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Anastassiadis
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Epigenetic regulation and genomic engineering


Previous and current research

Our work focuses on two complementary aspects of genomics,
(i) mechanisms of epigenetic regulation in eukaryotic chromatin and
(ii) technologies of genetic engineering.

EPIGENETIC REGULATION IN CHROMATIN.

Although the complete DNA sequence of an organism encodes the primary information, additional information is added by epigenetic regulation. In eukaryotic chromatin, epigenetic regulation is conveyed by covalent modifications of DNA (DNA methylation) and histone tails (acetylation, phosphorylation, methylation, ubiquitinylation). Much attention worldwide is now focused on the histone tails and the proposition that patterns of covalent modifications serve as an epigenetic code. Our approach to unravelling epigenetic mechanisms and hierarchies is based on complementary uses of the yeast, S. cerevisiae and the mouse as experimental systems. We apply advanced reverse genetic strategies, some of which were developed by us, to analyze select classes of epigenetic regulators in both organisms. In yeast, we are using protein-tagging and mass spectrometry to characterize complexes containing epigenetic regulators. Amongst other complexes that we have identified in the proteomic environment of chromatin, we have recently identified a new histone methyltransferase activity for lysine 4 of histone 3.

In mice, we are studying two candidate histone methyltransferases by knock-out and conditional strategies using Cre/lox, as well applying proteomic approaches to characterize the complexes. A future aspect of our mouse work is directed towards use of ES cell differentiation in culture as a model for epigenetic decisions and stem cell manipulations.

GENOMIC ENGINEERING

We have developed several aspects of genetic engineering technology using site specific and homologous recombination. We aim at more fluent manipulation of mammalian cells, particularly ES cells and in mice. Most recent work involves exploration and implementation of a novel homologous recombination system that we discovered in E.coli phages. This permits fluent engineering of BACs in E.coli, and may offer new routes for directly engineering eukaryotic cells.

Future prospects and goals

Further work on epigenetic regulators in eukaryotes will be accompanied by advanced engineering strategies to examine roles of epigenetic regulation in mammalian development, stem cells, ageing and disease.


Further Links



Selected Publications

Lubitz, S., Glaser, S., Schaft, J., Stewart, A.F., Anastassiadis, K. (2007) “Increased apoptosis and skewed differentiation in mouse ES cells lacking the histone methyltransferase, Mll2”, Mol. Biol. Cell.

Sarov, M., Pozniakovski, A., Schneider, S., Roguev, A., Ernst, S., Zhang, Y., Hyman, A.A. and Stewart, A.F. (2006) “A recombineering pipeline for protein tagging and functional analysis, as applied to Caenorhabtidis elegans” Nature Methods, 3, 839 -44.

Glaser, S., Schaft, J., Lubitz, S., Vintersten, K., van der Hoeven, F., Tufteland, K.R., Aasland, R., Anastassiadis, K., Ang, S.-L. and Stewart, A.F. (2006) “Multiple epigenetic maintenance factors implicated by the loss of Mll2 in mouse development” Development, 133, 1423 - 32.

Glaser, S, Anastasiadis, K. and Stewart A.F. (2005) “Current issues in mouse genome engineering” Nature Genetics, 37, 1187-93.

Roguev, A., Shevchenko, A., Schaft, D., Thomas, H., Stewart, A.F. and Shevchenko, A. (2004) “A comparative analysis of an orthologous proteomic environment in the yeasts S. cerevisiae and S. pombe” Mol. Cell. Proteomics 3, 125-32.

Testa, G., Schaft, J., van der Hoeven, F., Glaser, S., Anastassiadis, K., Zhang, Y., Hermann, T., Stremmel, W. and Stewart , A.F. (2004) “A reliable expression reporter cassette for multipurpose, knock-out/conditional mouse alleles” Genesis 38, 151-8.

Testa, G., Zhang, Y., Vintersten, K., van der Hoeven, F., Benes, V., Chambers, I., Smith, A.J.H., Smith, A.A. and Stewart, A.F. (2003) “Engineering the mouse genome with bacterial artificial chromosomes to create multi-purpose alleles”. Nature Biotechnology, 21, 443-447.

Anastassiadis, K., Kim, J., Daigle, N., Sprengel, R., Schöler, H.R. and Stewart, A.F. (2002) “A predictable ligand regulated expression strategy for stably integrated transgenes in mammalian cells in culture” Gene 298, 159-72

Casanova, E., Fehsenfeld, S., Greiner, E., Stewart, A.F. and Schütz, G. (2002) “Conditional mutagenesis of CamKIV.” Genesis. 32, 161-4.

Roguev, A., Schaft, D., Shevchenko, A., Pijnappel, W.W.M., Wilm, M., Aasland, R. and Stewart, A.F. (2001) “The S. cerevisiae Set1 complex includes an Ash2-like protein and methylates histone 3 lysine 4” EMBO J. 20, 7137-7148

Muyrers, JPP, Zhang, Y and Stewart AF (2001) Recombinogenic Engineering: new options for manipulating DNA. Trends in Biochemical Sciences, 26: 325-331.

Schaft, J, Ashery-Padan, R, van der Hoeven, F, Gruss, P and Stewart AF (2001) Efficient FLP recombination in mouse ES cells and oocytes. Genesis, 31: 6-10.

Pijnappel, WWM, Schaft, D, Roguev, A., Tekotte, H, Shevchenko, A, Wilm, M, Rigaut, G, Séraphin, B, Aasland, R, and Stewart, AF (2001) The S. cerevisiae Set3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program. Genes Dev., 15: 2991-3004.

Roguev, A, Schaft, D, Shevchenko, A, Pijnappel, WWM, Wilm, M, Aasland, R and Stewart, AF (2001) S. cerevisiae Set1 complex includes an Ash2-like protein and methylates histone 3 lysine 4. EMBO J., 20: (December).

Muyrers, JPP, Zhang, Y, Buchholz, F and Stewart, AF (2000) RecE/RecT and RedƒÑ/RedƒÒ initiate double stranded break repair by specifically interacting with their respective partners. Genes and Development, 14: 1971-1982.