Kenji Murakami, Ph.D.
Associate Professor of Biochemistry and Biophysics
Associate Professor, Penn Center for Genome Integrity, University of Pennsylvania
Associate professor, Institute of Structural Biology, University of Pennsylvania
Department: Biochemistry and Biophysics
Graduate Group Affiliations
Contact information
Department of Biochemistry and Biophysics
363 Clinical Research Building
Perelman School of Medicine at the University of Pennsylvania
Philadelphia, PA 19104
363 Clinical Research Building
Perelman School of Medicine at the University of Pennsylvania
Philadelphia, PA 19104
Office: 215-573-1125
Lab: 215-898-8863
Lab: 215-898-8863
Education:
B.Sc. (Physics)
University of Tokyo, 1999.
M.Sc. (Physics)
University of Tokyo, 2001.
Ph.D. (Physics)
University of Tokyo, 2004.
Permanent linkB.Sc. (Physics)
University of Tokyo, 1999.
M.Sc. (Physics)
University of Tokyo, 2001.
Ph.D. (Physics)
University of Tokyo, 2004.
Description of Research Expertise
Eukaryotic gene expression by RNA polymerase II (pol II) requires the orchestration of a large number of factors during each stage of transcription. Proper gene regulation underlies organismal development, environmental response, and can be disrupted in disease. The goal of our lab is to determine the mechanisms of pol II transitions between initiation, elongation, and re-initiation, and its regulations in the context of chromatin, which we will accomplish through structural (cryo-EM and cross-linking mass spectrometry) and biochemical dissection of these macromolecular complexes.Selected Publications
H.J. Kim, M.R. Szurgot, T. van Eeuwen, M.D. Ricketts, P. Basnet, A.L. Zhang, A. Vogt, S. Sharmin, C.D. Kaplan, B.A. Garcia, R. Marmorstein*, and K. Murakami*: Structure of the Hir histone chaperone complex. Molecular Cell 84(14): 601-2617.E12, 6 2024 Notes: * Co-corresponding authorsL. Palao III, K. Murakami*, and Y.W. Chang*: Combining per-particle cryo-ET and cryo-EM single particle analysis to elucidate heterogeneous heterogeneous DNA-protein organization. Current Opinion in Structural Biology 84: 102765, 2 2024 Notes: * Co-corresponding authors
J. Gorbea†, L. Palao III†, S.F. Chen, H.J. Kim, L. Snyder, Y.W. Chang✉, K.L. Tsai*, and K. Murakami*: Structural basis of a transcription pre-initiation complex on a divergent promoter. Molecular Cell 83(4): 574-588, 2 2023 Notes: † Co-first authors * Co-corresponding authors
C. Yang†, R. Fujiwara†, H.J. Kim, P. Basnet, Y. Zhu, J. Gorbea, S. Steimle, B.A. Garcia, C.D. Kaplan, and K. Murakami: Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Molecular Cell. † Co-first authors, 82(3): 660-676, 2 2022.
T. van Eeuwen, Y. Shim, H.J. Kim, T. Zhao, S. Basu, B.A. Garcia, C.D. Kaplan, J.H. Min✉, and K. Murakami✉: Cryo-EM Structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in Nucleotide Excision Repair. Nature Communications 12(1): 3338, 6 2021 Notes: ✉ Co-corresponding authors
T. van Eeuwen, T. Li, H.J. Kim, J. Gorbea, M.I. Parker, R.L. Dunbrack, B.A. Garcia, K.L. Tsai✉, and K. Murakami✉: Structure of TFIIK for phosphorylation of CTD of RNA polymerase II. Science Advances 7(15): eabd4420, 4 2021 Notes: ✉ Co-corresponding authors
S. Steimle, T. van Eeuwen, Y. Ozturk, H.J. Kim, M. Braitbard, N. Selamoglu, B.A. Garcia, D. Schneidman-Duhovny, K. Murakami✉, and F. Daldal✉: Cryo-EM Structures of Engineered Active bc1-cbb3 type CIII2CIV Super-complexes and Electronic Communication Between the Complexes. Nature Communications 12(1): 929, 2 2021 Notes: ✉ Co-corresponding authors; contributed to project design, structural analysis, and data interpretation.
R. Fujiwara, N. Damodaren, J.E. Wilusz, and K. Murakami : The capping enzyme facilitates promoter escape and assembly of a follow-on preinitiation complex for reinitiation. Proc. Natl Acad. Sci. USA 116(45): 22573-22582, 11 2019.
R. Fujiwara, K. Murakami: In vitro reconstitution of yeast RNA polymerase II transcription initiation with high efficiency. Methods. Elsevier, 159-160: 82-89, 4 2019.
Damodaren N, Van Eeuwen T, Zamel J, Lin-Shiao E, Kalisman N, Murakami K.: Def1 interacts with TFIIH and modulates RNA polymerase II transcription. Proc. Natl Acad. Sci. USA 114(50): 13230-13235, 12 2017.