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

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Alexandra P. Yan^1,2,a*, Paul A. Salnikov^1,2, Maria M. Gridina^1,2, Polina S. Belokopytova^1,2, and Veniamin S. Fishman^1,2,b*

¹Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia

²Novosibirsk State University, 630090 Novosibirsk, Russia

Received October 11, 2023; Revised February 1, 2024; Accepted March 2, 2024

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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.

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KEY WORDS: chromatin interactions, 4C, plasmid, extrachromosomal sequences, plasmid-genome interactions, chromosome conformation capture, transfection

DOI: 10.1134/S0006297924040059

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