Towards Development of the 4C-Based Method Detecting Interactions of Plasmid DNA with Host Genome

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Towards Development of the 4C-Based Method Detecting Interactions of Plasmid DNA with Host Genome. / Yan, Alexandra P.; Salnikov, Paul A.; Gridina, Maria M. et al.

In: Biochemistry (Moscow), Vol. 89, No. 4, 04.2024, p. 653-662.

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

BibTeX

@article{8e4f7a4d9dfa417c9d03fdc627f9e0de,

title = "Towards Development of the 4C-Based Method Detecting Interactions of Plasmid DNA with Host Genome",

abstract = "Abstract: Chromosome conformation capture techniques have revolutionized our understanding of chromatin architecture and dynamics at the genome-wide scale. In recent years, these methods have been applied to a diverse array of species, revealing fundamental principles of chromosomal organization. However, structural organization of the extrachromosomal entities, like viral genomes or plasmids, and their interactions with the host genome, remain relatively underexplored. In this work, we introduce an enhanced 4C-protocol tailored for probing plasmid DNA interactions. We design specific plasmid vector and optimize protocol to allow high detection rate of contacts between the plasmid and host DNA.",

keywords = "4C, chromatin interactions, chromosome conformation capture, extrachromosomal sequences, plasmid, plasmid-genome interactions, transfection",

author = "Yan, {Alexandra P.} and Salnikov, {Paul A.} and Gridina, {Maria M.} and Belokopytova, {Polina S.} and Fishman, {Veniamin S.}",

note = "We acknowledge infrastructure and resources provided by the collective usage center of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 121031800061-7 (Mechanisms of genetic control of development, physiological processes, and behavior in animals) for running next generation sequencing experiments. Computational data analysis was performed using the high-throughput computing nodes of the Novosibirsk State University (supported by the Ministry of Science and Higher Education of the Russian Federation, grant no. FSUS-2024-0018). This work was supported by the Russian Science Foundation (project no. 22-14-00242).",

year = "2024",

month = apr,

doi = "10.1134/S0006297924040059",

language = "English",

volume = "89",

pages = "653--662",

journal = "Biochemistry (Moscow)",

issn = "0006-2979",

publisher = "Maik Nauka-Interperiodica Publishing",

number = "4",

}

RIS

TY - JOUR

T1 - Towards Development of the 4C-Based Method Detecting Interactions of Plasmid DNA with Host Genome

AU - Yan, Alexandra P.

AU - Salnikov, Paul A.

AU - Gridina, Maria M.

AU - Belokopytova, Polina S.

AU - Fishman, Veniamin S.

N1 - We acknowledge infrastructure and resources provided by the collective usage center of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 121031800061-7 (Mechanisms of genetic control of development, physiological processes, and behavior in animals) for running next generation sequencing experiments. Computational data analysis was performed using the high-throughput computing nodes of the Novosibirsk State University (supported by the Ministry of Science and Higher Education of the Russian Federation, grant no. FSUS-2024-0018). This work was supported by the Russian Science Foundation (project no. 22-14-00242).

PY - 2024/4

Y1 - 2024/4

N2 - Abstract: Chromosome conformation capture techniques have revolutionized our understanding of chromatin architecture and dynamics at the genome-wide scale. In recent years, these methods have been applied to a diverse array of species, revealing fundamental principles of chromosomal organization. However, structural organization of the extrachromosomal entities, like viral genomes or plasmids, and their interactions with the host genome, remain relatively underexplored. In this work, we introduce an enhanced 4C-protocol tailored for probing plasmid DNA interactions. We design specific plasmid vector and optimize protocol to allow high detection rate of contacts between the plasmid and host DNA.

AB - Abstract: Chromosome conformation capture techniques have revolutionized our understanding of chromatin architecture and dynamics at the genome-wide scale. In recent years, these methods have been applied to a diverse array of species, revealing fundamental principles of chromosomal organization. However, structural organization of the extrachromosomal entities, like viral genomes or plasmids, and their interactions with the host genome, remain relatively underexplored. In this work, we introduce an enhanced 4C-protocol tailored for probing plasmid DNA interactions. We design specific plasmid vector and optimize protocol to allow high detection rate of contacts between the plasmid and host DNA.

KW - 4C

KW - chromatin interactions

KW - chromosome conformation capture

KW - extrachromosomal sequences

KW - plasmid

KW - plasmid-genome interactions

KW - transfection

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85192176112&origin=inward&txGid=cd67a2f6a8cfb6e16b1f4c45506f5b4f

UR - https://www.mendeley.com/catalogue/1d39e649-a880-3604-817a-34e1edb9d63a/

U2 - 10.1134/S0006297924040059

DO - 10.1134/S0006297924040059

M3 - Article

C2 - 38831502

VL - 89

SP - 653

EP - 662

JO - Biochemistry (Moscow)

JF - Biochemistry (Moscow)

SN - 0006-2979

IS - 4

ER -

ID: 61084322