Genome-Wide Profiling of Endogenous Single-Stranded DNA Using the SSiNGLe-P1 Method

Author:

Xu Dongyang1ORCID,Huang Yu1,Luo Lingcong1,Tang Lu1,Lu Meng1,Cao Huifen1,Wang Fang1,Diao Yong1ORCID,Lyubchenko Liudmila2,Kapranov Philipp13ORCID

Affiliation:

1. Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China

2. National Medical Research Center for Radiology, Ministry of Health of Russia, 125284 Moscow, Russia

3. State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China

Abstract

Endogenous single-stranded DNA (essDNA) can form in a mammalian genome as the result of a variety of molecular processes and can both play important roles inside the cell as well as have detrimental consequences to genome integrity, much of which remains to be fully understood. Here, we established the SSiNGLe-P1 approach based on limited digestion by P1 endonuclease for high-throughput genome-wide identification of essDNA regions. We applied this method to profile essDNA in both human mitochondrial and nuclear genomes. In the mitochondrial genome, the profiles of essDNA provide new evidence to support the strand-displacement model of mitochondrial DNA replication. In the nuclear genome, essDNA regions were found to be enriched in certain types of functional genomic elements, particularly, the origins of DNA replication, R-loops, and to a lesser degree, in promoters. Furthermore, interestingly, many of the essDNA regions identified by SSiNGLe-P1 have not been annotated and thus could represent yet unknown functional elements.

Funder

National Natural Science Foundation of China

Natural Science Foundation of Fujian Province, China

Fundamental Research Funds for the Central Universities of Huaqiao University

Scientific Research Funds of Huaqiao University

Research Fund for International Senior Scientists from the National Natural Science Foundation of China

Natural Science Foundation of Fujian Province

Publisher

MDPI AG

Subject

Inorganic Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Spectroscopy,Molecular Biology,General Medicine,Catalysis

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