After the completion of the Human genome project, the strategic direction of modern genetics shifted towards functional genomics, which also studies noncoding regions of DNA, located in heterochromatin. Most functions of heterochromatin are yet to be determined. Shortarm telomeres of each human acrocentric chromosome (13, 14, 15, 21, and 22) have satellite strands, called nucleolar organizer regions (NORs), which consist of heterochromatin. Human NORs contain from 250 to 670 gene replicas of ribosomal RNA (rRNA) and only 50 % of these replicas are transcribed. The satellite strands of chromatids in some acrocentric chromosomes are united, forming «satellite associations» (SAs), which are always transcriptionally active. The phenomenon of SA lies in the fact that it is a highly specific indicator of the structure and function of the nucleolus in the preceding interphase. rDNA in human genome may be subject to changes due to cancer. In this study, we determined the epigenetic variability of ribosomal cistrons in lung cancer (LC). It was found that the frequency of chromatid SAs per cell was reliably increased (p < 0.05) in patients with LC (1.76 ± 0.08) as compared with the similar index for clinically healthy persons, aged 22–45 (control group) (1.35 ± 0.03). The associative activity of chromatids of the 15th chromosome was decreased in the control group (p < 0.01) as compared with the activity of chromatids of other chromosomes. Contrary to the control group, in patients with LC the chromatids of the 15th chromosome manifested higher involvement in the associations (p < 0.05) than the chromatids of other acrocentric chromosomes, which corresponded to the order: 15> 13 = 14> 21> 22. A similar phenomenon was observed for the associations of chromatids of homologous chromosomes (15 : 15) in patients with LC, which reliably exceeded the index for this type of SA in healthy middleaged people (p < 0.001). Our results demonstrated that the differential activity of satellite strands of the chromatids of the 15th chromosome in patients with LC is subject to epigenetic variability which highlights the relevance of studying SAs for diagnostics and elaboration of treatment strategy. The studies on epigenetic variability of ribosomal cistrons of acrocentric chromatids under pathology is a new direction in medicine, aimed at diagnostics of diseases and determining a new treatment strategy in future.
Keywords: chromatid associations, heterochromatinization, lung cancer, NOR, satellite strands
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References
1. Baranov, V. and Kuznecova, T., Cytogenetics of Human Embryonic Development, Leningrad: Nauka, 2006, pp. 3–329.
2. Bartova, E., Structure and epigenetics nucleoli compared with an unusual nucleola compartments, J. Histochem. Cytochem., 2015, vol. 58, pp. 391–403.
3. Caudron-Herger, M. and Diederichs, S., Mitochondrial mutations in human cancer: duration of translation, RNA Biol., 2018, vol. 15, pp. 62–69.
4. Caudron-Herger, M., Pankert, T., Seiler, J., et al., Alu element-containing RNAs maintain nucleolar structure and function, EMBO J., 2015, vol. 34, pp. 2758–2774.
5. Cong, R., Das, S., Ugrinova, I., et al., Interaction of nucleolin with ribosomal RNA genes and its role in RNA polymerase 1 transcription, Nucleic Acids Res., 2012, vol. 19, pp. 9441–9454.
6. Donat, G., Montanaro, L., and Derenzini, M., Ribosome biogenesis and control of cell proliferation: p53 is not alone, Cancer Res., 2012, vol 72l, pp. 1602–1607.
7. Ginisty, H., Sicard, H., Roger, B., et al., Structure and functions of nucleolin, J. Cell Sci., 1999, vol. 12, pp. 761–772.
8. Grummt, I. and Pikaard, C., Epigenetic mechanisms controlling RNA polymerase I transcription, Nat. Rev. Mol. Cell Biol., 2003, vol. 4, pp. 641–649.
9. Hirota, K., Miyoshi, T., and Kugou, K., Stepwise chromatin remodeling by a cascade of transcription initiation of non-coding RNA, Nature, 2008, vol. 456, pp. 130–134.
10. Horn, L. and Lovely, C., Neoplasms of the lung, in Harrison’s Principles of Internal Medicine, Jameson, J.L., Eds., 20th ed., 2018, chapter 74.
11. Kadotani, T., Watanabe, Y., and Makino, S., Chromosome study in aging, Int. J. Hum. Genet., 2002, vol. 2, pp. 5–9.
12. Kim, J., Dilthey, A., Nagaraja, R., et al., Variation in human chromosome 21 ribosomal RNA gene is characterized by TAR cloning and long-read sequencing, Nucleic Acids Res., 2018, vol. 46, pp. 6712–6725.
13. Lezhava, T., Human Chromosomes and Aging: From 80 to 114 Years, New York: Nova Science Publisher, 2006, pp. 3–177.
14. Lezhava, T., Jokhadze, T., and Monaselidze, J., The functioning of “aged” heterochromatin, in Senescence, Nagata, T., Ed., Intech Open Science, 2012, chapter 26, pp. 631–664.
15. Lezhava, T., Buadze, T., Jokhadze, T., et al., Normalization of epigenetic change in the genome by peptide bioregulator (Ala-Glu-Asp-Glu) in pulmonary tuberculosis, Int. J. Pept. Res. Ther., 2019, vol. 25, pp. 555–563.
16. Lezhava, T., Buadze, T., Monaselidze, J., et al., Epigenetic changes of activity of the ribosomal cistrons of human acrocentric chromatids in fetuses, middle-aged (22–45 years) and old individuals (80–106 years), Cytol. Genet., 2020, vol. 54, pp. 233–242.
17. Malinovskaya, E., Ershova, E., Golimbet, V., et al., Copy number of human ribosomal genes with aging: unchanged mean, but narrowed range and decreased variance in elderly group, Front. Genet., 2018. https://doi.org/10.3389/fgene.2018.00306
18. Mattick, J. and Mehler, M., RNA editing, DNA recoding and the evolution of human cognition, Trends Neurosci., 2008, vol. 31, pp. 227–233.
19. Mayer, C., Neubert, M., and Grummt, I., The structure of NoRC-associated RNA is crucial for targeting the chromatin remodelling complex NoRC to the nucleolus, EMBO Rep., 2008, vol. 9, pp. 774–780.
20. Mazin, A., Suicidal function of DNA methylation in age-related genome disintegration, Ageing Res. Rev., 2009, vol. 8, no. 4, pp. 314–327.
21. Nemeth, A. and Langst, G., Genome organization in and around the nucleolus, Trends Genet., 2011, vol. 27, pp. 149–156.
22. Olson, M., The Nucleolus, Spinger Science LLC, 2011, pp. 105–278.
23. Pankaj, K. and Desai, B., Frequency of satellite associations of acrocentric chromosomes in oral squamous cell carcinoma patients after 5-FU and cisplatin treatments, Int. J. Mol. Med. Sci., 2016, vol. 6, pp. 1–5.
24. Porokhovnik, L. and Gerton, J., Ribosomal DNA-connecting ribosome biogenesis and chromosome biology, Chromosome Res., 2019, vol. 27, pp. 1–3.
25. Porokhovnik, L. and Lyapunova, N., Dosage effects of human ribosomal genes (rDNA) in health and disease, Chromosome Res., 2019, vol. 27, pp. 5–17.
26. Prokofeva-Belgovskay, A., Heterochromatin Regions of Chromosomes, Moscow: Nauka, 1986, pp. 3–431.
27. Santoro, R. and Grummt, I., Epigenetic mechanism of rRNA gene silencing: temporal order of NoRC mediated histone modification, chromatin remodeling, and DNA methylation, Mol. Cell Biol., 2005, vol. 25, pp. 2539–2546.
28. Savku, R. and Olson, M., Protein B23 endoribonuclease could play a role in pre-rRNA processing, Nucleic Acids Res., 1998, vol. 26, pp. 4508–4515.
29. Schmitz, K., Schmit, N., Hoffman-Robrer, U., et al., TAF12 recruits Gadd45a and the nucleotide excision repair complex to the promoter of rRNA genes leading to active DNA demethylation, Mol. Cell, 2009, vol. 33, pp. 344–353.
30. Shen, H., Zhu, M., and Wang, C., Precision oncology of lung cancer: genetic and genomic differences in Chinese population, NPJ Precis. Onc., 2019. https://doi.org/10.1038/s41698-019-0086-1
31. Sluis, M., Vuuren, C., Mangan, H., et al., NORs on human acrocentric chromosome p-arms are active by default and can associate with nucleoli independently of rDNA, Proc. Natl. Acad. Sci. U. S. A., 2020, vol. 117, pp. 10368–10377.
32. Storck, S., Shukla, M., Dimitrov, S., et al., Functions of the histone chaperone nucleolin in diseases, Biochemistry, 2007, vol. 41, pp. 25–44.
33. Valori, V., Tus, K., Laukaitis, C., et al., Human rDNA copy number is unstable in metastatic breast cancers, Epigenetics, 2020, vol. 15, pp. 85–106.