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PhD thesis: Genome-wide biochemistry of nucleosome positioning mechanisms

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Eukaryotes package their nuclear DNA into a complex protein-nucleic acid structure called chromatin. At the most basic level of chromatin, the DNA is wrapped around histone octamers forming nucleosomes. Genome-wide nucleosome maps in various organisms showed that a large fraction of nucleosomes is not randomly distributed but precisely positioned. What creates this ordered state? Moreover, as nucleosomes can occlude functional DNA elements, e.g., transcription factor binding sites, it is clear that nucleosome positioning along a chromosome is a very fundamental level of genome regulation. This is why chromatin directly impacts gene expression and thereby virtually all cell biology that is linked to changes in gene expression programs, for example, development, cancer or signaling. Therefore, there generally is a keen interest in understanding the establishment, maintenance and modulation of chromatin structures. Nonetheless, some of the most basic mechanisms are still not properly understood, for example, the very basic question of why nucleosomes are where they are. So we focus on the corresponding question: „What determines nucleosome positioning?“
We are a small, independent group in the larger context of the department of Molecular Biology (chair Prof. Dr. Peter B. Becker) at the BioMedical Center (BMC), LMU München. The BMC is newly built and we moved there just recently in July 2015. So we benefit from a completely new and state-of-the-art laboratory infrastructure embedded in the vibrant neighborhood of the HighTech Campus Grosshadern/Martinsried with other institutes like the Gene Center or the Max-Planck-Institute for Biochemistry close by. We study the role of chromatin in gene regulation and use the yeasts Saccharomyces cerevisiae (baker's yeast) and Schizosaccharomyces pombe (fission yeast) as model systems with powerful genetics and easy biochemical accessibility. (For a complete list of our publications search PubMed „korber p“. This search term is unique for us.) Our particular strength lies in the establishment of the only in vitro chromatin assembly system currently available that is able to generate in vivo-like nucleosome positioning across the whole S. cerevisiae genome (Krietenstein et al., 2012, Meth. Enzymol.; Zhang et al., 2011, Science). This approach has turned into a gold mine as it puts us into the unique position to study biochemically which factors determine nucleosome positioning in S. cerevisiae. Right now we are submitting the results of the follow up of our initial study (Zhang et al., 2011, Science) again to a top tier journal as we could further elucidate fundamental mechanisms of nucleosome positioning, especially the role of ATP-dependent remodeling enzymes and DNA sequence specific "barrier" factors. These are most exciting times!
Now, we are looking for a PhD student who will continue digging deeply into this gold mine and further define the molecular mechanisms of nucleosome positioning determinants. This will involve sophisticated biochemistry work, e.g., cloning of expression constructs, purification of endogenous and recombinant proteins, in vitro chromatin reconstitution, chromatin analysis by MNase digestion coupled to high throughput sequencing, as well as bioinformatics analyses of large genome-wide data sets. Therefore, a strong interest and background in biochemistry/molecular biology/bioinformatics is preferred. Payment will be according to 65% E13 and the project shall start in October or November the latest.

A special bonus for our group is the exceptionally comprehensive and supporting environment. In our department there are seven independent groups working on chromatin related projects ( and all these groups, together with ten more chromatin research groups, are also members of the Collaborative Research Center (Sonderforschungsbereich) SFB1064 “Chromatin Dynamics” ( The close proximity of many groups who also study chromatin and gene regulation mechanisms provides an exceptionally stimulating and collaborative working environment and offers an extensive resource of expertise, materials and core facility services (mass spectrometry, high-throughput sequencing, antibody generation, bioimaging). In addition to the connections within Munich, we collaborate extensively on the international level, for example with the groups of Frank Pugh (PennState University), Karl Ekwall (Karolinska Institute, Sweden) and Craig Peterson (Univ. of Massachusetts Medical School). We are also an associated Junior Group within the Bavarian Research Network for Molecular Biosystems ( and an Associate Member of „The European Network of Excellence EpiGeneSys“ (, which continues to be a great platform for the integration of chromatin and epigenetics research within Europe. In order to take advantage of our well-established local, regional and international connections we expect and encourage an explorative attitude and good communication skills, especially in English.
We accept applications from now on but due to vacation from August 1st to 23rd, we will probably invite for job interviews not before end of August.


Art des Bewerbungszugangs
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Kontakt für Bewerbungen
PD Dr. Philipp Korber
BioMedizinisches Centrum
LMU München
Großhadernerstr. 9
82152 Planegg-Martinsried bei München
+49-(0)89-21807435 phone
+49-(0)89-21807425 fax

Details der Stellenanzeige

Befristete Anstellung
Berufserfahrung nicht vorausgesetzt
Deutschland (Bayern)
82152 Planegg - Martinsried / München
Biologie & Life Sciences