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PLoS Comput Biol. 2009 Feb;5(2):e1000282. doi: 10.1371/journal.pcbi.1000282. Epub 2009 Feb 6.

Evidence for gene-specific rather than transcription rate-dependent histone H3 exchange in yeast coding regions.

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  • 1Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Berlin, Germany. gat-viks@molgen.mpg.de


In eukaryotic organisms, histones are dynamically exchanged independently of DNA replication. Recent reports show that different coding regions differ in their amount of replication-independent histone H3 exchange. The current paradigm is that this histone exchange variability among coding regions is a consequence of transcription rate. Here we put forward the idea that this variability might be also modulated in a gene-specific manner independently of transcription rate. To that end, we study transcription rate-independent replication-independent coding region histone H3 exchange. We term such events relative exchange. Our genome-wide analysis shows conclusively that in yeast, relative exchange is a novel consistent feature of coding regions. Outside of replication, each coding region has a characteristic pattern of histone H3 exchange that is either higher or lower than what was expected by its RNAPII transcription rate alone. Histone H3 exchange in coding regions might be a way to add or remove certain histone modifications that are important for transcription elongation. Therefore, our results that gene-specific coding region histone H3 exchange is decoupled from transcription rate might hint at a new epigenetic mechanism of transcription regulation.

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