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Koo CX, Kobiyama K, Shen YJ, LeBert N, Ahmad S, Khatoo M, Aoshi T, Gasser S, Ishii KJ. RNA polymerase III regulates cytosolic RNA:DNA hybrids and intracellular microRNA expression. J Biol Chem 2015; 290:7463-73. [PMID: 25623070 PMCID: PMC4367256 DOI: 10.1074/jbc.m115.636365] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
RNA:DNA hybrids form in the nuclei and mitochondria of cells as transcription-induced R-loops or G-quadruplexes, but exist only in the cytosol of virus-infected cells. Little is known about the existence of RNA:DNA hybrids in the cytosol of virus-free cells, in particular cancer or transformed cells. Here, we show that cytosolic RNA:DNA hybrids are present in various human cell lines, including transformed cells. Inhibition of RNA polymerase III (Pol III), but not DNA polymerase, abrogated cytosolic RNA:DNA hybrids. Cytosolic RNA:DNA hybrids bind to several components of the microRNA (miRNA) machinery-related proteins, including AGO2 and DDX17. Furthermore, we identified miRNAs that are specifically regulated by Pol III, providing a potential link between RNA:DNA hybrids and the miRNA machinery. One of the target genes, exportin-1, is shown to regulate cytosolic RNA:DNA hybrids. Taken together, we reveal previously unknown mechanism by which Pol III regulates the presence of cytosolic RNA:DNA hybrids and miRNA biogenesis in various human cells.
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Affiliation(s)
- Christine Xing'er Koo
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, the Laboratory of Adjuvant Innovation and
| | - Kouji Kobiyama
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Yu J Shen
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456
| | - Nina LeBert
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and
| | - Shandar Ahmad
- the Laboratory of Bioinformatics, National Institute of Biomedical Innovation (NIBIO), Ibaraki, Osaka 567-0085, Japan, and
| | - Muznah Khatoo
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and
| | - Taiki Aoshi
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Stephan Gasser
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456,
| | - Ken J Ishii
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
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