Publications
Peer-reviewed scientific journals:
1. Grigoryev, S.A. (2018) Chromatin higher-order folding: a perspective with linker DNA angles. Biophys. J. 114(10):2290-2297.
2. Nikitina T, Norouzi D, Grigoryev SA and Zhurkin VB (2017) DNA topology in chromatin is defined by nucleosome spacing. Science Adv. v.3: e1700957
3. Buckwalter JM, Norouzi D, Harutyunyan A, Zhurkin VB., and Grigoryev SA (2017) Regulation of chromatin folding by conformational variations of nucleosome linker DNA. Nucl. Acids Res. 45 (16), 9372-9387.
4. Salzberg AC, Harris-Becker A, Popova EY, Keasey N, Loughran TP, Claxton DF, Grigoryev SA. 2017. Genome-wide mapping of histone H3K9me2 in acute myeloid leukemia reveals large chromosomal domains associated with massive gene silencing and sites of genome instability. PLOS One 12: e0173723.
5. Adkins NL, Swygert SG, Kaur P, Niu H, Grigoryev SA, Sung P, Wang H, Peterson CL. 2017. Nucleosome-like, ssDNA-histone octamer complexes and the implication for DNA double-strand break repair. J Biol Chem. 292 (13), 5271-81.
6. Grigoryev S.A. Bascom G., Buckwalter J.M., Schubert M.B.,Woodcock, C.L., and Schlick, T. (2016) Evidence for Heteromorphic Chromatin Fibers from Analysis of Nucleosome Interactions. Proc. Natl. Acad. Sci. USA, 113 (5), 1238-1243.
7. Maher K, Jerič-Kokelj B, Butinar M, Mikhaylov G, Manček-Keber M, Stoka V, Vasiljeva O, Turk B, Grigoryev S.A., Kopitar-Jerala N. (2014) A role for stefin B (cystatin B) in inflammation and endotoxemia. J Biol Chem. 289(46), 31736-50.
8. Chakraborty, S. A., Kazi, A.A., Khan, T.M., and Grigoryev, S. A. (2014) Nucleosome-positioning sequence repeats impact chromatin silencing in yeast Minichromosomes. Genetics, 198 (3), 1015-1029
9. A.Luque, R. Collepardo-Guevara, S.A. Grigoryev, and T. Schlick (2014) Dynamic condensation of linker histone C-terminal domain regulates chromatin structure. Nucl. Acids Res. V. 42(12), 7553-7560.
10. Popova EY, Grigoryev S.A., Fan Y, Skoultchi AI, Zhang SS, Barnstable CJ. (2013) Developmentally Regulated Linker Histone H1c Promotes Heterochromatin Condensation and Mediates Structural Integrity of Rod Photoreceptors in Mouse Retina. J Biol Chem. 288(24), 17895-17907.
11. Nikitina T, Wang D, Gomberg M, Grigoryev S.A., Zhurkin VB. (2013) Combined Micrococcal Nuclease and Exonuclease III Digestion Reveals Precise Positions of the Nucleosome Core/Linker Junctions: Implications for High-Resolution Nucleosome Mapping. J Mol Biol. 2013 Jun 12;425(11):1946-60.
12. Lukášová,E., Kořistek, Z., Klabusay, M., Ondřej, V., Grigoryev, S.A., Bačíková, Řezáčová, A. M., Falk, M. Vávrová, J., Kohútová V., and Kozubek S. (2013). Granulocyte maturation determines ability to release chromatin NETs and loss of DNA damage response; these properties are absent in immature AML granulocytes. BBA – Molecular Cell Research, 1833, 767-779.
13. Grigoryev, S.A. (2012) Nucleosome spacing and chromatin higher-order folding. Nucleus, 3(6), 493-499.
14. Correll, S.J., Schubert, M.H., and Grigoryev, S.A. (2012) Short nucleosome repeats impose rotational modulations on chromatin fiber folding. EMBO Journal, 31(10), 2416-26.
15. Grigoryev, S.A. and Woodcock, C.L. (2012) The 30 nm fiber. Exp. Cell Res., 318(12), 1448-55.
16. Schlick, T., Hayes, J., and Grigoryev, S.A. (2012) Towards Convergence of Experimental Studies and Theoretical Modeling of the Chromatin Fiber. J Biol Chem, 287(8), 5183-5191.
17. Chakraborty, S. A., Simpson, R.T., and Grigoryev, S. A. (2011) A single heterochromatin boundary element imposes position-independent antisilencing activity in Saccharomyces cerevisiae minichromosomes. PLOS One, 6 (9), e24835
18. Arya, G., Maitra, A., and Grigoryev, S.A. (2010) A structural perspective on the where, how, why, and what of nucleosome positioning. J. Biomol. Structure and Dynamics 27, 803-820.
19. Rochman, M., Postnikov, Y., Correll, S., Malicet, C., Winkovitch, S., Karpova, T.S., McNally, J.G., Wu, X., Bubunenko, N. A. Grigoryev, S.A., and Bustin. M. (2009) The Interaction of NSBP1 With Nucleosomes In Euchromatin Counteracts Linker Histone-mediated Chromatin Compaction And Modulates Transcription. Molecular Cell 35, 642-656.
20. Grigoryev, S.A. Arya, G., Correll S., Woodcock, C.L., and Schlick, T. (2009) Evidence for Heteromorphic Chromatin Fibers from Analysis of Nucleosome Interactions. Proc. Natl. Acad. Sci. USA. 106, 13317-13322.
21. Zhao, Y., Wang, S., Popova, E.Y., Grigoryev, S.A. and Zhu, J. (2009) Rearrangement of Upstream Sequences of the hTERT Gene During Cellular Immortalization Genes, Chromosomes & Cancer 48, 963–974.
22. Ong P.C., Golding S.J., Pearce M.C., Irving J.A., Grigoryev S.A., Pike D., Langendorf C.G., Bashtannyk-Puhalovich T.A., Bottomley S.P., Whisstock J.C., Pike R.N., McGowan S.. (2009) Conformational change in the chromatin remodelling protein MENT. PLoS ONE. 4(3):e4727.
23. Popova, E.Y., Krauss, S.W. Short, S.A., Lee, G., Villalobos, J., Etzell, J., Koury, M.J. , Ney, P.A., Chasis, J.A., Grigoryev, S.A. (2009) Chromatin condensation in terminally differentiating mouse erythroblasts does not involve special architectural proteins but depends on histone deacetylation. Chromosome Res. 17, 47-64.
24. Wang, Y., Li, M., Stadler, S., Correll, S., Hayama, R., Leonelli, L., Li, P., Han, H., Nathan, C., Grigoryev, S.A., Allis, C.D., and Coonrod, S. (2009) Histone hypercitrullination mediates chromatin decondensation and neutrophil extracellular trap formation. J.Cell Biol. 184, 205-213.
25. Nikitina, T., Ghosh, R.P., Horowitz-Scherer, R.A., Hansen, J.C., Grigoryev, S.A, and Woodcock, C.L. (2007) MeCP2-chromatin interactions include the formation of chromatosome-like structures and are altered in mutations causing Rett syndrome. J Biol Chem. , 282, 28237-45.
26. Ong, P.C., McGowan S., Pearce M.C., Irving J.A., Kan W.T., Grigoryev S.A., Turk B., Silverman G.A., Brix K., Bottomley S.P., Whisstock J.C., Pike R.N. (2007) DNA accelerates the inhibition of human cathepsin V by serpins. J Biol Chem. 282, 28237-28245.
27. Bulynko, Y A. , Hsing , L.C., Mason, R.W., Tremethick, D., and Grigoryev, S.A. (2006) Cathepsin L stabilizes histone modification landscape on Y chromosome and pericentromeric heterochromatin.
Mol. Cell. Biol. 26, 4172-4184.
28. McGowan, S., Buckle, A.M., Irving, J.A.,, Ong, P-C., Bashtannyk-Puhalovich, T.A., Kan, W-T, Henderson, K.N. , Bulynko, Y.A., Popova, E.Y., Smith, A.I., Bottomley, S.P., Rossjohn, J., Grigoryev S.A., Pike, R.N., and Whisstock, J.C. (2006) X-ray crystal structure of MENT: Evidence for functional loop-sheet polymers in chromatin condensation. EMBO Journal, 25, 3144-3155.
29. Popova, E.Y., Claxton, D.F.,, Lukasova, E., Bird, P.I. and Grigoryev, S.A. (2006) Epigenetic Heterochromatin Markers Distinguish Terminally Differentiated Leukocytes From Incompletely Differentiated Leukemia Cells in Human Blood. Experimental Hematology 34, 453-462.
30. Grigoryev*, S.A., Bulynko, Y.A., Popova, E.Y. (2006) The end adjusts the means: heterochromatin remodeling during terminal cell differentiation. Chromosome Research, 14, 53-69.
31. Lukasova E, Koristek Z, Falk M, Kozubek S, Grigoryev S, Kozubek M, Ondrej V, Kroupova I. (2005) Methylation of histones in myeloid leukemias as a potential marker of granulocyte abnormalities. J Leukoc Biol. 77, 100-111.
32. Grigoryev, S. A., Nikitina, T., Pehrson, J.R., Singh, P.B., and Woodcock. C.L. (2004) Dynamic relocation of epigenetic chromatin markers reveals an active role of constitutive heterochromatin in the transition from proliferation to quiescence. J. Cell Sci., 117, 6153-62.
33. Grigoryev, S.A. (2004) Keeping fingers crossed: heterochromatin spreading through interdigitation of nucleosome arrays. FEBS Letters, 564, 4-8.
34. Springhetti, E. M., Istomina, N. E., Whisstock, J. C., Nikitina, T. V., Woodcock, C. L., and Grigoryev, S. A., (2003) Folding and Bridging of Nucleosome Arrays by a Developmentally Regulated Heterochromatin Protein, MENT: the Role of the M-loop and the RCL domains. Journal of Biol. Chem., 278, 43384-43393.
35. N. E. Istomina, S. S. Shushanov, E. S. Springhetti, V. L. Karpov, I. A.Krasheninnikov, K. Stevens, K. S. Zaret, P. B. Singh, and S. A. Grigoryev (2003) Insulation of the Chicken b-globin Chromosomal Domain from a Chromatin-Condensing Protein, MENT. Mol. Cell. Biol, 23, 6455-6468.
36. J.A. Irving, S.S. Shushanov, R.N. Pike, E.Y. Popova, D. Brömme, T. H. T. Coetzer, S.P. Bottomley, I.A. Boulynko , S.A. Grigoryev and J.C. Whisstock (2002) Inhibitory activity of a heterochromatin-associated serpin (MENT) against papain-like cysteine proteinases affects chromatin structure and blocks cell proliferation. Journal of Biol Chem. 277, 13192-13201.
37. Grigoryev, S.A. (2001) Higher Order Folding of Heterochromatin: Protein Bridges Span the Nucleosome Arrays. Biochem. and Cell Biol. 79, 227-241.
38. Bednar, J., Studitsky, V., Grigoryev, S.A., Woodcock, C.L., and Felsenfeld, G. (1999) Nature of the nucleosomal barrier to transcription: direct observation of paused intermediates by electron cryo-microscopy. Molecular Cell 4, 377-386.
39. Grigoryev, S.A., Bednar, J., and Woodcock, C.L. (1999) MENT, a heterochromatin protein that mediates higher order chromatin folding, is a new Serpin family member. Journal of Biol. Chem. 274, 5626-5636.
40. Bednar, J., Horowitz, R.A., Grigoryev, S.A., Carruthers, L.M., Hansen,J.C., Koster, A.J., and Woodcock, C.L. (1998) Nucleosomes, linker DNA and linker histone form a unique structural motif that directs the higher order folding and compaction of nucleosomal arrays. Proc. Natl. Acad. Sci.USA 95, 14173-14178.
41. Grigoryev, S.A., and Woodcock, C.L. (1998) Chromatin structure in granulocytes: a link between tight compaction and accumulation of aheterochromatin-associated protein (MENT). Journal of Biol. Chem. 273, 3082-3089.
42. Grigoryev S.A., Stuart A.E., Kwon Y-T., Arfin S.M., Bradshaw R.A., Jenkins, N.A., Copeland N.J., and Varshavsky A. (1996) A mouse amidase specific for N-terminal asparagine: the gene, the enzyme, and their function in the N-end rule pathway.
Journal of Biol. Chem. 271, 28521-28532.
43. Woodcock,C.L., Grigoryev,S.A., Horowitz, R.A., and Whitaker, N. (1993) A modelling approach to chromatin folding incorporating linker variability. Generation of fibers that mimic the native structures. Proc. Nat. Acad. Sci. USA 90, 9021-9025.
44. Grigoryev,S.A. and Woodcock,C.L. (1993) Stage-specific expression and localization of MENT, a nuclear protein associated with chromatin condensation in terminally differentiated avian erythroid cells. Exp.Cell Res. 206, 335-343.
45. Grigoryev,S.A., Solovieva,V.O., Spirin,K.S., and Krasheninnikov,I.A. (1992) A Novel nonhistone protein (MENT) promotes nuclear collapse at the terminal stage of avian erythropoiesis. Exp.Cell Res. 198, 268-275.
46. Grigoryev,S.A., Spirin,K.S., and Krasheninnikov,I.A. (1990) Loosened nucleosome linker folding in transcriptionally-active chromatin of chicken embryo erythrocyte nuclei. Nucl.Acids Res. 18, 7397-7406.
47. Grigoryev S.A., Spirin K.S., Solovieva V.O., and Krasheninnikov I.A. (1990) A novel basic nonhistone protein participates in the condensation of inactive chromatin at the terminal stage of chicken erythrocyte differentiation. Doklady AN USSR, vol.312,p.1266-1270.
48. Spirin K.S., Grigoryev S.A., and Krasheninnikov I.A. (1988) Mechanism of generation of associated oligonucleosomes in the course of electrophoresis. Molekuljarnaja Biologija (Molecular Biology, USSR), vol.22,p.490-493.
49. Spirin K.S., Grigoryev S.A. and Krasheninnikov I.A. (1988). The differencies in the structure of transcriptionally-active and inert chromatin as revealed by DNP-electrophoresis. Doklady AN USSR, vol.300,p.490-493.
50. Grigoryev S.A. (1984) A spatial model for transcription and the mechanism of RNA elongation. Biologicheskie Nauki (Biological Sciences, USSR), vol.12,p.17-24.
51. Grigoryev S.A. and Krasheninnikov, I.A. (1983) A topological model fortranscription and a role for nucleosome linkers.FEBS Letters 162, 1-4.
52. Ananieva N.M., Grigoryev S.A., Ermokhina T.M., and Krasheninnikov I.A. (1983). Isolation and characterization of nucleosomes from the mold Neurospora crassa. Doklady AN USSR, vol.272, p.1252-1254.
53. Grigoryev S.A. and Krasheninnikov I.A. (1983) Geometry of nucleosome DNA and the linking number problem. Doklady AN USSR, vol.268,p.1494-1497.
54. Grigoryev S.A. and Krasheninnikov I.A. (1982) Transient unfolding of trypsin-digested nucleosome core particles. European J. Biochem., vol.129,p.119-125.
55. Grigoryev, S.A., and Krasheninnikov, I.A. (1982) Products of limited proteolysis of chromatin core particles. Biokhymija (Biochemistry, USSR) vol. 47, p.707-712.
56. Grigoryev S.A. and Ioffe L.B. (1981) The dependence of the linking number of a circular minichromosome upon the shape and the orientation of its nucleosomes. FEBS Letters., vol.130, p.43-46.
57. Grigoryev S.A., and Krasheninnikov I.A. (1981) Reversible conformational transitions of proteolized chromatin core-particles. Doklady AN USSR, vol.258,p.232-236.
Book chapters and conference papers:
58. Walker SI, Callahan BJ, Arya G, Barry JD, Bhattacharya T, Grigoryev S, Pellegrini M, Rippe K, Rosenberg SM. (2013) Evolutionary dynamics and information hierarchies in biological systems. Ann N Y Acad Sci. 1305: 1-17
59. Grigoryev S., McGowan S. (2011) Isolation and Characterization of the Nuclear Serpin MENT. Methods Enzymol. 2011;501:29-47.
60. Grigoryev S.A., Bulynko, Y.A., Pike, R.N., and Whisstock, J.C. (2007) MENT, a chromatin-associated serpin from avian blood cells: structure and function. In: Molecular and Cellular Aspects of the Serpinopathies and Disorders in Serpin Activity. Eds: G.Silverman and D.Lomas. World Scientific Publishing Co., London.
61. Varshavsky, A., Byrd, C., Davydov, I.V., Dohmen, J., Ghislain, M., Gonzales, M., Grigoryev, S., Johnson, E.S., Johnsson, N., Johnston, J.A., Kwon, Y.T., Levy, F., Lomovskaya, O., Madura, K., Rumenaph, T., Shrader, T., Suzuki, T., Turner, G., and Webster, A. (1998) The N-end rule pathway. in: Ubiquitin and the Biology of the Cell, eds.: Peters, J,-M., Harris, J.R. & Finley, D. Plenum, New York.