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Title: Understanding the role of CFP1 at CpG islands
Author: Brown, David
Awarding Body: University of Oxford
Current Institution: University of Oxford
Date of Award: 2014
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Vertebrate genomes are punctuated by CpG islands regions, which have an elevated frequency of CpG dinucleotides. CpG islands are associated with over 70% of mammalian promoters suggesting they may contribute to the regulation of transcription. However, despite being discovered over 30 years ago, the function of CpG islands is still not understood. Unlike the majority of the genome, CpG islands are resistant to DNA methylation. This provides a binding site for CFP1 which binds specifically to non-methylated DNA via its zinc-finger CXXC (zf-CXXC) domain. CFP1 is a subunit of the SET1 methyltransferase complex, and is thought to direct the activating histone modification H3K4me3 to CpG islands. Interestingly, CFP1 also contains a PHD domain which is proposed to bind the H3K4me3 mark, potentially producing a feedback loop between H3K4me3 and the SET1 complex. Although the structural basis for discrimination of non-methylated CpGs is known, it is not clear how zf-CXXC proteins distinguish CpG islands amongst the irregular nucleosomal landscape which exists within the nucleus. This thesis is focused on the role of CFP1 in the relationship between CpG islands, SET1 and H3K4me3. To address these questions, it was important to mechanistically dissect the contribution of the PHD and zf-CXXC domains. The proposal that the PHD domain of CFP1 binds selectively to H3K4me3 was confirmed by in vitro experiments, however this study demonstrates that the PHD domain is insufficient for stable interactions with chromatin. Using complementary genome-wide and live cell imaging approaches, the zf-CXXC domain shown to be required for PHD-dependent interactions. Genome-wide snapshots of binding interactions, together with spatial and temporal details, expose a surprising contribution of the SET1 complex to the nuclear mobility of CFP1, providing a new perspective on the role of CFP1 in H3K4 methylation.
Supervisor: Klose, Rob; Schermelleh, Lothar Sponsor: Wellcome Trust
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: Biochemistry ; Cell Biology ; Mammalian chromosome ; Biology (medical sciences) ; CpG Islands ; Chromatin ; DNA methylation ; Histone ; Methyltransferase ; ChIP ; genome