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Methods Mol Biol. 2012;809:291-301. doi: 10.1007/978-1-61779-376-9_20.

Chromatin endogenous cleavage and psoralen crosslinking assays to analyze rRNA gene chromatin in vivo.

Author information

1
Naturwissenschaftliche Fakultät III, Institut für Biochemie III, Universität Regensburg, Regensburg, Germany. joachim.griesenbeck@vkl.uni-r.de

Abstract

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.

PMID:
22113284
DOI:
10.1007/978-1-61779-376-9_20
[Indexed for MEDLINE]

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