Transcription is an essential process for life that constitutes the first step of gene expression in the cell and a crucial checkpoint for the control f critical biological events, including cell growth, differentiation, and oncogenesis. In eukaryotes, this highly regulated process is carried out by RNA polymerase II (Pol II). To transcribe the DNA, this enzyme must overcome the physical barriers imposed by the nucleosomal organization of the genetic material. Moreover, Pol II must transcribe torsionally constrained DNA segments that require the enzyme to translocate against increasing torques. Various mechanisms participate in the control and regulation of transcription, including structural changes of chromatin, various transcription factors, the polymerase ability to generate torque, and the activity of ATP-dependent chromatin remodeler complexes. In this application we propose to characterize these mechanisms of transcription control using a combination of single molecule manipulation and visualization approaches. Specifically, we propose: 1) Investigate the dynamics of transcription through nucleosomal arrays to elucidate the contribution of internucleosomal elements to the barrier. 2) Determine the mechanisms by which transcription factors IIS (TFIIS) and IIF (TFIIF) enhance nucleosomal transcription. 3) Characterize the relationship between the torsional strain in DNA and the ability of Pol II to transcribe through a nucleosome. 4) Characterize the nucleosome-remodeling mechanism, mechanochemical properties, and torque generation of the SWI/SNF complex.
Oncogenesis and a large variety of developmental pathologies are associated with disruption of transcription, the central point of control for the regulation of gene expression. In this application we propose to characterize the dynamics of individual molecules of Pol II transcribing through arrays of nucleosomes, the effect of the enzyme's torque-generating capabilities on transcription throughput, the contribution of transcription factors to the ability of the enzyme to overcome the nucleosomal barrier, and the nucleosome remodeling mechanism of SWI/SNF. The insights that our experiments provide on transcription will lead to a better understanding of the basic molecular mechanisms of control of gene expression and they will support the first steps in the development of future therapies for transcription-based pathologies.
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