The eukaryotic chromatin structure compacts and protects the genome, but also restricts direct access to the DNA. Chromatin modifying activities can open the chromatin structure and provide regulated access to specific genomic loci. Chromatin characteristics, such as the positions and turnover-rate of nucleosomes, histone modifications and other chromatin marks establish an elaborate genomic indexing mechanism, which is responsible for defining functional units in the genome. Several mutations have been identified that lead to a defect in chromatin organization and as a result, countless new promoters appear throughout the genome. Consequently, these mutations lead to transcription initiation events from gene coding- and intergenic-regions, and to a dramatic increase in pervasive transcription and to strong accumulation of ncRNA transcripts.

To identify factors that have a role in repressing pervasive transcription in the fission yeast Schizosaccharomyces pombe (S. pombe), we screened a deletion library for chromatin-related factors and tested their effect on pervasive transcription. From our screening efforts and from previously identified mutants, we collected a panel of S. pombe mutants that show increased genome-wide pervasive transcription. Although all of these mutants accumulate cryptic transcripts, our data demonstrates that the underlying mechanisms are remarkably different (Hennig et al., 2012; Hennig & Fischer, 2013). Our goal is to unravel the molecular mechanisms underlying these phenotypes, especially focusing on the changes in the nucleosome structure. Nucleosomes are the basic building blocks of the chromatin, and the position, occupancy and turn-over rate of nucleosomes at a given genomic locus ultimately determines the accessibility of the underlying DNA sequence. Despite the central role of nucleosomes in transcription regulation, our knowledge about the effects of different histone modifications and histone variants on the nucleosome organization is very limited.

These studies will not only help us to further understand the mechanisms involved in repressing pervasive transcription, but will also provide a more general understanding of how genomic indexing mechanisms define correct transcription units. The long-term goal of this project is to understand the interplay between chromatin modifications, nucleosome-positions, -turnover and -occupancy, and perhaps other as yet unknown chromatin characteristics, that allow the dynamic regulation of the eukaryotic genome.

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The regularly organized nucleosome arrays in gene coding regions are disrupted in the hrp1∆hrp3∆ strain. Two-dimensional plots of nucleosomes along 3,778 genes in WT and hrp1∆hrp3∆ strains. Positions of the first and last nucleosomes were determined for each gene in an independent experiment with the WT strain. These annotations were used for the analysis of all data sets. Each row represents a gene; genes were sorted vertically (shortest at the top and longest genes at the bottom) according to the distance between the first and last nucleosome of the gene and were aligned at the mid-point. Blue dots correspond to the centre of identified nucleosomes.