Dmitry Fyodorov, Ph.D.

 

Assistant Professor, Department of Cell Biology Chanin Bldg., Room 414 718 430-4021 dfyodoro@aecom.yu.edu Biosketch Complete list of publications

Research interests BIOCHEMISTRY AND GENETICS OF CHROMATIN ASSEMBLY In the eukaryotic nucleus, hundreds of millions of base pairs of DNA are packed into chromosomes. Chromatin, the central nucleoprotein filament of a chromosome, has many different forms and organization levels, which range from the 10 nm oligonucleosome filament to highly condensed metaphase chromatin. Chromatin is the natural state of DNA in the nucleus and the native substrate for nuclear processes such as DNA replication, recombination, repair and transcription. The assembly of DNA into chromatin and dynamic conversion between its different forms are critical steps in the maintenance and regulation of the eukaryotic genome. The ultimate goal of our research is to understand how chromosomes are assembled and how chromatin assembly regulates the structure and activity of eukaryotic chromosomes. The crucial first step in this direction is a systematic study of enzymes that mediate the assembly of chromatin. In our work we use biochemical approaches to analyze mechanisms of chromatin assembly by a SWI/SNF-like factor ACF. In addition, we dissect its function in vivo by methods of Drosophila genetics. We also use biochemistry and genetics to identify novel assembly factors in Drosophila. Thus, we are trying to uncover the intricate network of chromatin assembly factors and their roles in the hierarchical organization of the chromosome, from the nucleosome to higher-order structures. 1. Molecular mechanisms of chromatin assembly ACF (ATP-utilizing chromatin assembly and remodeling factor) was identified on the basis of its ability to mediate ATP-dependent reconstitution of chromatin in vitro. ACF consists of two subunits, an SNF2-like ATPase ISWI and another evolutionary conserved polypeptide termed Acf1. We study ACF as a prototype assembly factor to elucidate elementary molecular events that take place during ATP-dependent assembly of nucleosomes.  In the presence of a core histone chaperone NAP-1, ACF mediates deposition of histone octamers on the DNA and forms arrays of regularly spaced nucleosomes. Upon reaction initiation, ACF commits to the DNA template and assembles nucleosomes as a processive, ATP-driven, DNA-translocating motor. Multiple conserved polypeptide domains of ACF subunits are involved in this reaction. 2. Biological function of chromatin assembly factors In Drosophila, ACF is an integral component of interphase chromatin. It is the major (but not the only) ATP-dependent chromatin assembly factor in the fly embryo. In order to expose its biological function, we study Drosophila mutants that do not express ACF. It appears that the enzymatic activity of ACF in vivo is directed towards the assembly of nucleosomes as well as repressive, higher-order chromatin. For instance, ACF-deficient animals have reduced nucleosome periodicity in bulk embryonic chromatin and exhibit suppressed pericentric position effect variegation (PEV). 3. Reconstitution of chromatin in vitro During chromatin assembly, ACF can mediate deposition of both core and linker histones. Therefore, ACF can assemble the 30 nm chromatin fiber in a defined system in vitro. In order to reconstitute other higher-order chromatin structures, we are trying to incorporate various components, such as posttranslationally modified core histones, histone variants and heterochromatin proteins, into the defined assembly system. In vitro assembled chromatin vectors can turn into useful tools in research and therapy. Among other outcomes, these studies will eventually lead to the discovery of molecular techniques to reconstitute functional metazoan chromosomes.

Recent publications Konev AY, Tribus M, Park SY, Podhraski V, Lim CY, Emelyanov AV, Vershilova E, Pirrotta V, Kadonaga JT, Lusser A, Fyodorov DV. CHD1 motor protein is required for deposition of histone variant H3.3 into chromatin in vivo. Science. 2007 Aug 24;317(5841):1087-90. Fyodorov, D.V., Blower, M.D., Karpen, G.H., and Kadonaga, J.T. (2004). Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo. Genes Dev. 18, 170-183. Fyodorov, D.V., and Kadonaga, J.T. (2003). Chromatin assembly in vitro with purified recombinant ACF and NAP-1 [37]. Meth. Enzymol. 371, 499-515. Fyodorov, D.V., and Kadonaga, J.T. (2002). Dynamics of ATP-dependent chromatin assembly by ACF. Nature 418, 896-900. Fyodorov, D.V., and Levenstein, M.E. (2002). Chromatin assembly using Drosophila systems. Unit 21.7. in “Current Protocols in Molecular Biology”, John Wiley & Sons, New York. Fyodorov, D.V., and Kadonaga, J.T. (2002). Binding of Acf1 to DNA involves a WAC motif and is important for ACF-mediated chromatin assembly. Mol. Cell. Biol. 22, 6344-6353. Fyodorov, D.V., and Kadonaga, J.T. (2001). The many faces of chromatin remodeling: SWItching beyond transcription. Cell 106, 523-525. Ito, T.*, Levenstein, M.E.*, Fyodorov, D.V.*, Kutach, A.L., Kobayashi, R., and Kadonaga, J.T. (1999). ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly. Genes Dev. 13, 1529-1539.

Dmitry Fydorov: Research interests | Biosketch Faculty research at a glance Birshtein | Bouhassira | Edelmann | Fyodorov | Keogh | Kielian | Kitsis | Nathenson | Query Scharff | Schildkraut | Shafritz | Singer | Skoultchi | Stanley | Steidl |Warner | Ye   Home