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Analysis of the Mechanism of Transcript Elongation through Chromatin by Pol II

Daria A. Gaykalova
MS, 2005
Lomonosov Moscow State University
Moscow, Russia

Thesis Advisor: Vasily M. Studitsky, PhD
Graduate Program: Cellular & Molecular Pharmacology

Research Tower
Room V-10

Wednesday, August 5, 2009
10:00 am


Nucleosome is the basic structural unit of chromatin. The degree of chromatin compaction and stability of nucleosome structure determines DNA accessibility and play a regulatory role during transcription initiation and perhaps during transcript elongation. Nucleosomes are present on the majority of coding regions of RNA polymerase II (Pol II)-transcribed genes, and are displaced from DNA only during extensive transcription. Thus, on moderately transcribed genes Pol II has to deal with DNA packed into nucleosomes.

It has become apparent that transcript elongation is a highly regulated stage of the transcription cycle. Thus in vivo Pol II is paused during early transcript elongation on thousands of genes. This distribution of paused Pol II overlaps with the first well positioned nucleosome on the transcribed regions. Moreover a single nucleosome was shown to present an absolute barrier to transcription in vitro. Numerous experiments in vivo and in vitro have also shown that the nucleosomal barrier can be removed in activator-dependent manner. Such data demonstrate that chromatin likely plays a critical role in determination of Pol II elongation rate. The nature of nucleosomal barrier to transcribing polymerases and the mechanisms mediating its regulation remain to be analyzed.

Results in vitro and in vivo showed that there are at least two different mechanisms (Pol II- and Pol III-specific) of transcription through nucleosome. The Pol II-specific mechanism is characterized by high nucleosomal barrier to transcription, quantitative displacement of one H2A/H2B dimer, and survival of the remaining histone hexamer at the original position on DNA. The mechanism of overcoming the nucleosomal barrier by Pol II without disruption of the nucleosomal structure was unknown and was one of the primary targets of this thesis.

The major goal of this dissertation work is to determine and describe the exiting and unprecedented molecular mechanism of Pol II transcription through chromatin, the nature of the nucleosomal barrier to transcription, and to evaluate the contribution of different factors to the height of the barrier and its possible regulation.

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