20944/preprints202402.1301.v1

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preprints.org > biology and life sciences > biochemistry and molecular biology > doi: 10.20944/preprints202402.1301.v1

Preprint Review Version 1 Preserved in Portico This version is not peer-reviewed

Emerging Approaches to Profile Accessible Chromatin from Ffpe Sections

Vishnu Udayakumar Sunita Kumary

Bryan J Venters

Karthikeyan Raman

Sagnik Sen

Pierre-Olivier Estève

Martis W Cowles

Michael-Christopher Keogh

^* ,

Sriharsa Pradhan

Version 1 : Received: 22 February 2024 / Approved: 22 February 2024 / Online: 23 February 2024 (08:25:28 CET)

How to cite: Sunita Kumary, V.U.; Venters, B.J.; Raman, K.; Sen, S.; Estève, P.; Cowles, M.W.; Keogh, M.; Pradhan, S. Emerging Approaches to Profile Accessible Chromatin from Ffpe Sections. Preprints 2024, 2024021301. https://doi.org/10.20944/preprints202402.1301.v1 Sunita Kumary, V.U.; Venters, B.J.; Raman, K.; Sen, S.; Estève, P.; Cowles, M.W.; Keogh, M.; Pradhan, S. Emerging Approaches to Profile Accessible Chromatin from Ffpe Sections. Preprints 2024, 2024021301. https://doi.org/10.20944/preprints202402.1301.v1

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MDPI and ACS Style

Sunita Kumary, V.U.; Venters, B.J.; Raman, K.; Sen, S.; Estève, P.; Cowles, M.W.; Keogh, M.; Pradhan, S. Emerging Approaches to Profile Accessible Chromatin from Ffpe Sections. Preprints 2024, 2024021301. https://doi.org/10.20944/preprints202402.1301.v1

APA Style

Sunita Kumary, V.U., Venters, B.J., Raman, K., Sen, S., Estève, P., Cowles, M.W., Keogh, M., & Pradhan, S. (2024). Emerging Approaches to Profile Accessible Chromatin from Ffpe Sections. Preprints. https://doi.org/10.20944/preprints202402.1301.v1

Chicago/Turabian Style

Sunita Kumary, V.U., Michael-Christopher Keogh and Sriharsa Pradhan. 2024 "Emerging Approaches to Profile Accessible Chromatin from Ffpe Sections" Preprints. https://doi.org/10.20944/preprints202402.1301.v1

Abstract

Nucleosomes are non-uniformly distributed across eukarytic genomes, with stretches of ‘open’ chromatin strongly associated with transcriptionally active promoters and enhancers. Understanding chromatin accessibility patterns in normal tissue and how they are altered in pathologies can provide critical insights to development and disease. With the advent of high-throughput sequencing, a variety of strategies have been devised to identify open regions across the genome, including DNase-seq, MNase-seq, FAIRE-seq, ATAC-seq, and NicE-seq. However, the broad application of such methods to FFPE (formalin-fixed paraffin embedded) tissues has been curtailed by the major technical challenges imposed by highly fixed and damaged genomic material. Here we review the most common approaches for mapping open chromatin regions, recent optimizations to overcome the challenges of working with FFPE tissue, and a brief overview of a typical data pipeline with analysis considerations.

Keywords

Chromatin; FFPE; Nucleosome; Nucleosome-free region; Nucleosome-depleted region

Subject

Biology and Life Sciences, Biochemistry and Molecular Biology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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