Writers and readers of histone H3 methylation

Abstract

The synthesis of RNA from a DNA template in eukaryotic cells is a complex process which is regulated at several stages. This is accomplished by RNA polymerase II and a horde of other transcription factors which together comprise the transcription machinery. Accessing information from DNA in the nucleus is restricted by chromatin structures. Chromatin comprises of DNA wrapped around a histone octamer (two copies each of histones H2A, H2B, H3 and H4) and the linker histone H1. The structural entity of chromatin known as nucleosome contains protruding N-terminal ends of histones. These histone tails are subject to post-translational modifications like acetylation, methylation, phosphorylation and methylation. Histone modifications may act alone or in concert in a context-dependent manner to facilitate or repress transcription. They may also influence one another such that one modification recruits or activates chromatin-modifying complexes to generate a different histone modification and this forms the theme of histone ‘cross talk’. Genomic-scale analyses of histone modifications show general correlations between different modification states, their genomic loci and gene expression levels. Histone modification patterns are regulated by enzymes that add, remove or read the covalent modifications. Trimethylation of lysine 4 on histone H3 (H3K4me3) is a mark associated with active transcription at promoters and the MLL families of histone methyltransferases are mainly responsible for writing this mark. Menin, an integral subunit of the MLL1/MLL2 complexes critically links H3K4me3 and estrogen-receptor mediated transcription. H3K4me3 can recruit plant homeodomain (PHD)-containing effector proteins to chromatin and thereby facilitate downstream effects. Basal transcription factor TFIID has been identified as one such reader of H3K4me3. To further explore the mechanism of menin and nuclear- receptor mediated transcription as well as the regulation of TFIID mediated recognition of H3K4me3 we addressed these two questions in this thesis. In chapter 2 we review the current knowledge of several histone lysine methyltransferase and demethylase pathways relevant to cancer. We also summarize the current status and future opportunities for development of 'epidrugs' targeting histone modifications for cancer therapy. The menin protein is encoded by the Multiple Endocrine Neoplasia type 1 (MEN1) tumor suppressor gene. In chapter 3 we address the role of menin in PPAR γ -dependent transcription and adipocyte differentiation. Next, in chapter 4, we investigate the global levels of H3K4me3 in parathyroid adenomas and also the effect of menin on the function of VDR. We establish that aberrant gene expression in MEN1 tumors is caused by specific effects on genes that are regulated by menin-interacting proteins, such as VDR. In chapter 5 we show that H3K4me3 binding of TFIID is decreased by phosphorylation of the preceding threonine residue in the histone H3 tail and this coincides with mitotic inhibition of transcription. Based on our observations we propose that a histone H3 phospho-methyl switch regulates TFIID mediated transcription during mitotic progression of the cell cycle. In conclusion, I have addressed the importance of H3K4me3 and menin in molecular pathways regulating gene expression and I have also identified a novel form of cross talk at the histone H3 tail in regulating transcription by TFIID during mitosis