We are interested in the role of chromatin in the epigenetic transmission of cellular phenotypes. We have two main projects to study the mechanisms of chromatin structure maintenance after genome replication and cell division:
1.Chromatin dynamics during DNA replication
(ERC- consolidator grant NChIP 647618; 2015- 2020)
Chromatin assembly is a fundamental cellular process necessary for the maintenance of genome integrity and transcriptional programs. Understanding the effect of DNA replication on histone protein dynamics is also a prerequisite for understanding the role of chromatin in epigenetic inheritance. Epigenetic phenomena are thought to influence cellular differentiation and cancer formation, as well as the impact of environmental factors on early development and later predispositions to disease. While epigenetic inheritance of chromatin components is, in theory, accepted as the driver of such phenomena, chromatin state inheritance per se has only been demonstrated for a few specific cases. Not much is known about histone “inheritance” beyond the facts that bulk maternal histones distribute equally among the daughter strands and are diluted two-fold after replication with newly synthesized “unmarked” histones, and that the majority of H3/H4 tetramers do not split before reassembly. We have shown previously that maternal nucleosomes stay on average within 400bp of their original binding site, implying that any potentially heritable chromatin encoded information, has to be inherited in ~1kb blocs, as smaller nucleosome domains would rapidly be diluted by new nucleosomes.
We are developing high throughput techniques (such as NChAP-Nascent Avidin Chromatin Pulldown; Figure 1) for directly measuring movements of histones and chromatin regulators during genomic replication in S.cerevisiae to determine, how chromatin states survive the perturbations associated with replication. This will allow us to assess locus specific differences in the spread of maternal nucleosomes after replication, the effects of leading and lagging strand replication on nucleosome positioning and maternal nucleosome distribution, the renewal dynamics of posttranslational histone marks and chromatin binding proteins, and the kinetics of chromatin footprint re-establishment and gene (re)activation.
2.Asymmetric Segregation of Chromatin components
(ANR GENCHROSEG; 2014-2018)
Asymmetric cell division is a prerequisite for cellular differentiation and stem cell maintenance. Phenotypic transformation during differentiation is a poorly understood epigenetic phenomenon, in which chromatin, as a transcriptional regulator, theoretically plays a role. The underlying assumption that chromatin components segregate asymmetrically in asymmetric divisions has however not been systematically tested. Budding yeast also undergoes asymmetric divisions producing mother and daughter cells. The mother can generate 20-30 daughters during its replicative lifespan, and most of the factors that determine the phenotypic identity of the mother cell are unknown. The high conservation of chromatin components among eukaryotes and the availability of powerful genetic tools make S. cerevisiae an ideal system for identifying chromatin components involved in
asymmetric division and elucidating the underlying molecular mechanisms, using whole genome and single cell approaches (Figure 2).