Animal Bioscience

  • 제37권6호
  • /
  • Pages.1021-1030
  • /
  • 2024
  • /
  • 2765-0189(pISSN)
  • /
  • 2765-0235(eISSN)
아세아태평양축산학회 (Asian Australasian Association of Animal Production Societies)
권호 표지
DOI QR코드

DOI QR Code

RNA helicase DEAD-box-5 is involved in R-loop dynamics of preimplantation embryos

  • Hyeonji Lee (Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University) ;
  • Dong Wook Han (Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University) ;
  • Seonho Yoo (Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University) ;
  • Ohbeom Kwon (Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University) ;
  • Hyeonwoo La (Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University) ;
  • Chanhyeok Park (Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University) ;
  • Heeji Lee (Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University) ;
  • Kiye Kang (Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University) ;
  • Sang Jun Uhm (Department of Animal Science, Sangji University) ;
  • Hyuk Song (Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University) ;
  • Jeong Tae Do (Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University) ;
  • Youngsok Choi (Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University) ;
  • Kwonho Hong (Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University)
  • 투고 : 2023.10.06
  • 심사 : 2023.12.07
  • 발행 : 2024.06.01
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

Objective: R-loops are DNA:RNA triplex hybrids, and their metabolism is tightly regulated by transcriptional regulation, DNA damage response, and chromatin structure dynamics. R-loop homeostasis is dynamically regulated and closely associated with gene transcription in mouse zygotes. However, the factors responsible for regulating these dynamic changes in the R-loops of fertilized mouse eggs have not yet been investigated. This study examined the functions of candidate factors that interact with R-loops during zygotic gene activation. Methods: In this study, we used publicly available next-generation sequencing datasets, including low-input ribosome profiling analysis and polymerase II chromatin immunoprecipitation-sequencing (ChIP-seq), to identify potential regulators of R-loop dynamics in zygotes. These datasets were downloaded, reanalyzed, and compared with mass spectrometry data to identify candidate factors involved in regulating R-loop dynamics. To validate the functions of these candidate factors, we treated mouse zygotes with chemical inhibitors using in vitro fertilization. Immunofluorescence with an anti-R-loop antibody was then performed to quantify changes in R-loop metabolism. Results: We identified DEAD-box-5 (DDX5) and histone deacetylase-2 (HDAC2) as candidates that potentially regulate R-loop metabolism in oocytes, zygotes and two-cell embryos based on change of their gene translation. Our analysis revealed that the DDX5 inhibition of activity led to decreased R-loop accumulation in pronuclei, indicating its involvement in regulating R-loop dynamics. However, the inhibition of histone deacetylase-2 activity did not significantly affect R-loop levels in pronuclei. Conclusion: These findings suggest that dynamic changes in R-loops during mouse zygote development are likely regulated by RNA helicases, particularly DDX5, in conjunction with transcriptional processes. Our study provides compelling evidence for the involvement of these factors in regulating R-loop dynamics during early embryonic development.

키워드

과제정보

The authors are indebted to all the members of the KH lab for helpful discussion.

참고문헌

  1. Ing-Simmons E, Rigau M, Vaquerizas JM. Emerging mechanisms and dynamics of three-dimensional genome organisation at zygotic genome activation. Curr Opin Cell Biol 2022;74:37-46. https://doi.org/10.1016/j.ceb.2021.12.004
  2. Eckersley-Maslin MA, Alda-Catalinas C, Reik W. Dynamics of the epigenetic landscape during the maternal-to-zygotic transition. Nat Rev Mol Cell Biol 2018;19:436-50. https://doi.org/10.1038/s41580-018-0008-z
  3. Wang C, Chen C, Liu X, et al. Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation. Cell Res 2022;32:801-13. https://doi.org/10.1038/s41422-022-00652-8
  4. Abe KI, Funaya S, Tsukioka D, et al. Minor zygotic gene activation is essential for mouse preimplantation development. Proc Natl Acad Sci USA 2018;115:E6780-8. https://doi.org/10.1073/pnas.1804309115
  5. Liu B, Xu Q, Wang Q, et al. The landscape of RNA Pol II binding reveals a stepwise transition during ZGA. Nature 2020;587:139-44. https://doi.org/10.1038/s41586-020-2847-y
  6. Core L, Adelman K. Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation. Genes Dev 2019;33:960-82. https://doi.org/10.1101/gad.325142.119
  7. Abuhashem A, Garg V, Hadjantonakis AK. RNA polymerase II pausing in development: orchestrating transcription. Open Biol 2022;12:210220. https://doi.org/10.1098/rsob.210220
  8. Price DH. Transient pausing by RNA polymerase II. Proc Natl Acad Sci USA 2018;115:4810-2. https://doi.org/10.1073/pnas.1805129115
  9. Shao W, Zeitlinger J. Paused RNA polymerase II inhibits new transcriptional initiation. Nat Genet 2017;49:1045-51. https://doi.org/10.1038/ng.3867
  10. Castillo-Guzman D, Chedin F. Defining R-loop classes and their contributions to genome instability. DNA Repair (Amst) 2021;106:103182. https://doi.org/10.1016/j.dnarep.2021.103182
  11. Zhang X, Chiang HC, Wang Y, et al. Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis. Nat Commun 2017;8:15908. https://doi.org/10.1038/ncomms15908
  12. Zardoni L, Nardini E, Brambati A, et al. Elongating RNA polymerase II and RNA:DNA hybrids hinder fork progression and gene expression at sites of head-on replication-transcription collisions. Nucleic Acids Res 2021;49:12769-84. https://doi.org/10.1093/nar/gkab1146
  13. Gan W, Guan Z, Liu J, et al. R-loop-mediated genomic instability is caused by impairment of replication fork progression. Genes Dev 2011;25:2041-56. https://doi.org/10.1101/gad.17010011
  14. Pohjoismaki JL, Holmes JB, Wood SR, et al. Mammalian mitochondrial DNA replication intermediates are essentially duplex but contain extensive tracts of RNA/DNA hybrid. J Mol Biol 2010;397:1144-55. https://doi.org/10.1016/j.jmb.2010.02.029
  15. Huertas P, Aguilera A. Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol Cell 2003;12:711-21. https://doi.org/10.1016/j.molcel.2003.08.010
  16. Yu K, Chedin F, Hsieh CL, Wilson TE, Lieber MR. R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells. Nat Immunol 2003;4:442-51. https://doi.org/10.1038/ni919
  17. Ohle C, Tesorero R, Schermann G, Dobrev N, Sinning I, Fischer T. Transient RNA-DNA hybrids are required for efficient double-strand break repair. Cell 2016;167:1001-13. https://doi.org/10.1016/j.cell.2016.10.001
  18. Aguilera A, Garcia-Muse T. R loops: from transcription byproducts to threats to genome stability. Mol Cell 2012;46:115-24. https://doi.org/10.1016/j.molcel.2012.04.009
  19. Brickner JR, Garzon JL, Cimprich KA. Walking a tightrope: the complex balancing act of R-loops in genome stability. Mol Cell 2022;82:2267-97. https://doi.org/10.1016/j.molcel.2022.04.014
  20. Petermann E, Lan L, Zou L. Sources, resolution and physiological relevance of R-loops and RNA-DNA hybrids. Nat Rev Mol Cell Biol 2022;23:521-40. https://doi.org/10.1038/s41580-022-00474-x
  21. Cristini A, Groh M, Kristiansen MS, Gromak N. RNA/DNA hybrid interactome identifies DXH9 as a molecular player in transcriptional termination and R-loop-associated DNA damage. Cell Rep 2018;23:1891-905. https://doi.org/10.1016/j.celrep.2018.04.025
  22. Mosler T, Conte F, Longo GMC, et al. R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability. Nat Commun 2021;12:7314. https://doi.org/10.1038/s41467-021-27530-y
  23. Mersaoui SY, Yu Z, Coulombe Y, et al. Arginine methylation of the DDX5 helicase RGG/RG motif by PRMT5 regulates resolution of RNA:DNA hybrids. EMBO J 2019;38:e100986. https://doi.org/10.15252/embj.2018100986
  24. Saha S, Yang X, Huang SN, et al. Resolution of R-loops by topoisomerase III-beta (TOP3B) in coordination with the DEAD-box helicase DDX5. Cell Rep 2022;40:111067. https://doi.org/10.1016/j.celrep.2022.111067
  25. Dou P, Li Y, Sun H, et al. C1orf109L binding DHX9 promotes DNA damage depended on the R-loop accumulation and enhances camptothecin chemosensitivity. Cell Prolif 2020;53:e12875. https://doi.org/10.1111/cpr.12875
  26. Chakraborty P, Huang JTJ, Hiom K. DHX9 helicase promotes R-loop formation in cells with impaired RNA splicing. Nat Commun 2018;9:4346. https://doi.org/10.1038/s41467-018-06677-1
  27. Yuan W, Al-Hadid Q, Wang Z, et al. TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution. Nucleic Acids Res 2021;49:8573-91. https://doi.org/10.1093/nar/gkab642
  28. Abdelhaleem M, Maltais L, Wain H. The human DDX and DHX gene families of putative RNA helicases. Genomics 2003;81:618-22. https://doi.org/10.1016/s0888-7543(03)00049-1
  29. Bourgeois CF, Mortreux F, Auboeuf D. The multiple functions of RNA helicases as drivers and regulators of gene expression. Nat Rev Mol Cell Biol 2016;17:426-38. https://doi.org/10.1038/nrm.2016.50
  30. Putnam AA, Jankowsky E. DEAD-box helicases as integrators of RNA, nucleotide and protein binding. Biochim Biophys Acta Gene Regul Mech 2013;1829:884-93. https://doi.org/10.1016/j.bbagrm.2013.02.002
  31. Fuller-Pace FV. DExD/H box RNA helicases: multifunctional proteins with important roles in transcriptional regulation. Nucleic Acids Res 2006;34:4206-15. https://doi.org/10.1093/nar/gkl460
  32. Kang HJ, Eom HJ, Kim H, Myung K, Kwon HM, Choi JH. Thrap3 promotes R-loop resolution via interaction with methylated DDX5. Exp Mol Med 2021;53:1602-11. https://doi.org/10.1038/s12276-021-00689-6
  33. Villarreal OD, Mersaoui SY, Yu Z, Masson JY, Richard S. Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution. Life Sci Alliance 2020;3:e202000762. https://doi.org/10.26508/lsa.202000762
  34. Skourti-Stathaki K, Proudfoot NJ, Gromak N. Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination. Mol Cell 2011;42:794-805. https://doi.org/10.1016/j.molcel.2011.04.026
  35. Zhao DY, Gish G, Braunschweig U, et al. SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination. Nature 2016;529:48-53. https://doi.org/10.1038/nature16469
  36. Yu Z, Mersaoui SY, Guitton-Sert L, et al. DDX5 resolves R-loops at DNA double-strand breaks to promote DNA repair and avoid chromosomal deletions. NAR Cancer 2020;2:zcaa028. https://doi.org/10.1093/narcan/zcaa028
  37. Sessa G, Gomez-Gonzalez B, Silva S, et al. BRCA2 promotes DNA-RNA hybrid resolution by DDX5 helicase at DNA breaks to facilitate their repairdouble dagger. EMBO J 2021;40:e106018. https://doi.org/10.15252/embj.2020106018
  38. Leszczynska KB, Dzwigonska M, Estephan H, et al. Hypoxia-mediated regulation of DDX5 through decreased chromatin accessibility and post-translational targeting restricts R-loop accumulation. Mol Oncol 2023;17:1173-91. https://doi.org/10.1002/1878-0261.13431
  39. Zhang C, Wang M, Li Y, Zhang Y. Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition. Sci Adv 2022;8:eabj3967. https://doi.org/10.1126/sciadv.abj3967
  40. Dang Y, Li S, Zhao P, et al. The lysine deacetylase activity of histone deacetylases 1 and 2 is required to safeguard zygotic genome activation in mice and cattle. Development 2022;149:dev200854. https://doi.org/10.1242/dev.200854
  41. Ma P, Pan H, Montgomery RL, Olson EN, Schultz RM. Compensatory functions of histone deacetylase 1 (HDAC1) and HDAC2 regulate transcription and apoptosis during mouse oocyte development. Proc Natl Acad Sci USA 2012;109:E481-9. https://doi.org/10.1073/pnas.1118403109
  42. Matsubara K, Lee AR, Kishigami S, et al. Dynamics and regulation of lysine-acetylation during one-cell stage mouse embryos. Biochem Biophys Res Commun 2013;434:1-7. https://doi.org/10.1016/j.bbrc.2013.03.083
  43. Wang M, Chen Z, Zhang Y. CBP/p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos. EMBO J 2022;41:e112012. https://doi.org/10.15252/embj.2022112012
  44. Wu D, Dean J. Maternal factors regulating preimplantation development in mice. Curr Top Dev Biol 2020;140:317-40. https://doi.org/10.1016/bs.ctdb.2019.10.006
  45. Aoki F. Zygotic gene activation in mice: profile and regulation. J Reprod Dev 2022;68:79-84. https://doi.org/10.1262/jrd.2021-129
  46. Aoshima K, Inoue E, Sawa H, Okada Y. Paternal H3K4 methylation is required for minor zygotic gene activation and early mouse embryonic development. EMBO Rep 2015;16:803-12. https://doi.org/10.15252/embr.201439700
  47. Lee H, You SY, Han DW, et al. Dynamic change of R-loop implicates in the regulation of zygotic genome activation in mouse. Int J Mol Sci 2022;23:14345. https://doi.org/10.3390/ijms232214345
  48. Suo L, Zhou YX, Jia LL, et al. Transcriptome profiling of human oocytes experiencing recurrent total fertilization failure. Sci Rep 2018;8:17890. https://doi.org/10.1038/s41598-018-36275-6