Kenji Murakami, Ph.D.

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Assistant Professor of Biochemistry and Biophysics
Department: Biochemistry and Biophysics
Graduate Group Affiliations

Contact information
Department of Biochemistry and Biophysics
364 Clinical Research Building
Perelman School of Medicine at the University of Pennsylvania
Philadelphia, PA 19104
Office: 215-573-1125
Lab: 215-573-1128
Education:
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

Transcription initiation by RNA polymerase II (pol II) is the first step in gene expression, and an end point of many signal transduction pathways. Approximately sixty proteins assemble in a 3-million Dalton complex at all mRNA promoters before every round of transcription. About half of these proteins, some 30 in number [the subunits of pol II and the general transcription factors (GTFs; TBP, TFIIA, TFIIB, TFIIE, TFIIF, TFIIH)], form a pre-initiation complex (PIC) that can recognize a promoter, open the double-stranded DNA, select a transcription start site, and synthesize a nascent transcript (Fig. 1). The remaining proteins are needed for the regulation of transcription. Emerging evidence from recent genome-wide studies points to the transition from initiation to elongation as the most widespread regulatory mechanism of transcription. In humans, this transition is the basis for regulation during environmental stress, immunological signaling and development, and is targeted by a variety of transcription factors (e.g., DSIF, NELF, P-TEFb, mRNA capping enzyme) (Fig. 1). Therefore, the elucidation of this mechanism of action is critical for finding novel targets for cancer therapies.

initation to elongation

Figure 1. A model for the transition from initiation to elongation of RNA polymerase II.

Previous studies were performed with nuclear extracts or with partially purified GTFs assembled on immobilized promoter DNA. Due to the poor efficiency of the reaction and trace amounts of protein involved, detection was only possible by the synthesis of a radiolabeled transcript and by immunoblotting techniques. In an important advance during my postdoctoral work with Dr. Roger Kornberg at Stanford University, we overcame this limitation by succeeding in reconstituting milligram quantities of a complete 32-subunit PIC that included all the GTFs and pol II. This has more than 30-fold greater transcription activity than that obtained by simple mixing of components, as routinely done in the past (Murakami et al., 2012, PNAS, Murakami et al., 2013, JBC; Murakami et al., 2015, in press, Mol. Cell). It opened the way to definitive biochemical and structural studies of the entire transcription initiation machinery. In the first of such studies, we have determined the structure of the PIC at the closed state by cryo-electron microscopy (cryo-EM) at 15 Å resolution (Murakami et al., 2013, Science) and subnanometer resolution (Murakami et al., 2015, Manuscript in preparation). The way is now open to dissect the post-initiation process by single-molecule studies and to determine the structures of post-initiation intermediates by cryo-electron microscopy (cryo-EM).

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 U S A 114(50): 13230-13235, 12 2017.

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.

Murakami K, Tsai KL, Kalisman N, Bushnell DA, Asturias FJ, Kornberg RD.: Structure of an RNA polymerase II preinitiation complex. Proc Natl Acad Sci U S A 112(44): 13543-8, 11 2015 Notes: DOI: 10.1073/pnas.1518255112.

Murakami K, Mattei PJ, Davis RE, Jin H, Kaplan CD, Kornberg RD.: Uncoupling promoter opening from start-site scanning. Mol. 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 U S A 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: DOI: 10.1126/science.1238724.

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 Notes: DOI: 10.1074/jbc.M109.059881.

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 Notes: DOI: 10.1073/pnas.0801950105.

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: 04/14/2021
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