The impact of oncomutations and post-translational modifications of linker histone H1 on the chromatosome structure and stability
Abstract
In this work, we investigated the chromatosome stability under the influence of oncomutations and post-translational modifications. A chromatosome is formed during the interaction of a nucleosome with linker histone. This interaction may be characterized by the binding free energy. We hypothesized that oncomutations may be associated with changing of the binding free energy and subsequent changes in chromatin compaction state and gene expression levels. Calculations of the binding free energy were performed using the FoldX program algorithms. Screening of the positions of post-translational modifications for potential steric constraints was also performed. The analysis of the data allowed us to identify the oncomutations and post-translational modifications, which can significantly change the binding free energy of the linker histone with the nucleosome, thereby, possibly, affecting the structure of chromatin.
About the Authors
M. V. Bass
Lomonosov Moscow State University
Russian Federation
Russian Federation
Department of Bioengineering, School of Biology
Leninskiye gory 1–12, Moscow, 119234
G. A. Armeev
Lomonosov Moscow State University
Russian Federation
Russian Federation
Department of Bioengineering, School of Biology
Leninskiye gory 1–12, Moscow, 119234
K. V. Shaitan
Lomonosov Moscow State University
Russian Federation
Russian Federation
Department of Bioengineering, School of Biology
Leninskiye gory 1–12, Moscow, 119234
A. K. Shaytan
Lomonosov Moscow State University
Russian Federation
Russian Federation
Department of Bioengineering, School of Biology
Leninskiye gory 1–12, Moscow, 119234
References
1. Zhou B.-R., Jiang J., Feng H., Ghirlando R., Xiao T.S., Bai Y. Structural mechanisms of nucleosome recognition by linker histones // Mol. Cell. 2015. Vol. 59. N 4. P. 628–638.
2. Bednar J., Garcia-Saez I., Boopathi R., et al. Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1 // Mol. Cell. 2017. Vol. 66. N 3. P. 384–397.
3. Gorkovets T.K., Armeev G.A., Shaitan K.V., Shaytan A.K. Joint effect of histone H1 amino acid sequence and DNA nucleotide sequence on the structure of chromatosomes: analysis by molecular modeling methods // Moscow Univ. Biol. Sci. Bull. 2018. Vol. 73. N 2. P. 82–87.
4. Draizen E.J., Shaytan A.K., Mariсo-Ramírez L., Talbert P.B., Landsman D., Panchenko A.R. HistoneDB 2.0: a histone database with variants— an integrated resource to explore histones and their variants // Database (Oxford). 2016. Vol. 2016: baw014. DOI: 10.1093/database/baw014.
5. Kuzmichev A., Jenuwein T., Tempst P., Reinberg D. Different Ezh2-containing complexes target methylation of histone H1 or nucleosomal histone H3 // Mol. Cell. 2004. Vol. 14. N 2. P. 183–193.
6. Th’ng J.P.H., Sung R., Ye M., Hendzel M.J. H1 family histones in the nucleus. Control of binding and localization by the C-terminal domain // J. Biol. Chem. 2005. Vol. 280. N 30. P. 27809–27814.
7. Li H., Kaminski M.S., Li Y., et al. Mutations in linker histone genes HIST1H1 B, C, D, and E; OCT2 (POU2F2); IRF8; and ARID1A underlying the pathogenesis of follicular lymphoma // Blood. 2014. Vol. 123. N 10. P. 1487–1498.
8. Tatton-Brown K., Loveday C., Yost S., et al. Mutations in epigenetic regulation genes are a major cause of overgrowth with intellectual disability // Am. J. Hum. Genet. 2017. Vol. 100. N 5. P. 725–736.
9. Sjöblom T., Jones S., Wood L.D., et al. The consensus coding sequences of human breast and colorectal cancers // Science. 2006. Vol. 314. N 5797. P. 268–274.
10. Th’ng J.P., Guo X.W., Swank R.A., Crissman H.A., Bradbury E.M. Inhibition of histone phosphorylation by staurosporine leads to chromosome decondensation // J. Biol. Chem. 1994. Vol. 269. N 13. P. 9568–9573.
11. Clausell J., Happel N., Hale T.K., Doenecke D., Beato M. Histone H1 subtypes differentially modulate chromatin condensation without preventing ATP-dependent remodeling by SWI/ SNF or NURF // PLOS One. 2009. Vol. 4. N 10: e0007243.
12. Christophorou M.A., Castelo-Branco G., Halley-Stott R.P., Oliveira C.S., Loos R., Radzisheuskaya A., Mowen K.A., Bertone P., Silva J.C.R., Zernicka-Goetz M., Nielsen M.L., Gurdon J.B., Kouzarides T. Citrullination regulates pluripotency and histone H1 binding to chromatin // Nature. 2014. Vol. 507. N 7490. P. 104–108.
13. Dai L., Peng C., Montellier E., et al. Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark // Nat. Chem. Biol. 2014. Vol. 10. N 5. P. 365–370.
14. Xie Z., Zhang D., Chung D., et al. Metabolic regulation of gene expression by histone lysine β-hydroxybutyrylation // Mol. Cell. 2016. Vol. 62. N 2. P. 194–206.
15. Nacev B.A., Feng L., Bagert J.D., Lemiesz A.E., Gao J., Soshnev A.A., Kundra R., Schultz N., Muir T.W., Allis C.D. The expanding landscape of ‘oncohistone’ mutations in human cancers // Nature. 2019. Vol. 567. N 7749. P. 473.
16. Webb B., Sali A. Protein structure modeling with MODELLER // Protein Structure Prediction. Methods in Molecular Biology (Methods and Protocols), vol 1137 / Eds. D. Kihara. N.Y.: Humana Press, 2014. P. 1–15.
17. Schymkowitz J., Borg J., Stricher F., Nys R., Rousseau F., Serrano L. The FoldX web server: an online force field // Nucleic Acids Res. 2005. Vol. 33. Suppl. 2. P. W382–W388.
18. Tate J.G., Bamford S., Jubb H.C., et al. COSMIC: the catalogue of somatic mutations in cancer // Nucleic Acids Res. 2019. Vol. 47. N D1. P. D941–D947.
19. Adzhubei I.A., Schmidt S., Peshkin L., Ramensky V.E., Gerasimova A., Bork P., Kondrashov A.S., Sunyaev S.R. A method and server for predicting damaging missense mutations // Nature Methods. 2010. Vol. 7. N 4. P. 248–249.
20. UniProt: a worldwide hub of protein knowledge // Nucleic Acids Res. 2019. Vol. 47. N D1. P. D506–D515.
21. Margreitter C., Petrov D., Zagrovic B. Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications // Nucleic Acids Res. 2013. Vol. 41. N W1. P. W422–W426.
22. Hanwell M.D., Curtis D.E., Lonie D.C., Vandermeersch T., Zurek E., Hutchison G.R. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform // J. Cheminform. 2012. Vol. 4: 17.
23. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. UCSF Chimera – a visualization system for exploratory research and analysis // J. Comput. Chem. 2004. Vol. 25. N 13. P. 1605–1612.
24. Bozic I., Antal T., Ohtsuki H., Carter H., Kim D., Chen S., Karchin R., Kinzler K.W., Vogelstein B., Nowak M.A. Accumulation of driver and passenger mutations during tumor progression // Proc. Natl. Acad. Sci. U.S.A. 2010. Vol. 107. N 43. P. 18545–18550.
25. Schwartzentruber J., Korshunov A., Liu X.Y., et al. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma // Nature. 2012. Vol. 482. N 7384. P. 226–231.
26. Kumar N.M., Walker I.O. The binding of histones H1 and H5 to chromatin in chicken erythrocyte nuclei // Nucleic Acids Res. 1980. Vol. 8. N 16. P. 3535–3552.
Review
For citations:
Bass M.V., Armeev G.A., Shaitan K.V., Shaytan A.K. The impact of oncomutations and post-translational modifications of linker histone H1 on the chromatosome structure and stability. Vestnik Moskovskogo universiteta. Seriya 16. Biologiya. 2019;74(3):156-162. (In Russ.)
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