Abstract #80

Distribution of RNA Polymerase II on yeast chromosomes and its perturbation by a substitution in Sen1 helicase. Eric J. Steinmetz¹, Christopher L. Warren², Bahman Panbehi¹, Aseem Z. Ansari², David A. Brow¹. 1) Dept Biomolecular Chemistry and; 2) Dept Biochemistry, Univ Wisconsin, Madison, WI.
   The functional engagement of RNA polymerase (Pol) II with eukaryotic chromosomes is a complex and highly regulated process. Evidence is accumulating for the involvement of non-coding Pol II transcripts both in positive and negative control of transcription. To better understand the mechanisms underlying the regulation of Pol II recruitment, we have mapped the distribution pattern of Pol II on all 16 chromosomes of the yeast S. cerevisiae at 100-200 base pair resolution, both in a wild-type strain and in a strain with a substitution in the Sen1 helicase. Sen1 is a Pol II termination factor for non-coding RNA genes, and mutations in the gene encoding its human ortholog, Senataxin, cause the neuromuscular disorders AOA2 and ALS4. The wild-type pattern of Pol II distribution confirms known aspects of Pol II regulation and reveals possible new mechanisms of regulation. For example, telomeric silencing excludes Pol II primarily from ORFs and not intergenic regions, suggesting that initiation of silencing requires transcription. Likewise, rDNA silencing does not uniformly exclude Pol II across the entire repeat. Throughout the genome, we have identified Pol II peaks over regions without annotated genes, and some of these regions produce stable transcripts. A substitution in Sen1 that disrupts Pol II termination on snoRNA genes causes significant changes in Pol II distribution over much of the genome, establishing an important function of Sen1 helicase in the regulation of transcription. We find that Sen1 is important for termination on some protein-coding genes as well as non-coding genes, and mediates attenuation-like regulation of several protein-coding genes. Sen1 also appears to function in the exclusion of Pol II from Pol I and Pol III transcription units. We expect our data to lead to many new insights into the regulation of Pol II activity.

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