Expanding the list of sequence-agnostic enzymes for chromatin conformation capture assays with S1 nuclease

Author:

Maria Gridina,Andrey Popov,Artem Shadskiy,Nikita Torgunakov,Andrey Kechin,Evgeny Khrapov,Oxana Ryzhkova,Maxim Filipenko,Veniamin Fishman

Abstract

AbstractThis study presents a novel approach for mapping global chromatin interactions using S1 nuclease, a sequence-agnostic enzyme. We develop and outline a protocol that leverages S1 nuclease's ability to effectively introduce breaks into both open and closed chromatin regions, allowing for comprehensive profiling of chromatin properties. Our S1 Hi–C method enables the preparation of high-quality Hi–C libraries, marking a significant advancement over previously established DNase I Hi–C protocols. Moreover, S1 nuclease's capability to fragment chromatin to mono-nucleosomes suggests the potential for mapping the three-dimensional organization of the genome at high resolution. This methodology holds promise for an improved understanding of chromatin state-dependent activities and may facilitate the development of new genomic methods.

Funder

Russian Science Support Foundation

Publisher

Springer Science and Business Media LLC

Subject

Genetics,Molecular Biology

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