The eukaryotic chromatin structure compacts and protects the genome but also limits the accessibility of the underlying DNA. Chromatin modifying activities can open the chromatin and provide regulated access to specific genomic loci. 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 determine the accessibility of the underlying DNA sequence. Defects in nucleosome organization lead to increased levels of pervasive transcription outside of genetically defined transcription units. Despite the central role of nucleosomes in transcription regulation, our knowledge about the effects of different histone modifications and histone variants on nucleosome organization is very limited. We are studying the impact of various histone modifications on the position, occupancy and turn-over rate of nucleosomes and their effect on pervasive transcription. Increased pervasive transcription and the resulting nuclear accumulation of non-coding transcripts can lead to excessive RNA-DNA hybrid formation in the genome and subsequent genomic instability. Interestingly, we have recently identified an additional role for pervasive transcription in the DNA double-strand break repair pathway, thus revealing a surprising, positive role in genomic stability.