The organization, regulation and functions of genes in the pericentric heterochromatin of the Drosophila melanogaster third chromosome

Alterations to chromatin through the post-translational modification of histone proteins or the binding of non-histone proteins is important for the tight control and specification of nuclear processes (e.g. transcription) occurring at most chromosomal regions. In this thesis, I report on the roles of enzymes responsible for adding methyl groups to histone H3 at lysine 4 (H3K4)—a modification pattern which is found at most active genes. I focus on a functional characterization of dSet1, which I show is responsible for most di- and trimethylation of H3K4. I also present evidence that dSet1 interacts with members of an evolutionarily conserved complex and that complex members are collectively required for H3K4 methylation. This work establishes a model system for better understanding functions of methyl-H3K4 in metazoans. Given that the dSet1 gene was found in pericentric heterochromatin, I became interested in the regulation, functions and organization of other genes in this specialized genomic compartment. Pericentric heterochromatin encompasses approximately 1/3 of the Drosophila melanogaster DNA sequences, yet contains just over 1% of Drosophila genes. Since pericentric heterochromatin has a low gene density, remains condensed throughout the cell cycle, and ‘silences’ most genes ectopically placed within it, it has in the past been mistakenly regarded as transcriptionally inert. However, there are still approximately 200 transcribed genes present in pericentric regions, and many of these genes are essential and/or expressed ubiquitously throughout development. Here I report a broad requirement for structural components of heterochromatin (Su(var) proteins) in the expression of genes in Drosophila pericentric heterochromatin, expanding on previous work reporting that Su(var) proteins and a heterochromatic environment are required for the expression of genes in this region. Due to difficulties arising in sequencing, mapping and genetically manipulating heterochromatic regions, much work remains in order to fully characterize the heterochromatic genome. I have assisted in these efforts by identifying and characterizing essential functions in 3rd chromosome pericentric heterochromatin by sequencing genetic mutants and through gene-targeting using RNA interference (RNAi). Together my data will contribute to collaborative efforts to obtain a basic understanding of the regulation, organization and functions of genes in pericentric heterochromatin.