Chromatin and DNA replication

 Marta RADMAN-LIVAJA

 CRBM - UMR 5535

 1919, route de Mende, 34293 Montpellier

Phone: +33 4 34 35 96 67

Email: marta.radman-livaja@igmm.cnrs.fr

Website

Our group is interested in the mechanisms of chromatin patterns re-establishment after DNA replication. Despite important implications that chromatin reassembly has for our understanding of the role of chromatin in epigenetic phenomena, these processes have not yet been explored on a genomic scale, mainly due to the absence of appropriate high-throughput methods. We are using S.Cerevisiae as a model system for developing methods to map chromatin architecture dynamics following perturbations caused by the passage of the replication fork. We are following three principal axes of inquiry: 1) Heterochromatin inheritance-We are measuring turnover rates of the heterochromatic Sir complex before and after replication genome wide, thus directly testing whether the Sir proteins are maintained locally after replication as might be expected. 2) Tracking maternal nucleosomes at targeted genomic loci-We are developing a method to measure replication-mediated dispersion of maternal nucleosomes within defined chromatin domains, with the goal to better understand the epigenetic potential of nucleosomes. 3) Chromatin configuration re-establishment after DNA replication-In order to map changes in chromatin features, such as nucleosome positions and histone modifications, in the wake of the replication fork, we are developing a method for isolating chromatin assembled on newly replicated DNA.

Keywords: chromatin, genomics, DNA replication, epigenetics, yeast

Main publications :

• Vasseur P., Tonazzini S., Ziane R.,  Camasses A., Rando O.J., and  Radman Livaja M. Dynamics of nucleosome positioning maturation following genomic replication. Cell Reports, 16(10): 2651-2665,2016.
• Soares L, Radman-Livaja M, Lin SG, Rando OJ, and Buratowski S. Feedback Control of Set1 Protein Levels Is Important for Proper H3K4 Methylation Patterns. Cell Reports. 6(6):961-72, 2014.
• Watanabe S, Radman-Livaja M, Rando OJ, Peterson CL. A Histone Acetylation Switch Regulates H2A.Z Deposition by the SWR-C Remodeling Enzyme Science 340:195-199, 2013.
• Radman-Livaja M, Quan T K, Valenzuela L, Armstrong J A, van Welsem T, Kim T, Lee L J, Buratowski S, van Leeuwen F, Rando O J, Hartzog GA. A key role for chd1 in histone h3 dynamics at the 3' ends of long genes in yeast. PLoS Genet., 8: e1002811, 2012.
• Radman-Livaja M, Verzijlbergen K, Weiner A, van Welsem T, Friedman N, Rando OJ, and van Leeuwen F. Patterns and mechanisms of ancestral histone protein inheritance in budding yeast. PLoS Biology, 9: e1001075, 2011.
• Radman-Livaja M, Ruben G, Weiner A, Friedman N, Kamakaka R, and Rando OJ. Dynamics of Sir3 spreading in budding yeast: secondary recruitment sites and euchromatic localization. EMBO J., 30: 1012-1026, 2011.
• Radman-Livaja M, Liu CL, Schreiber SL, and Rando OJ. Replication and active demethylation represent partially overlapping mechanisms for erasure of H3K4me3 in budding yeast. PLoS Genet., 6: e1000837, 2010.
• Radman-Livaja M, and Rando OJ. Nucleosome positioning: how is it established, and why does it matter? Dev. Biol., 339: 258-266, 2009.(review)
• Sun X, Mierke D, Biswas T, Lee SY, Landy A, and Radman-Livaja M. Architecture of the 99 bp DNA - Six Protein Regulatory Complex of the λ att Site. Mol. Cell, 24:569-580, 2006.
• Radman-Livaja M, Biswas T, Mierke D, and Landy A. Architecture of Recombination Intermediates Visualized by In-gel FRET of λ Integrase-Holliday Junction-Arm-DNA Complexes. Proc. Natl. Acad. Sci. U S A, 102:3913-20, 2005.
• Biswas T, Aihara A, Radman-Livaja M, Filman D, Landy A, and Ellenberger T. A structural basis for allosteric control of DNA recombination by λ integrase. Nature, 435:1059-66, 2005.
• Radman-Livaja M, Shaw C, Azaro M, Biswas T, Ellenberger T, and Landy A. Arm sequences contribute to the architecture and catalytic function of a λ Integrase-Holliday Junction complex. Molecular Cell, 11:783-794, 2003.