Transcription constitutes the central point of control for gene expression in the cell. The eukaryotic Pol II enzyme must transcribe in the presence of the physical barriers present in nucleosomal DNA and both this enzyme and its prokaryotic counterpart must transcribe torsionally constrained DNA segments that require the enzymes to translocate against increasing torques. Moreover, during transcription elongation these two highly structurally homologous enzymes perform a mechanochemical cycle in which a nucleotide condensation reaction is coupled to the mechanical tasks of movement, force, and torque generation. In this application we propose to use a combination of imaging and single molecule manipulation approaches to: a) Investigate the dynamics of transcription through nucleosomal DNA by yeast Pol II. b) Determine the effect of elongation factors on nucleosomal transcription. c) Investigate the effect of histone modification on the dynamics of nucleosomal transcription. d) Investigate the effect of remodeling factors on the dynamics of Pol II through nucleosomal DNA. We also propose to continue our previous studies of the prokaryotic E. coli RNA polmerase enzyme to investigate: a) Its generation of torque during transcription of torsionally constrained DNA, and b) The details of its mechanochemical cycle at high spatial resolution.

Public Health Relevance

Transcription constitutes the central point of control for regulation of gene expression. Disruption of this process is associated with congenital heart disease, oncogenesis, and a large variety of developmental pathologies. The insights that our experiments provide on transcription will support the first steps in the development of future therapies.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Macromolecular Structure and Function C Study Section (MSFC)
Program Officer
Lewis, Catherine D
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California Berkeley
Organized Research Units
United States
Zip Code
Gabizon, Ronen; Lee, Antony; Vahedian-Movahed, Hanif et al. (2018) Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates. Nat Commun 9:2930
Liu, Ninning; Chistol, Gheorghe; Cui, Yuanbo et al. (2018) Mechanochemical coupling and bi-phasic force-velocity dependence in the ultra-fast ring ATPase SpoIIIE. Elife 7:
Tafoya, Sara; Liu, Shixin; Castillo, Juan P et al. (2018) Molecular switch-like regulation enables global subunit coordination in a viral ring ATPase. Proc Natl Acad Sci U S A 115:7961-7966
Schöneberg, Johannes; Pavlin, Mark Remec; Yan, Shannon et al. (2018) ATP-dependent force generation and membrane scission by ESCRT-III and Vps4. Science 362:1423-1428
Righini, Maurizio; Lee, Antony; Cañari-Chumpitaz, Cristhian et al. (2018) Full molecular trajectories of RNA polymerase at single base-pair resolution. Proc Natl Acad Sci U S A 115:1286-1291
Lee, Antony; Tsekouras, Konstantinos; Calderon, Christopher et al. (2017) Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis. Chem Rev 117:7276-7330
Bustamante, Andrés; Sotelo-Campos, Juan; Guerra, Daniel G et al. (2017) The energy cost of polypeptide knot formation and its folding consequences. Nat Commun 8:1581
San Martín, Álvaro; Rodriguez-Aliaga, Piere; Molina, José Alejandro et al. (2017) Knots can impair protein degradation by ATP-dependent proteases. Proc Natl Acad Sci U S A 114:9864-9869
Herrera-Asmat, Omar; Lubkowska, Lucyna; Kashlev, Mikhail et al. (2017) Production and characterization of a highly pure RNA polymerase holoenzyme from Mycobacterium tuberculosis. Protein Expr Purif 134:1-10
Rodriguez-Aliaga, Piere; Ramirez, Luis; Kim, Frank et al. (2016) Substrate-translocating loops regulate mechanochemical coupling and power production in AAA+ protease ClpXP. Nat Struct Mol Biol 23:974-981

Showing the most recent 10 out of 114 publications