Библиография

1. 1. Abakir A., Giles T. C., Cristini A., Foster J. M., Dai N., Starczak M., Crutchley J., Flatt L., Young L., Gaffney D. J., Denning C., Dalhus B., Emes R. D., Gackowski D., Corrêa I. R. Jr., Garcia-Perez J.L., Klungland A., Gromak N., Ruzov A. N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells // Nat. Genet. 2020. V. 1. P. 48-55. https://doi.org/10.1038/s41588-019-0549-x
2. 2. Boguslawski S. J., Smith D. E., Michalak M. A., Mickelson K. E., Yehle C. O., Patterson W. L., Carrico R. J. Characterization of monoclonal antibody to DNA.RNA and its application to immunodetection of hybrids // J. Immunol. Methods. 1986. V. 89. P. 123-130. https://doi.org/10.1016/0022-1759 (86)90040-2
3. 3. Brochu J., Vlachos-Breton E.Â., Sutherland S., Martel M., Drolet M. Topoisomerases I and III inhibit R-loop formation to prevent unregulated replication in the chromosomal Ter region of Escherichia coli // PLoS Genet. 2018. V. 14. Art. e1007668. https://doi.org/10.1371/journal.pgen.1007668
4. 4. Drolet M., Phoenix P., Menzel R., Masse E., Liu L. F., Crouch R. J. Overexpression of RNase H partially complements the growth defect of an Escherichia coli ∆topA mutant: R-loop formation is a major problem in the absence of DNA topoisomerase I // Proc. Natl. Acad. Sci. USA. 1995. V. 92. P. 3526-3530. https://doi.org/10.1073/pnas.92.8.3526
5. 5. Ewels P., Magnusson M., Lundin S., Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report // Bioinformatics. 2016. V. 32. P. 3047-3048. https://doi.org/10.1093/bioinformatics/btw354
6. 6. Gan W., Guan Z., Liu J., Gui T., Shen K., Manley J. L., Li X. R-loop-mediated genomic instability is caused by impairment of replication fork progression // Genes Dev. 2011. V. 25. P. 2041-2056. https://doi.org/10.1101/gad.17010011
7. 7. Garcia-Muse T., Aguilera A. R loops: from physiological to pathological roles // Cell. 2019. V. 179. P. 604-618. https://doi.org/10.1016/j.cell.2019.08.055
8. 8. Ginno P. A., Lott P. L., Christensen H. C., Korf I., Chédin F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters // Mol. Cell. 2012. V. 45. P. 814-825. https://doi.org/10.1016/j.molcel.2012.01.017
9. 9. Holt I.J. R-loops and mitochondrial DNA metabolism // Methods Mol. Biol. 2022. V. 2022:2528. P. 173-202. https://doi.org/10.1007/978-1-0716-2477-7_12
10. 10. Huertas P., Aguilera A. Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination // Mol. Cell. 2003. V. 12. P. 711-721. https://doi.org/10.1016/j.molcel.2003.08.010
11. 11. Jenuth J. P. The NCBI. Publicly available tools and resources on the web // Bioinformatics methods and protocols. Methods in Molecular Biology™ / Eds. Misener S., Krawetz S.A. V. 132. Totowa, NJ: Humana Press, 1999. P. 301-312. https://doi.org/10.1385/1-59259-192-2:301
12. 12. Jordan S. W., Cronan J. E., Jr. The Escherichia coli lipB gene encodes lipoyl (octanoyl)-acyl carrier protein: protein transferase // J. Bacteriol. 2003. V. 185. P. 1582-1589. https://doi.org/10.1128/JB.185.5.1582-1589.2003
13. 13. Kim S., Kim Y., Yoon S. Y. Overexpression of YbeD in Escherichia coli enhances thermotolerance // J. Microbiol. Biotechnol. 2019. V. 29. P. 401-409. https://doi.org/10.4014/jmb.1901.01036
14. 14. Kozlov G., Elias D., Semesi A., Yee A., Cygler M., Gehring K. Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains // J. Bacteriol. 2004. V. 186. P. 8083-8088. https://doi.org/10.1128/jb.186.23.8083-8088.2004
15. 15. Leela J. K., Raghunathan N., Gowrishankar J. Topoisomerase I essentiality, DnaA-independent chromosomal replication, and transcription-replication conflict in Escherichia coli // J. Bacteriol. 2021. V. 203. Art. e0019521. https://doi.org/10.1128/jb.00195-21
16. 16. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. The Sequence Alignment/Map format and SAMtools // Bioinformatics. 2009. V. 25 P. 2078-2079. https://doi.org/10.1093/bioinformatics/btp352
17. 17. Li R., Liu B., Yuan X., Chen Z. A bibliometric analysis of research on R-loop: landscapes, highlights and trending topics // DNA Repair (Amst). 2023. V. 127. Art. 103502. https://doi.org/10.1016/j.dnarep.2023.103502
18. 18. Raghunathan N., Kapshikar R. M., Leela J. K., Mallikarjun J., Bouloc P., Gowrishankar J. Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli // Nucleic Acids Res. 2018. V. 46. P. 3400-3411. https://doi.org/10.1093/nar/gky118
19. 19. Ramírez F., Dündar F., Diehl S., Grüning B.A., Manke T. deepTools: a flexible platform for exploring deep-sequencing data // Nucleic Acids Res. 2014. V. 42 (W1). P. W187-W191. https://doi.org/10.1093/nar/gku365
20. 20. Renaudin X., Venkitaraman A. R. A mitochondrial response to oxidative stress mediated by unscheduled RNA- DNA hybrids (R-loops) // Mol. Cell. Oncol. 2021. V. 8. Art. 2007028. https://doi.org/10.1080/23723556.2021.2007028
21. 21. Sanz L. A., Hartono S. R., Lim Y. W., Steyaert S., Rajpurkar A., Ginno P. A., Xu X., Chédin F. Prevalent, dynamic, and conserved R-loop structures associate with specific epigenomic signatures in mammals // Mol. Cell. 2016. V. 63. P. 167-178. https://doi.org/10.1016/j.molcel.2016.05.032
22. 22. Skourti-Stathaki K., Proudfoot N. J., Gromak N. Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination // Mol Cell. 2011. V. 42. P. 794-805. https://doi.org/10.1016/j.molcel.2011.04.026
23. 23. Thomas M., White R. L., Davis R. W. Hybridization of RNA to double-stranded DNA: formation of R-loops // Proc. Natl. Acad. Sci. USA. 1976. V. 73. P. 2294-2298. https://doi.org/10.1073/pnas.73.7.2294
24. 24. Tripathi D., Oldenburg D. J., Bendich A. J. Ribonucleotide and R-loop damage in plastid DNA and mitochondrial DNA during maize development // Plants (Basel). 2023. V. 12. Art. 3161. https://doi.org/10.3390/plants12173161
25. 25. Xu W., Xu H., Li K., Fan Y., Liu Y., Yang X., Sun Q. The R-loop is a common chromatin feature of the Arabidopsis genome // Nature Plants. 2017. V. 3. P. 704-714. https://doi.org/10.1038/s41477-017-0004-x
26. 26. Yu G., Wang L. G., He Q. Y. ChIPseeker: an R/Biocon-ductor package for ChIP peak annotation, comparison and visualization // Bioinformatics. 2015. V. 31. P. 2382-2383. https://doi.org/10.1093/bioinformatics/btv145
27. 27. Zeller P., Padeken J., van Schendel R., Kalck V., Tijsterman M., Gasser S. M. Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability // Nature Genet. 2016. V. 48. P. 1385-1395. https://doi.org/10.1038/ng.3672
28. 28. Zhang Y., Liu T., Meyer C. A., Eeckhoute J., Johnson D. S., Bernstein B. E., Liu X. S. Model-based analysis of ChIP-Seq (MACS) // Genome Biol. 2008. V. 9. Art. R137. P. 1-9. https://doi.org/10.1186/gb-2008-9-9-r137