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

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Expanding the list of sequence-agnostic enzymes for chromatin conformation capture assays with S1 nuclease. / Maria, Gridina; Andrey, Popov; Artem, Shadskiy et al.

In: Epigenetics & chromatin, Vol. 16, No. 1, 48, 11.12.2023.

Research output: Contribution to journal › Article › peer-review

BibTeX

@article{2417f509780a4c959a2fda2ff4324a51,

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

abstract = "This 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.",

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

note = "We acknowledge the Ministry of Science and Higher Education of the Russian Federation (state project FWNR-2022-0019) for providing access to the computational facilities. The access to public resources and data sets was provided by the Novosibirsk State University, supported by the Ministry of Education and Science of Russian Federation, grant #2019-0546 (FSUS-2020-0040). The original manuscript text was composed by authors; proofreading was done with assistance of the chatGPT version 4. The text was corrected and edited by authors after chatGPT proofreading. {\textcopyright} 2023. The Author(s).",

year = "2023",

month = dec,

day = "11",

doi = "10.1186/s13072-023-00524-4",

language = "English",

volume = "16",

journal = "Epigenetics and Chromatin",

issn = "1756-8935",

publisher = "BioMed Central Ltd.",

number = "1",

}

RIS

TY - JOUR

T1 - Expanding the list of sequence-agnostic enzymes for chromatin conformation capture assays with S1 nuclease

AU - Maria, Gridina

AU - Andrey, Popov

AU - Artem, Shadskiy

AU - Nikita, Torgunakov

AU - Andrey, Kechin

AU - Evgeny, Khrapov

AU - Oxana, Ryzhkova

AU - Maxim, Filipenko

AU - Veniamin, Fishman

N1 - We acknowledge the Ministry of Science and Higher Education of the Russian Federation (state project FWNR-2022-0019) for providing access to the computational facilities. The access to public resources and data sets was provided by the Novosibirsk State University, supported by the Ministry of Education and Science of Russian Federation, grant #2019-0546 (FSUS-2020-0040). The original manuscript text was composed by authors; proofreading was done with assistance of the chatGPT version 4. The text was corrected and edited by authors after chatGPT proofreading. © 2023. The Author(s).

PY - 2023/12/11

Y1 - 2023/12/11

N2 - This 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.

AB - This 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.

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85179336129&origin=inward&txGid=9f98dcac72245676bfcc45ffca3588d6

U2 - 10.1186/s13072-023-00524-4

DO - 10.1186/s13072-023-00524-4

M3 - Article

C2 - 38072950

VL - 16

JO - Epigenetics and Chromatin

JF - Epigenetics and Chromatin

SN - 1756-8935

IS - 1

M1 - 48

ER -

ID: 59334941