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Emmy Noether Junior Research Group - Understanding the regulatory mechanisms governing combinatorial chromatin states

  • Project Leader: Dr. Guillermo Rodrigo VillaseƱor Molina
  • Affiliation: Chair of Molecular Biology, Biomedical Center (BMC)
  • Funding: since 2021

At the time of writing, 22 types of histone modifications have been described, including acetylation, citrullination, methylation, phosphorylation, and ubiquitination. With eight modifiable amino acid residues at about 138 positions on five canonical histone variants, more than 550 possible histone modifications have been reported. Several of these chemical marks can coexist on the same nucleosome resulting in an immense theoretical number of combinatorial possibilities.

Bivalent chromatin and its associated histone modifications, H3K4me3 and H3K27me3, is perhaps the best-described example of a combinatorial chromatin state known to date. Despite years of intense research on bivalent chromatin, many fundamental questions remain unanswered. How is bivalent chromatin established and maintained in pluripotent cells? How are bivalent sites kept accessible and hence transcriptionally responsive? Are the same factors associated with bivalent chromatin in different cell types?

In the first two aims of this proposal, my group will combine experimental and computational approaches to answer these fundamental questions in a quantitative and comprehensive manner. On the experimental side, my group will combine genome-wide assays with rapid protein depletion strategies to carry out mechanistic studies at unprecedented temporal control under defined conditions in mouse embryonic stem cells. In the final part of this project, we will venture into new territory. To date, only a few examples of new combinatorial chromatin states are known. However, these results open the exciting possibility for the existence of more combinatorial options in mammalian cells. In Aim3 of this project, my team will employ a robust and quantitative chromatin-proteomics approach to explore large combinatorial possibilities at single-nucleosome resolution in three distinct cell types and functionally characterize novel examples.

In the future, my team will expand our chromatin-proteomics approach to other cell types and cancer cells to elucidate more combinatorial chromatin modifications.