Our laboratory is interested in understanding the mechanisms controlling mammalian development and cell differentiation.  We study the epigenetic functions of chromatin proteins and transcription factors in control of gene expression in embryonic stem cells, in red blood cells, and in Drosophila. Our approaches involve directed gene inactivation and transgenesis in mice and Drosophila.  We also study control of proliferation and differentiation in red blood cell progenitors and in leukemia cells in which normal development is disrupted.  Currently there are two major projects underway in the lab.

Role of H1 Linker Histones and Chromatin Remodeling Factors in Chromatin Structure, DNA Methylation, the Histone Code, Gene Expression and Development in Mice and Drosophila.  Recent studies show that posttranslational modifications of core histones (H2A, H2B, H3, H4) (the Histone Code) play a very important role in control of gene expression.  The H1 linker histones are more diverse than the core histones.  Mice contain 8 H1 histone subtypes including differentiation-specific and tissue-specific subtypes, whereas Drosophila has only one type of H1.  H1’s are thought to be responsible for the final level of packaging DNA into the compact chromatin structure but we know very little about their role in gene expression and development.  We are studying the functional roles of H1 linker histones by inactivating (knocking-out) specific H1 genes in mice and the single H1 in Drosophila.  We are also reintroducing mutant H1 linker histones into H1 depleted mouse cells and flies, to perform structure-function studies.  We have also established a new role for H1 histone in DNA methylation, genomic imprinting and establishment of the histone code.  We are also studying the chromatin remodeling factor that assembles H1 histone into chromatin.

Control of Proliferation and Differentiation in Normal and Leukemic Blood Cells: In this project we are investigating how cell proliferation and differentiation are coordinated in normal blood cell development and how this coordination is disrupted in leukemia.  We have investigating the molecular mechanisms for the cross talk between these two cellular programs in normal and leukemic blood cells.  Our studies are focused on the relationships between the master transcription factors that control blood cell development and the cell cycle regulators (cyclins, cyclin-dependent kinases (cdks), cdk inhibitors and RB) that regulate the cell division cycle proliferation.  This project includes genome-wide approaches involving chromatin immunoprecipitation and high throughput sequencing (ChIP-Seq) and gene expression profiling by RNA-Seq.

Willcockson, M. A., Healton, S. E., Weiss, C. N., Bartholdy, B. A., Botbol, Y., Mishra, L. N., Sidhwani, D. S., Wilson, T. J., Pinto, H. B., Maron, M. I., Skalina, K. A., Toro, L. N., Zhao, J., Lee, C. H., Hou, H., Yusufova, N., Meydan, C., Osunsade, A., David, Y., Cesarman, E., Melnick, A. M., Sidoli, S., Garcia, B. A., Edelmann, W., Macian, F. & Skoultchi, A. I. H1 histones control the epigenetic landscape by local chromatin compaction. Nature 589, 293-298, (2021). doi:10.1038/s41586-020-3032-z. [PDF Full Text]

Healton, S. E., Pinto, H. D., Mishra, L. N., Hamilton, G. A., Wheat, J. C., Swist-Rosowska, K., Shukeir, N., Dou, Y., Steidl, U., Jenuwein, T., Gamble, M. J. & Skoultchi, A. I. H1 linker histones silence repetitive elements by promoting both histone H3K9 methylation and chromatin compaction. Proc Natl Acad Sci U S A 117, 14251-14258, (2020). doi:10.1073/pnas.1920725117. [PDF Full Text]

Willcockson, M. A., Taylor, S. J., Ghosh, S., Healton, S. E., Wheat, J. C., Wilson, T. J., Steidl, U. & Skoultchi, A. I. Runx1 promotes murine erythroid progenitor proliferation and inhibits differentiation by preventing Pu.1 downregulation. Proc Natl Acad Sci U S A 116, 17841-17847, (2019). doi:10.1073/pnas.1901122116. [PDF Full Text]

Fyodorov DV, Zhou BR, Skoultchi AI, Bai Y. Emerging roles of linker histones in regulating chromatin structure and function Nat Rev Mol Cell Biol. Mar;19(3):192-206, (2018). PMCID: PMC5897046. [PDF Full Text]

Andreyeva EN, Bernardo TJ, Kolesnikova TD, Lu X, Yarinich LA, Bartholdy BA, Guo X, Posukh OV, Healton S, Willcockson MA, Pindyurin AV, Zhimulev IF, Skoultchi AI, Fyodorov DV. Regulatory functions and chromatin loading dynamics of linker histone H1 during endoreplication in Drosophila. Genes Dev. Mar 15;31(6):603-616, (2017). PMCID: PMC5393055. [PDF Full Text]

Kavi H., X. Lu, N. Xu, B.A. Bartholdy, E. Vershilova, A.I. Skoultchi and D.V. Fyodorov. A Genetic Screen and Transcript Profiling Reveal a Shared Regulatory Program for Drosophila Linker Histone H1 and Chromatin Remodeler CHD1. G3: Genes Genomes Genetics Jan 27 (2015). PMID: 25628309 PMCID: PMC4390582. [PDF Full Text]

Xu N., A.V. Emelyanov, D.V. Fyodorov, and A.I. Skoultchi. Drosophila linker histone H1 coordinates STAT-dependent organization of heterochromatin and suppresses tumorigenesis caused by hyperactive JAK-STAT signaling. Epigenetics Chromatin. Jul 28;7:16. (2014). PMCID: PMC4149798. [PDF Full Text]

Alvarez-Saavedra M., Y. De Repentigny, P.A. Lagali, E.V. Raghu Ram, K. Yan, E. Hashem, D. Ivanochko, M.S. Huh, D. Yang, A.J. Mears, M.A. Todd, C.P. Corcoran, E.A. Bassett, N.J. Tokarew , J. Kokavec, R. Majumder, I. Ioshikhes , V.A. Wallace, R. Kothary, E. Meshorer, T. Stopka, A.I. Skoultchi and D.J. Picketts. Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation. Nat Commun. 20;5:4181, (2014). PMCID: PMC4083431. [PDF Full Text]

Lu, X., S.N. Wontakal, H. Kavi, B,J. Kim, P.M. Guzzardo, A.V. Emelyanov, N. Xu, G.J. Hannon, J. Zavadil, D.V. Fyodorov and A.I. Skoultchi. Drosophila H1 regulates the genetic activity of heterochromatin by recruitment of Su(var)3-9. Science 340(6128): 78-81, (2013). PMCID: PMC3756538. [PDF Full Text]

Yang S.M., B.J. Kim, L. Norwood-Toro and A.I. Skoultchi. H1 linker histone promotes epigenetic silencing by regulating both DNA methylation and histone H3 methylation. Proc Natl Acad Sci U S A, 110(5):1708-13, (2013). PMCID: PMC3562819. [PDF Full Text]

Wontakal S.N., X. Guo, C. Smith, T. MacCarthy. E.H. Bresnick, A. Bergman , M.P. Snyder, S.M. Weissman, D. Zheng and A.I. Skoultchi. A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation. Proc Natl Acad Sci USA, 6;109(10):3832-7, (2012). PMCID: PMC3309740. [PDF Full Text]

Wontakal S.N., X. Guo, B. Will, M. Shi, D. Raha, M.C. Mahajan, S. Weissman, M. Snyder, U. Steidl, D. Zheng and A.I. Skoultchi. A Large Gene Network in Immature Erythroid Cells Is Controlled by the Myeloid and B Cell Transcriptional Regulator PU.1. PLoS Genet 7(6), e1001392. (2011). PMCID: PMC3111485. [PDF Full Text]

Maclean J,A,, A. Bettegowda, B.J. Kim, C.H. Lou, S.M. Yang, A. Bhardwaj, S. Shanker, Z. Hu, Y. Fan, S. Eckardt, K.J. McLaughlin, A.I. Skoultchi, and M.F. Wilkinson. The rhox homeobox gene cluster is imprinted and selectively targeted for regulation by histone h1 and DNA methylation. Mol Cell Biol. 31(6):1275-87, (2011). Epub 2011 Jan 18. PMCID: PMC3067900. [PDF Full Text]

Choe, K.S., O. Ujhelly, S.N. Wontakal and A.I. Skoultchi. PU.1 directly regulates CDK6 gene expression, linking the cell proliferation and differentiation programs in erythroid cells. J. Biol. Chem. 285(5):3044-52, (2009). PMCID: PMC2823399. [PDF Full Text]

Lu, X., S.N. Wontakal, A.V. Emelyanov, P. Morcillo, A.Y. Konev, D.V. Fyodorov and A.I. Skoultchi. Linker histone H1 is essential for Drosophila development, the establishment of pericentric heterochromatin, and a normal polytene chromosome structure. Genes Dev. Feb 15;23(4):452-65, (2009). PMCID: PMC2648648. [PDF Full Text]

Woodcock, C.L., A.I. Skoultchi and Y. Fan. Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length. Chromosome Res 14, 17-25, (2006). PMID: 16506093. [PDF Full Text]

Fan, Y., T. Nikitina, J. Zhao, T.J. Fleury, R. Bhattacharyya, E.E. Bouhassira, A. Stein, C.L. Woodcock and A.I. Skoultchi. Histone H1 depletion in mammals alters global chromatin structure but causes specific changes in gene regulation. Cell 123, 1199-1212, (2005). PMID: 16377562. [PDF Full Text]