Kenji Murakami, Ph.D.

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Assistant Professor of Biochemistry and Biophysics
assistant professor, Penn Center for Genome Integrity, University of Pennsylvania
assistant 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
Office: 215-573-1125
Lab: 215-898-8863
B.Sc. (Physics)
University of Tokyo, 1999.
M.Sc. (Physics)
University of Tokyo, 2001.
Ph.D. (Physics)
University of Tokyo, 2004.
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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

Tsai KL, Yu X, Gopalan S, Chao TC, Zhang Y, Florens L, Washburn MP, Murakami K, Conaway RC, Conaway JW, Asturias FJ.: Mediator structure and rearrangements required for holoenzyme formation. Nature 544(7649): 196-201, 4 2017 Notes: DOI: 10.1038/nature21393.

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 Notes: DOI: 10.1073/pnas.1707955114

Fazal FM†, Meng CA†, Murakami K†, Kornberg RD, Block SM: Real-Time Observation of the Initiation of RNA Polymerase II Transcription. Nature 525(7568): 274-277, 9 2015 Notes: † Co-first authors.

Murakami K†, Tsai K-L†, Kalisman N, Bushnell DA, Asturias FJ, Kornberg RD.: Structure of an RNA polymerase II preinitiation complex. Proc. Natl Acad. Sci. USA 112(44): 13543-8, 11 2015 Notes: † Co-first authors.

Murakami K, Mattei PJ, Davis RE, Jin H, Kaplan CD, Kornberg RD: Uncoupling promoter opening from start-site scanning. Molecular Cell 59(1): 133–138, 7 2015 Notes: DOI: 10.1016/j.molcel.2015.05.021.

Pai DA, Kaplan CD, Kweon HK, Murakami K, Andrews PC, Engelke DR: RNAs nonspecifically inhibit RNA polymerase II by preventing binding to the DNA template. RNA 20(5): 644-655, 5 2014 Notes: DOI: 10.1261/rna.040444.113.

Schweikhard V, Meng C, Murakami K, Kaplan CD, Kornberg RD, Block SM: Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms. Proc. Natl Acad. Sci. USA 111(18): 6642-6647, 5 2014 Notes: DOI: 10.1073/pnas.1405181111.

Murakami K†, Elmlund H†, Kalisman N†, Bushnell DA, Adams CM, Azubel M, Elmlund D, Levi-Kalisman Y, Liu X, Gibbons BJ, Levitt M, Kornberg RD: Architecture of an RNA Polymerase II Transcription Pre-Initiation Complex. Science 342(6159): 1238724, 11 2013 Notes: † Co-first authors.

Murakami K, Calero G, Brown CR, Liu X, Davis RE, Boeger H, Kornberg RD: Formation and Fate of a Complete 31-Protein RNA polymerase II Transcription Preinitiation Complex. J. Biol. Chem. 288(9): 6325-6332, 3 2013 Notes: DOI: 10.1074/jbc.M112.433623.

Murakami K, Gibbons BJ, Davis RE, Nagai S, Liu X, Robinson PJ, Wu T, Kaplan CD, Kornberg RD: Tfb6, a previously unidentified subunit of the general transcription factor TFIIH, facilitates dissociation of Ssl2 helicase after transcription initiation. Proc. Natl Acad. Sci. USA 109(13): 4816-4821, 3 2012 Notes: DOI: 10.1073/pnas.1201448109.

Gibbons BJ, Brignole EJ, Azubel M, Murakami K, Voss NR, Bushnell DA, Asturias FJ, Kornberg RD: Subunit architecture of general transcription factor TFIIH. Proc. Natl Acad. Sci. USA 109(6): 1949-1954, 2 2012 Notes: DOI: 10.1073/pnas.1105266109.

Murakami K, Yasunaga T, Noguchi TQ, Gomibuchi Y, Ngo KX, Uyeda TQ, Wakabayashi T: Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release. Cell 143(2): 275-287, 10 2010 Notes: DOI: 10.1016/j.cell.2010.09.034.

Noguchi TQ, Gomibuchi Y, Murakami K, Ueno H, Hirose K, Wakabayashi T, Uyeda TQ: Dominant negative mutant actins identified in flightless Drosophila can be classified into three classes. J. Biol. Chem. 285(7): 4337-47, 2 2010.

Murakami K, Stewart M, Nozawa K, Tomii K, Kudou N, Igarashi N, Shirakihara Y, Wakatsuki S, Yasunaga T, Wakabayashi T: Structural basis for tropomyosin overlap in thin (actin) filaments and the generation of a molecular swivel by troponin-T. Proc. Natl Acad. Sci. USA 105(20): 7200-7205, 5 2008.

Murakami K, Yumoto F, Ohki SY, Yasunaga T, Tanokura M, Wakabayashi T: Structural basis for Ca2+-regulated muscle relaxation at interaction sites of troponin with actin and tropomyosin. J. Mol. Biol. 351(1): 178-201, 9 2005.

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Last updated: 04/24/2024
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