Understanding Nucleosome Assembly Regulation in Drosophila melanogaster

Abstract

Nucleosomes consist of a complex of DNA and an octameric core of histone proteins, which represent the basic subunit of chromatin. The N-terminal tails of histones are target for chemical modifications, which play an important role in chromatin structure and the control of gene activity shaping the epigenome of a cell which was defined by Cold Spring Harbor Laboratories in 2008 as the “Stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence” (1). “Heritable” implies, that the epigenetic landscape needs to be maintained or re-established during or after cell division. During DNA replication, pre-existing or parental nucleosomes are disrupted and re-assembled behind the replication fork together with newly synthesized histones. However, it is not well understood how parental histones decorated with posttranslational modifications are recycled and positioned during the assembly of nucleosomes in the course of DNA replication. In this study I have addressed the question whether modified parental histones ‘remember’ their position after replication. For this purpose, I used a Drosophila melanogaster mutant that lacks all canonical histone genes (encoding histone H1, H2A, H2B, H3, and H4). This mutant, referred to as HisC mutant, is therefore not able to express new histones during replication. Owing to special characteristics of the early embryonic development, I analysed the first cell cycle when zygotic histone synthesis is required during embryonic development, and the histone deletion exerts its effect. Chapter I represents the main findings of my study. I show that upon lack of histone synthesis in homozygous HisC mutant embryos, parental histones are faithfully recycled, but they are not sufficient to re-establish the characteristic chromatin landscape. This results in reduced nucleosome occupancy and increased inter dyad distances ultimately resulting in increased chromatin accessibility. Arrays of nucleosomes at transcription start sites (TSS) were irregular, with the +2 and +3 nucleosomes shifted downstream. This is accompanied by a drastic upregulation of genes, spurious transcription within gene bodies and intergenic regions, as well as a potential premature release of RNA polymerase II (RNAPII) towards productive elongation from the TSS. Consistently, active chromatin marks were strongly reduced in the mutant, whereas repressive marks maintained similar enrichment levels. Interestingly, however, in both cases, the enrichment patterns and peak calling suggests that decorated parental histones are incorporated in close vicinity of their original location. This observation suggests a positional memory of epigenetic marks during DNA replication. In chapter II, I address the question how histone depletion affects cell cycle progression. HisC mutant embryos, which fail to zygotically express canonical histones, arrest in cell cycle 15 during the G2/M15 transition, which normally is driven by StringCdc25. In HisC mutants, string mRNA is downregulated, which is controlled by the RNA binding protein called Held-out-wings (How). How is expressed in two isoforms (long and short How, respectively). Long How, which was shown to destabilize target RNAs, is upregulated in HisC mutant embryos. Deletion of the How binding site in string mRNA results in an increased string mRNA abundance. Thus, my data suggests that in the absence of histone synthesis, the cell cycle arrests at the G2/M transition by destabilizing string mRNA based on a How-dependent regulatory mechanism.