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The influence of DNA sequence on the epigenome (ATRUN)
Date du début: 1 avr. 2014, Date de fin: 31 mars 2016 PROJET  TERMINÉ 

Epigenetic regulation of transcription has emerged as a fundamental mechanism in developmental biology, stem cell biology and reprogramming and is frequently impaired in disease. Owing to recent advances in sequencing technology the genome wide distribution of epigenetic marks in different biological settings is being defined in unprecedented detail. Functional chromatin domains display distinct epigenetic marks and a variety of enzymatic activities depositing these marks has been identified. However, the mechanisms that determine locus specific setup of chromatin domains and their significance are incompletely understood. The proposed project is designed to shed light on the molecular mechanisms directing DNA methylation and histone modifications to specific loci. Using locus-specific integration of foreign DNA sequences with different base compositions and lengths, coupled to state of the art chromatin immunoprecipitation assays, DNA sequence determinants of de novo methylation and histone modifications will be explored. In a complementary approach, DNA pulldown assays coupled to mass spectrometry will be used to identify binding proteins of the respective sequences. In particular, I will analyze sequence motifs containing runs of A/T base pairs that are bound by AT-hook domains. AT-runs are a widespread sequence motif and a large number of DNA/chromatin binding proteins contain AT-hook domains, but their role in shaping the epigenome remains largely elusive to date. Our approach will not only identify new factors that contribute to the setup of the epigenome, but also yield valuable insights into the interplay between DNA binding proteins and chromatin modifiers that results in the specificity of the epigenomic landscape.