Nuclear re-localization of Dicer in primary mouse embryonic fibroblast nuclei following DNA damage

English version České info

Cytoplasmic Dicer is a key component of the canonical micro (mi)RNA biogenesis pathway. However, a growing body of evidence points toward localisation and activity of mammalian Dicer in the nucleus. A recent study by Much et al., employed an endogenously HA-tagged Dicer knock-in mouse cell line to show that Dicer is exclusively cytoplasmic. This paper challenges several studies reporting various RNA metabolic functions of Dicer in human nuclei. Given the controversy about Dicer’s subcellular localisation, it is essential to address this issue. Employing the same cells as used by Much and colleagues, we combined super-resolution microscopy followed by 3D reconstitution and biochemical assays to show that endogenously tagged HA-Dicer prominently localises in the nucleus under physiological conditions. We demonstrate that DNA damage triggers accumulation of phosphorylated HA-Dicer in the nucleus, confirming previous observations in human cells. Our data indicate evolutionary conservation of nuclear Dicer localisation and function in mammals in response to DNA damage.

Vyšlo v časopise: Nuclear re-localization of Dicer in primary mouse embryonic fibroblast nuclei following DNA damage. PLoS Genet 14(2): e32767. doi:10.1371/journal.pgen.1007151
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1007151

Souhrn

Zdroje

1. Rybak-Wolf A, Jens M, Murakawa Y, Herzog M, Landthaler M, Rajewsky N. A variety of dicer substrates in human and C. elegans. Cell. 2014;159(5):1153–67. doi: 10.1016/j.cell.2014.10.040 25416952.

2. Ha M, Kim VN. Regulation of microRNA biogenesis. Nature reviews Molecular cell biology. 2014;15(8):509–24. doi: 10.1038/nrm3838 25027649.

3. Burger K, Gullerova M. Swiss army knives: non-canonical functions of nuclear Drosha and Dicer. Nat Rev Mol Cell Biol. 2015;16(7):417–30. Epub 2015/05/29. doi: 10.1038/nrm3994 26016561.

4. Kanellopoulou C, Muljo SA, Kung AL, Ganesan S, Drapkin R, Jenuwein T, et al. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes & development. 2005;19(4):489–501. doi: 10.1101/gad.1248505 15713842; PubMed Central PMCID: PMC548949.

5. Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ, Schultz RM, et al. Critical roles for Dicer in the female germline. Genes & development. 2007;21(6):682–93. doi: 10.1101/gad.1521307 17369401; PubMed Central PMCID: PMC1820942.

6. Sinkkonen L, Hugenschmidt T, Filipowicz W, Svoboda P. Dicer is associated with ribosomal DNA chromatin in mammalian cells. PloS one. 2010;5(8):e12175. doi: 10.1371/journal.pone.0012175 20730047; PubMed Central PMCID: PMC2921364.

7. Ando Y, Tomaru Y, Morinaga A, Burroughs AM, Kawaji H, Kubosaki A, et al. Nuclear pore complex protein mediated nuclear localization of dicer protein in human cells. PloS one. 2011;6(8):e23385. doi: 10.1371/journal.pone.0023385 21858095; PubMed Central PMCID: PMC3156128.

8. Haussecker D, Proudfoot NJ. Dicer-dependent turnover of intergenic transcripts from the human beta-globin gene cluster. Molecular and cellular biology. 2005;25(21):9724–33. doi: 10.1128/MCB.25.21.9724-9733.2005 16227618; PubMed Central PMCID: PMC1265824.

9. Gagnon KT, Li L, Chu Y, Janowski BA, Corey DR. RNAi factors are present and active in human cell nuclei. Cell reports. 2014;6(1):211–21. doi: 10.1016/j.celrep.2013.12.013 24388755; PubMed Central PMCID: PMC3916906.

10. Redfern AD, Colley SM, Beveridge DJ, Ikeda N, Epis MR, Li X, et al. RNA- induced silencing complex (RISC) Proteins PACT, TRBP, and Dicer are SRA binding nuclear receptor coregulators. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(16):6536–41. doi: 10.1073/pnas.1301620110 23550157; PubMed Central PMCID: PMC3631673.

11. Skourti-Stathaki K, Kamieniarz-Gdula K, Proudfoot NJ. R-loops induce repressive chromatin marks over mammalian gene terminators. Nature. 2014. doi: 10.1038/nature13787 25296254.

12. Neve J, Burger K, Li W, Hoque M, Patel R, Tian B, et al. Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation. Genome research. 2015. doi: 10.1101/gr.193995.115 26546131.

13. Morris KV, Chan SW, Jacobsen SE, Looney DJ. Small interfering RNA- induced transcriptional gene silencing in human cells. Science. 2004;305(5688):1289–92. doi: 10.1126/science.1101372 15297624.

14. Cernilogar FM, Di Giaimo R, Rehfeld F, Cappello S, Lie DC. RNA interference machinery-mediated gene regulation in mouse adult neural stem cells. BMC neuroscience. 2015;16:60. doi: 10.1186/s12868-015-0198-7 26386671; PubMed Central PMCID: PMC4575781.

15. Cheng W, Qi Y, Tian L, Wang B, Huang W, Chen Y. Dicer promotes tumorigenesis by translocating to nucleus to promote SFRP1 promoter methylation in cholangiocarcinoma cells. Cell death & disease. 2017;8(2):e2628. doi: 10.1038/cddis.2017.57 28230864.

16. Doyle M, Badertscher L, Jaskiewicz L, Guttinger S, Jurado S, Hugenschmidt T, et al. The double-stranded RNA binding domain of human Dicer functions as a nuclear localization signal. Rna. 2013;19(9):1238–52. doi: 10.1261/rna.039255.113 23882114; PubMed Central PMCID: PMC3753931.

17. Lau PW, Guiley KZ, De N, Potter CS, Carragher B, MacRae IJ. The molecular architecture of human Dicer. Nature structural & molecular biology. 2012;19(4):436–40. doi: 10.1038/nsmb.2268 22426548; PubMed Central PMCID: PMC3319852.

18. Kennedy EM, Whisnant AW, Kornepati AV, Marshall JB, Bogerd HP, Cullen BR. Production of functional small interfering RNAs by an amino-terminal deletion mutant of human Dicer. Proceedings of the National Academy of Sciences of the United States of America. 2015;112(50):E6945–54. doi: 10.1073/pnas.1513421112 26621737; PubMed Central PMCID: PMC4687602.

19. Much C, Auchynnikava T, Pavlinic D, Buness A, Rappsilber J, Benes V, et al. Endogenous Mouse Dicer Is an Exclusively Cytoplasmic Protein. PLoS genetics. 2016;12(6):e1006095. doi: 10.1371/journal.pgen.1006095 27254021; PubMed Central PMCID: PMC4890738.

20. Comazzetto S, Di Giacomo M, Rasmussen KD, Much C, Azzi C, Perlas E, et al. Oligoasthenoteratozoospermia and infertility in mice deficient for miR-34b/c and miR-449 loci. PLoS genetics. 2014;10(10):e1004597. doi: 10.1371/journal.pgen.1004597 25329700; PubMed Central PMCID: PMC4199480.

21. White E, Schlackow M, Kamieniarz-Gdula K, Proudfoot NJ, Gullerova M. Human nuclear Dicer restricts the deleterious accumulation of endogenous double- stranded RNA. Nat Struct Mol Biol. 2014;21(6):552–9. Epub 2014/05/13. doi: 10.1038/nsmb.2827 24814348; PubMed Central PMCID: PMCPMC4129937.

22. Passon N, Gerometta A, Puppin C, Lavarone E, Puglisi F, Tell G, et al. Expression of Dicer and Drosha in triple-negative breast cancer. Journal of clinical pathology. 2012;65(4):320–6. doi: 10.1136/jclinpath-2011-200496 22259182.

23. Khalil AM, Driscoll DJ. Epigenetic regulation of pericentromeric heterochromatin during mammalian meiosis. Cytogenetic and genome research. 2010;129(4):280–9. doi: 10.1159/000315903 20606401; PubMed Central PMCID: PMC3202914.

24. Burger K, Schlackow M, Potts M, Hester S, Mohammed S, Gullerova M. Nuclear phosphorylated Dicer processes double-stranded RNA in response to DNA damage. J Cell Biol. 2017;216(8):2373–89. Epub 2017/06/24. doi: 10.1083/jcb.201612131 28642363.

25. Chitale S, Richly H. DICER and ZRF1 contribute to chromatin decondensation during nucleotide excision repair. Nucleic acids research. 2017. doi: 10.1093/nar/gkx261 28402505.

26. Drake M, Furuta T, Suen KM, Gonzalez G, Liu B, Kalia A, et al. A requirement for ERK-dependent Dicer phosphorylation in coordinating oocyte-to-embryo transition in C. elegans. Dev Cell. 2014;31(5):614–28. Epub 2014/12/10. doi: 10.1016/j.devcel.2014.11.004 25490268; PubMed Central PMCID: PMCPMC4261158.

27. Ward IM, Minn K, van Deursen J, Chen J. p53 Binding protein 53BP1 is required for DNA damage responses and tumor suppression in mice. Mol Cell Biol. 2003;23(7):2556–63. Epub 2003/03/18. doi: 10.1128/MCB.23.7.2556-2563.2003 12640136; PubMed Central PMCID: PMCPMC150747.

28. Giglia-Mari G, Zotter A, Vermeulen W. DNA damage response. Cold Spring Harbor perspectives in biology. 2011;3(1):a000745. doi: 10.1101/cshperspect.a000745 20980439; PubMed Central PMCID: PMC3003462.

29. Kastan MB, Lim DS. The many substrates and functions of ATM. Nature reviews Molecular cell biology. 2000;1(3):179–86. doi: 10.1038/35043058 11252893.

30. Marechal A, Zou L. DNA damage sensing by the ATM and ATR kinases. Cold Spring Harbor perspectives in biology. 2013;5(9). doi: 10.1101/cshperspect.a012716 24003211; PubMed Central PMCID: PMC3753707.

31. Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER, 3rd, Hurov KE, Luo J, et al. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science. 2007;316(5828):1160–6. doi: 10.1126/science.1140321 17525332.

32. Beshore EL, McEwen TJ, Jud MC, Marshall JK, Schisa JA, Bennett KL. C. elegans Dicer interacts with the P-granule component GLH-1 and both regulate germline RNPs. Developmental biology. 2011;350(2):370–81. doi: 10.1016/j.ydbio.2010.12.005 21146518; PubMed Central PMCID: PMC3031674.