Our research program is strongly integrated with graduate education at Penn State College of Medicine. I am a member of graduate Program in Biomedical Science ( https://med.psu.edu/biomedical-sciences-phd ). I am keen on providing new opportunities for cutting-edge graduate research training in the area of chromatin structure and function with emphasis on collaborations with computational scientists and neuroscientists thus giving the students a broad perspective for cross-disciplinary research. I am planning to continue inviting graduate students from the Biomedical Science program for rotations and thesis projects in my lab. I expect that the students choosing my laboratory would take BCHEM 522 course “Molecular Genetics: Genes to Genomes” and other classes under the option in Biochemistry and Molecular Genetics. Six PhD students and two MS students have successfully completed their thesis projects in my laboratory and authored publications in leading scientific journals. My student’s works were recognized by several prestigious awards such as Dean’s Graduate Education award (Bulynko), Moskowitz Family Endowment Award for Graduate Research Excellence (Correll), Charles Hill award (Springhetti and Bulynko), as well as American Heart Associations fellowships (Bulynko and Correll) and American Association of University Women fellowship (Chakraborty).
Graduate students sponsored:
Abigail Harris Becker, M.S. 2018
Thesis title: Epigenetic and gene expression changes mediated by histone H3 methylation in acute myeloid leukemia.
1. 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.
Jenna Buckwalter, Ph.D. 2017
Thesis title: Role of linker DNA conformations
in chromatin higher-order structure
1.Grigoryev, S.A., Bascom, G., Buckwalter J.M., Schubert, M., Woodcock, C.L., and Schlick, T. (2016) Proc. Natl. Acad. Sci. USA, 113, (5), 1238-1243.
2.J. M. Buckwalter, D. Norouzi, A. Haratyunyan, V. B. Zhurkin, and S. A. Grigoryev. (2017)Regulation of chromatin folding by conformational variations of nucleosome linker DNA. Nucleic Acids Res., 45 (16), 9372-9387.
Michael Schubert, M.S. 2015
Thesis title: Role of linker DNA length and linker histone occupancy in chromatin compaction
1. Grigoryev, S.A., Bascom, G., Buckwalte,r J.M., Schubert, M., Woodcock, C.L., and Schlick, T. (2016) Proc. Natl. Acad. Sci. USA, 113, pii: 201518280. PMID: 26787893
2. Correll, S.J., Schubert, M., and Grigoryev, S.A. (2012) EMBO Journal, 31(10), 2416-26.
Sangita Chakraborty, Ph.D. 2012
Thesis title: Construction and characterization of a minichromosome reporter system to study chromatin boundaries in S. cerevisiae
Graduate Award: American Association of University Women (AAUW) Doctoral Fellowship Award
1. Chakraborty, S. A., Kazi, A.A., Khan, T.M., and Grigoryev, S. A. (2014) Genetics, 198 (3), 1015-1029
2. Chakraborty, S. A., Simpson, R.T., and Grigoryev, S. A. (2011) PLOS One, 6 (9), e24835
Sarah Correll, Ph.D. 2011
Thesis title: Molecular and structural determinants of chromatin folding
Graduate Award: Moskowitz Family Endowment Award for Graduate Research Excellence.
1. Correll, S., Schubert, M., and Grigoryev, S.A. (2012) EMBO Journal, 31(10), 2416-26.
2. 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) Molecular Cell 35, 642-656.
3. Grigoryev, S.A. Arya, G., Correll S., Woodcock, C.L., and Schlick, T. (2009) Proc. Natl. Acad. Sci. USA. 106, 13317-13322.
4. 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) J.Cell Biol. 184, 205-213.
5. S. A. Grigoryev, S. Correll, and Christopher L. Woodcock (2009) J. Biomol. Structure and Dynamics vol. 26, p. 908.
Yaroslava Bulynko, Ph.D. 2006
Thesis title: Role of cysteine protease cathepsin L in maintenance of epigenetic histone modifications and constitutive heterochromatin
Graduate Awards: Charles W. Hill Graduate Fellowship Award ; Dean’s Award for Excellence in Graduate Education
1. Bulynko, Y A. , Hsing , L.C., Mason, R.W., Tremethick, D., and Grigoryev, S.A. (2006) Mol. Cell. Biol. 26, 4172-4184.
2. 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). EMBO Journal, 25, 3144-3155.
3. Grigoryev, S.A., Bulynko, Y.A., Popova, E.Y. (2006) Chromosome Research, 14, 53-69.
4. 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) Journal of Biol Chem. 277, 13192-13201
5. Bulynko, Y.A., and Grigoryev, S.A. (2003) Mol. Biol. Cell. Vol. 14(suppl.) p.370a
Natalia Istomina, Ph.D. 2006
Thesis title: Role of nonhistone proteins in organization of chromatin at the boundaries of beta-globin gene
1. 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). Mol. Cell. Biol, 23, 6455-6468.
2. Springhetti, E. M., Istomina, N. E., Whisstock, J. C., Nikitina, T. V., Woodcock, C. L., and Grigoryev, S. A., (2003) Journal of Biol. Chem. 278, 43384-43393.
Evelyn Springhetti, Ph.D. 2003
Thesis title: The molecular mechanism of developmentally-regulated chromatin condensation by MENT
Graduate Award: Charles W. Hill Graduate Fellowship Award
1. Springhetti, E. M., Istomina, N. E., Whisstock, J. C., Nikitina, T. V., Woodcock, C. L., and Grigoryev, S. A., (2003) Journal of Biol. Chem. 278, 43384-43393.
2. 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). Mol. Cell. Biol, 23, 6455-6468.
3. Springhetti, E.M., Shushanov, S.S., and Grigoryev S.A. (2001) Mol. Biol. Cell. Vol. 12(suppl.) p.494a.
My laboratory welcomes undergraduate research training and internship. At Hershey, I have been advisor to fourteen undergraduates while they performed their research projects in my lab. The PI is committed to continuing participation in undergraduate studies as an undergraduate mentor and a member of Summer Undergraduate Research Internship (SURIP) advisory board. I am planning to continue inviting student research assistants from the undergraduate students that apply for research internships at our SURIP program every year. This program is intended for college students who are interested in pursuing a career in the biological sciences (https://med.psu.edu/surip). My current National Science Foundation – funded research can provide several projects especially suited for undergraduate research. These include constructing multiple nucleosome array and their reconstitution into circular minichromosomes, preparation of a yeast shuttle vector, transfection into yeast cells and its phenotypic characterization by growing on selective yeast media. These projects have clear goals achievable during a period of summer training and are also excellent for forming a junior mentor (graduate student)/undergraduate trainee team. The undergraduate interns are encouraged to return to the lab in subsequent summer or break periods to complete their projects, to present at national conferences, and participate in peer-reviewed publications. The results of the summer projects are usually presented at our yearly Summer Undergraduate Research Symposia. I am also planning to sponsor undergraduate presentations at national research meeting such as Penn State Summer Symposium on Chromatin in 2019 and support undergraduate student co-authorship on peer-reviewed research publications. The examples of our recent research papers co-authored by undergraduate interns Anna Harutyunyan and Tamreen Khan are:
- 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.
- 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
Undergraduate student Valentina Kostyuk (Hunter College of CUNY, New York) presents her research on nucleosome DNA conformations