Chromatin Endogenous Cleavage and Psoralen Crosslinking Assays to Analyze rRNA Gene Chromatin In Vivo
In eukaryotes, multiple copies of ribosomal RNA (rRNA) genes co-exist in two different chromatin states: actively transcribed (nucleosome depleted) chromatin, and nontranscribed (nucleosomal) chromatin. The presence of two rRNA gene populations compromises the interpretation of analyses obtained by the standard biochemical methods that are used to study chromatin structure (e.g., nuclease digestion and chromatin immunoprecipitation). Here, we provide a protocol to investigate the specific association of proteins with the two rRNA gene chromatin populations in vivo, using Saccharomyces cerevisiae as a model eukaryote.
Key wordsChromatin Chromatin endogenous cleavage Psoralen crosslinking rDNA Ribosomal DNA Ribosomal RNA genes RNA polymerase I
This work was supported by a mobility program accompanied by the Bavarian Research Alliance GmbH as an assignment from the Bavarian State Chancellery to J.G. and by the Ministère des Relations Internationales du Québec to A.C. M.W. is a recipient of a fellowship from the Elitenetzwerk Bayern and R.C. is supported by the Natural Sciences and Engineering Research Council of Canada (NSERC No. 326873-2009) to A.C.
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