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2018 Scientific Report

  • Text
  • Institute
  • Biology
  • Methylation
  • Molecular
  • Mechanisms
  • Epigenetic
  • Michigan
  • Vari
  • Scientific

Center for Epigenetics

Center for Epigenetics HUILIN LI, Ph.D. Dr. Li earned his Ph.D. in electron crystallography from the University of Science and Technology Beijing, where he trained with the late K. H. Kuo. He joined VARI in 2016 from Stony Brook University, New York. RESEARCH INTERESTS The work of our lab focuses on the structural basis of DNA replication, the bacterial proteasome system, and the regulation and modification of the Notch receptor. STAFF Lin Bai, Ph.D. Xiang Feng, Ph.D. Hao-Chi Hsu, Ph.D. Amanda Kovach, B.S. Hua Li, Ph.D. Michelle Martin, A.A. Yanting Yin, Ph.D. Hongjun Yu, Ph.D. Eukaryotic DNA replication Replication initiation is tightly regulated, because failure to ensure once-only initiation per cell cycle can result in uncontrolled proliferation and genomic instability, which are hallmarks of tumorigenesis. We use structural and biochemical approaches to uncover the molecular mechanisms underlying eukaryotic chromosomal replication. Work in our lab over the past year has revealed how ORC, with the help of Cdc6, loads the Mcm2-7 hexamer and how the Mcm2-7 double-hexamer binds the origin DNA. In the S phase of the cell cycle, the active Cdc45–Mcm2-7–GINS helicase (CMG) works with the leading strand polymerase epsilon, the lagging strand polymerase delta, and the primase-polymerase alpha to synthesize new DNA. We also determined the structure of the 11-protein yeast CMG helicase and have shown how the helicase interacts with the replication fork DNA. Proteostasis in Mycobacterium tuberculosis Tuberculosis kills some 1.5 million people globally every year. Mycobacterium tuberculosis can be killed by nitric oxide (NO) of the host immune system. The Mtb proteasome is a key to the organism’s resistance to such attack and thus is a promising target for the development of anti-TB chemotherapeutics. In the past year, we have solved the structure of the ATPase-dependent proteasomal activator Mpa and the ATP-independent proteasomal activator PafE. We also uncovered the structural basis for the species-selective binding of six N,C-capped dipeptides to the Mtb proteasome. Our work illuminates the bacterial proteasome system and facilitates anti-TB chemotherapeutic development efforts. STUDENTS Minge Du, M.S. Ruda Santos, M.S. Zuanning Yuan, M.S. 26 | VAN ANDEL RESEARCH INSTITUTE SCIENTIFIC REPORT

GERD PFEIFER, Ph.D. Dr. Pfeifer earned his M.S. in pharmacology in 1981 and his Ph.D. in biochemistry in 1984 from Goethe University in Frankfurt, Germany. He most recently held the Lester M. and Irene C. Finkelstein Chair in Biology at the City of Hope in Duarte, California, before joining VARI in 2014 as a Professor. RESEARCH OVERVIEW The laboratory studies epigenetic mechanisms of human diseases, with a focus on DNA methylation and the role of 5-methylcytosine oxidation by the TET protein family. STAFF Zhijun Huang, Ph.D. Seung-Gi Jin, Ph.D. Jennifer Johnson, M.S. Amy Nelson Zhi-Qiang (Ken) Wang, Ph.D. DNA methylation in cancer This work centers on the hypothesis that CpG islands are protected from methylation in normal cells by a set of specific proteins, such as 5-methylcytosine oxidases, CXXC proteins, and the polycomb complex. The protection breaks down during early stages of malignancy. We investigate mechanisms of DNA hypermethylation using DNA-methylation mapping and chromatin mapping in both normal and malignant cells, as well as bioinformatic approaches and functional studies employing gene inactivation in tissue culture. TET3 and related proteins in basic biology and human disease The removal of methyl groups from DNA has been recognized as an important pathway in cancer and possibly in other diseases. Our lab studies mechanisms of 5-methylcytosine oxidation. We have identified three isoforms of the TET3 5-methylcytosine oxidase and characterized them using biochemical, functional, and genetic approaches. We observed that one isoform of TET3 specifically binds to 5-carboxylcytosine, thus establishing an anchoring mechanism of TET3 to its reaction product, which may aid in localized 5-methylcytosine oxidation and removal. We also study several TET3-associated proteins, trying to understand their biological roles. TET3 has a rather limited genomic distribution and is targeted to the transcription start sites of defined sets of genes, many of which function within the lysosome and autophagy pathways. We are exploring the mechanistic consequences of 5-methylcytosine oxidation in these genes, with the long-term goal of determining whether neurodegeneration has an epigenetic origin. In another project, we are exploring the function of a TET3-binding protein and its effect on TET-mediated processes in embryonic stem cells and in myoblasts. This work has implications for understanding the mechanisms underlying muscular dystrophy. VAN ANDEL RESEARCH INSTITUTE SCIENTIFIC REPORT | 27

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