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Cells 2019, 8(2), 111; https://doi.org/10.3390/cells8020111

Identification of Extrachromosomal Linear microDNAs Interacted with microRNAs in the Cell Nuclei

1
Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China
2
Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
3
Institute for Translational Medicine, Qingdao University, Qingdao 266071, China
*
Authors to whom correspondence should be addressed.
Received: 18 December 2018 / Revised: 17 January 2019 / Accepted: 31 January 2019 / Published: 1 February 2019
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Abstract

Extrachromosomal DNA exists in two forms: Covalently closed circular and linear. While diverse types of circular extrachromosomal DNA have been identified with validated in vivo functions, little is known about linear extrachromosomal DNA. In this study, we identified small, single-stranded linear extrachromosomal DNAs (SSLmicroDNAs) in the nuclei of mouse hearts, mouse brains, HEK293, and HeLa cells. We used a pull-down system based on the single-stranded DNA binding protein RecAf. We found that SSLmicroDNAs aligned predominantly to intergenic and intragenic regions of the genome, owned a variety of single nucleotide polymorphism sites, and strongly associated with H3K27Ac marks. The regions were tens to hundreds of nucleotides long, periodically separated by AT, TT, or AA dinucleotides. It has been demonstrated that SSLmicroDNAs in the nuclei of normal cells target microRNAs, which regulate biological processes. In summary, our present work identified a new form of extrachromosomal DNAs, which function inside nuclei and interact with microRNAs. This finding provides a possible research field into the function of extrachromosomal DNA. View Full-Text
Keywords: extrachromosomal DNAs; small single-stranded linear extrachromosomal DNAs (SSLmicroDNAs); sequence analysis; microRNAs; cell nucleus extrachromosomal DNAs; small single-stranded linear extrachromosomal DNAs (SSLmicroDNAs); sequence analysis; microRNAs; cell nucleus
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Sun, T.; Wang, K.; Liu, C.; Wang, Y.; Wang, J.; Li, P. Identification of Extrachromosomal Linear microDNAs Interacted with microRNAs in the Cell Nuclei. Cells 2019, 8, 111.

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