Dr. Christian Beisel

Christian Beisel is group leader at the ETH Zürich Department of Biosystems Science and Engineering in Basel (D-BSSE). He is also heading the Laboratory of Quantitative Genomics, a core research and service unit at D-BSSE, providing next generation sequencing technology. His main research area focuses on epigenetic gene regulation during development and disease. In particular he is interested in the molecular interplay of Polycomb and Trithorax group (PcG/TrxG) proteins, which are major determinants of the chromatin based (epigenetic) gene regulatory network, governing lineage commitment, maintenance and stem cell biology. By means of proteomics and functional genomics approaches his group aims at a deeper understanding of how the PcG/TrxG system is embedded within the cellular signalling network, how it responds to environmental cues and how gene expression states can be maintained or switched.

Current Group Members

Tobias Kockmann (PhD student)
Moritz Gerstung (iPhD project in collaboration with Niko Beerenwinkel)
Dr. Makiko Seimiya (Technical Assistance)
Ina Nissen (Technical Assistance, Laboratory of Quantitative Genomics)
Manuel Kohler (IT specialist, Laboratory of Quantitative Genomics, associated with CISD)

Publications

Sakoparnig T, Kockmann T, Paro R, Beisel C, Beerenwinkel N (2012). Binding profiles of chromatin-modifying proteins are predictive for transcriptional activity and promoter-proximal pausing. J Computational Biology (in press).

Tiwari VK, Stadler MB, Wirbelauer C, Paro R, Schübeler D, Beisel C (2011). A chromatin-modifying function of JNK during stem cell differentiation. Nature Genetics 44, 94-100.

Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmstrom L, Aebersold R, Rinn B. (2011). openBIS: a flexible framework for managing and analyzing complex data in biology research. BMC Bioinformatics 12, 468.

Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C, Spillane C, Nordborg M, Rehmsmeier M and Köhler C. (2011). High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Arabidopsis Endosperm. PLoS Genetics 7, e1002126.

Struebbe G, Popp C, Schmidt A, Pauli A, Ringrose L, Beisel C, Paro R (2011). Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners. Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5572-7. [Epub 2011 Mar 17].

Beisel C, Paro R (2011). Silencing chromatin: comparing modes and mechanisms. Nat Rev Genet 2011 Feb;12(2):123-135. Review. [Epub 2011 Jan 11].

Enderle D*, Beisel C*, Stadler MB, Gerstung M, Athri P, Paro R (2011). Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. Genome Res 2011 Feb;21(2):216-226. [Epub 2010 Dec 22]. *Shared first authorship

Buller F, Steiner M, Scheuermann J, Mannocci L, Nissen I, Kohler M, Beisel C and Neri D (2010). High-throughput sequencing for the identification of binding molecules from DNA-encoded chemical libraries. Bioorg Med Chem Lett 2010 Jul 15; 20(14):4188-4192. [Epub 2010 May 20].

Brykczynska U, Hisano M, Erkek S, Ramos L, Oakeley EJ, Roloff TC, Beisel C, Schübeler D, Stadler MB and Peters AHFM (2010). Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa. Nat Struct Mol Biol 2010 Jun;17(6):679-687. [Epub 2010 May 16].

Bell O, Schwaiger M, Oakeley EJ., Lienert F, Beisel C, Stadler MB and Schübeler D (2010). Accessibility of the Drosophila genome discriminates PcG repression H4K16 acetylation and replication timing. Nat Struct Mol Biol 2010 Jul;17(7):894-900. [Epub 2010 Jun 20].

Beisel C*, Paro R (2009). Dissection of gene regulatory networks in embryonic stem cells by means of high-throughput sequencing. Biol Chem 2009 Nov;390(11):1139-44. Review. *Corresponding author

Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E (2009). Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol 2009;10(7):R79.

Tariq M, Nussbaumer U, Chen Y, Beisel C, Paro R (2009). Trithorax requires Hsp90 for maintenance of active chromatin at sites of gene expression. PNAS 2009 Jan 27;106(4):1157-62.

Beisel C, Buness A, Roustan-Espinosa IM, Koch B, Schmitt S, Haas SA, Hild M, Katsuyama T, Paro R (2007). Comparing active and repressed expression states of genes controlled by the Polycomb/Trithorax group proteins. PNAS 2007 Oct 16;104(42):16615-20.

Lyko F, Beisel C, Marhold J, Paro R (2006). Epigenetic regulation in Drosophila. Current Topics in Microbiology and Immunology: “DNA methylation”, editor Doerfler W, 310:23-44.

Belz T, Pham AD, Beisel C, Anders N, Bogin J, Kwozynski S, Sauer F (2002). In vitro assays to study protein ubiquitination in transcription. Methods 2002 Mar;26(3):233-44.

Laufen T, Mayer MP, Beisel C, Klostermeier D, Mogk A, Reinstein J, Bukau B (1999). Mechanism of regulation of hsp70 chaperones by DnaJ cochaperones. PNAS 1999 May 11;96(10):5452-5457.

Honors and Awards

GFM award for best PhD thesis 2003 in molecular biology at the University of Heidelberg, Germany (2004)

PhD, Faculty of Natural Sciences and Mathematics, University of Heidelberg, Germany (2003): Summa cum laude

Scholarship holder of the Klaus-Tschira Foundation (since 2001)

PhD Fellowship, Deutsche Forschungsgemeinschaft (1998-2001)

GFM award for best Diploma thesis 1998 in molecular biology at the University of Heidelberg, Germany (1999)