PgmNr Y3084: Defects in the nucleosome entry-exit site impair transcription termination.

Authors:
A. Elizabeth Hildreth; Karen M. Arndt


Institutes
University of Pittsburgh, Pittsburgh, PA.


Keyword: Chromatin

Abstract:

In eukaryotes, the chromatin template acts as a restrictive barrier to RNA polymerase II (Pol II), the molecular machine that transcribes protein coding and some noncoding RNAs. Chromatin consists of repeating nucleosomes, which contain approximately 147 bp of DNA surrounding an octamer of histone proteins H2A, H2B, H3, and H4. Transcription is controlled by factors that remove or modify these nucleosome barriers, allowing Pol II to contact otherwise occluded DNA. The mechanisms by which chromatin is modified are well understood in regard to transcription initiation and elongation. Despite a few studies showing that transcription-coupled histone modifications and select chromatin remodelers are important for proper termination, little else is known about the role of chromatin at this final termination step. We are investigating the role of chromatin in transcription termination using Saccharomyces cerevisiae as a model. To screen for histone H3 and H4 residues required for proper termination, we have made use of a plasmid library encoding histones with all possible alanine substitutions and a well-characterized, growth-based termination reporter. Our unbiased screen has identified ten residues in H3 and H4, which when mutant, cause defects in termination. Interestingly, many of these residues reside in or near the DNA entry-exit site of the nucleosome. This protein surface, including portions of histones H3 and H2A, is responsible for coordinating the first 30 bp of DNA, thus regulating the stability of the protein-DNA complex. Analysis of strains harboring these mutant histones has revealed transcriptional read-through at endogenous genes, altered nucleosome occupancy at candidate loci, and defects in the placement of a transcription-coupled histone modification previously implicated in termination and repression of cryptic transcription. Research in other labs has shown that conditions that speed up the rate of transcription elongation cause termination factors that associate with Pol II to effectively miss the appropriate termination window. We have begun assessing the elongation rates of Pol II in mutant yeast strains to determine whether altered transcriptional rates contribute to the observed termination defects. Additionally, we have begun screening H2A residues within the DNA entry-exit site for similar defects. Together, these data implicate the DNA entry-exit site as an important player in proper termination of transcription.