PD Dr. Philipp Korber
Nucleosome positioning mechanisms in yeasts
Models for the regulation of eukaryotic genomes have to include models for the most basic level of genome organization: the positioning of nucleosomes. Nucleosomes impede access to DNA and their positioning relative to functional DNA elements fundamentally regulates genomes. Recent genome-wide nucleosome maps underscored the high prevalence of well-positioned nucleosomes. However, the nucleosome positioning mechanisms are still unclear. Even more, we generated the first nucleosome map for the fission yeast S. pombe and showed by comparison with the budding yeast S. cerevisiae, that positioning mechanisms are not universal but evolutionarily plastic. So we need to unravel which mechanistic elements govern nucleosome positioning in different species. Recently, we established the genome-wide in vitro reconstitution of in vivo-like nucleosome positioning for S. cerevisiae. This system is a unique tool for biochemical and quantitative studies of nucleosome positioning mechanisms. Now we extend this approach to S. pombe for the biochemical identification of nucleosome positioning determinants in a comparative genomics cross-species approach.
Publications within BioSysNet
Musladin S, Krietenstein N, Korber P, Barbaric S (2014). The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening. Nucleic Acids Res 42(7):4270-82.
Pointner J, Persson J, Prasad P, Norman-Axelsson U, Strålfors A, Khorosjutina O, Krietenstein N, Svensson JP, Ekwall K, Korber P (2012). CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe. EMBO J 31(23):4388-403.
Publications before BioSysNet
Korber,P. and Hörz,W. (2004). SWRred not shaken; mixing the histones. Cell 117, 5-7.
Korber,P., Luckenbach,T., Blaschke,D., and Hörz,W. (2004). Evidence for histone eviction in trans upon induction of the yeast PHO5 promoter. Mol. Cell. Biol. 24, 10965-10974.
Korber,P. and Hörz,W. (2004). In vitro assembly of the characteristic chromatin organization at the yeast PHO5 promoter by a replication-independent extract system. J. Biol. Chem. 279, 35113-35120.
Schermer,U.J., Korber,P., and Hörz,W. (2005). Histones are incorporated in trans during reassembly of the yeast PHO5 promoter. Mol. Cell 19, 279-285.
Hertel,C.B., Längst,G., Hörz,W., and Korber,P. (2005). Nucleosome stability at the yeast PHO5 and PHO8 promoters correlates with differential cofactor requirements for chromatin opening. Mol. Cell. Biol. 25, 10755-10767.
Korber,P., Barbaric,S., Luckenbach,T., Schmid,A., Schermer,U.J., Blaschke,D., and Hörz,W. (2006). The histone chaperone Asf1 increases the rate of histone eviction at the yeast PHO5 and PHO8 promoters. J. Biol. Chem. 281, 5539-5545.
Barbaric,S., Luckenbach,T., Schmid,A., Blaschke,D., Hörz,W., and Korber,P. (2007). Redundancy of chromatin remodeling pathways for the induction of the yeast PHO5 promoter in vivo. J. Biol. Chem. 282, 27610-27621.
Lantermann,A., Stralfors,A., Fagerstrom-Billai,F., Korber,P., and Ekwall,K. (2009). Genome-wide mapping of nucleosome positions in Schizosaccharomyces pombe. Methods 48, 218-225.
Wippo,C.J., Krstulovic,B.S., Ertel,F., Musladin,S., Blaschke,D., Sturzl,S., Yuan,G.C., Hörz,W., Korber,P., and Barbaric,S. (2009). Differential cofactor requirements for histone eviction from two nucleosomes at the yeast PHO84 promoter are determined by intrinsic nucleosome stability. Mol. Cell. Biol. 29, 2960-2981.
Korber,P. and Becker,P.B. (2010). Nucleosome dynamics and epigenetic stability. Essays Biochem. 48, 63-74.
Ertel,F., Dirac-Svejstrup,A.B., Hertel,C.B., Blaschke,D., Svejstrup,J.Q., and Korber,P. (2010). In vitro reconstitution of PHO5 promoter chromatin remodeling points to a role for activator-nucleosome competition in vivo. Mol. Cell. Biol. 30, 4060-4076.
Lantermann,A.B., Straub,T., Stralfors,A., Yuan,G.C., Ekwall,K., and Korber,P. (2010). Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nat. Struct. Mol. Biol. 17, 251-257.
Wippo,C.J., Israel,L., Watanabe,S., Hochheimer,A., Peterson,C.L., and Korber,P. (2011). The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes. EMBO J. 30, 1277-1288.
Zhang,Z., Wippo,C.J., Wal,M., Ward,E., Korber,P., and Pugh,B.F. (2011). A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 332, 977-980.
Wippo,C.J. and Korber,P. (2012). In vitro reconstitution of in vivo-like nucleosome positioning on yeast DNA. Methods Mol. Biol. 833, 271-287.
Korber,P. (2012). Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution. Biochem. Soc. Trans. 40, 377-382.