Investigating H3K4 methylation by SET1/MLL complexes

Thesis

H3K4 methylation is a histone modification which often correlates well with active transcription. In mammals, the SET1/MLL complexes are responsible for H3K4 methylation. The conventional view holds that SET1A/B complexes deposit the majority of H3K4me3 at highly-transcribed genes, MLL1/2 complexes deposit H3K4me3 at a subset of lowly-transcribed genes, and MLL3/4 complexes deposit H3K4me1/2 at enhancers. In mammals, H3K4me3 is found at CpG islands - short stretches of DNA with high CpG density that remain unmethylated in an otherwise pervasively methylated genome. The SET1A/B and MLL1/2 complexes all contain a zinc-finger CXXC domain that targets them specifically to CpG islands. Over 70% of all promoters contain a CpG island, and SET1A/B and MLL1/2 complexes were thought to promote transcription by creating a permissive chromatin state through H3K4me3 deposition. However, recent work has shown that SET1A/B complexes can support transcription through an H3K4me3-independent mechanism, and their removal results in surprisingly modest reductions in H3K4me3. Therefore, our understanding of the how SET1/MLL complexes deposit H3K4 methylation and how they regulate transcription is lacking.

Here, I aim to understand how SET1/MLL complexes methylate H3K4 in mouse embryonic stem cells (mESCs) using degrons to rapidly deplete SET1/MLL proteins. Using cell lines in which SET1A/B, MLL1/2, and MLL3/4 can be rapidly depleted on their own, I dissect their contributions to H3K4 methylation. I find that SET1A/B and MLL1/2 have modest contributions to H3K4me3 on their own, but rather synergise to deposit half of all H3K4me3. Using a cell line in which these complexes can be simultanously depleted together, I find that SET1/MLL methyltransferases collectively implement half of all H3K4 methylation in mESCs. I find that the remaining H3K4 methylation is partially dependent on transcription and entirely dependent on shared subunits of SET1/MLL complexes. Surprisingly, I identify a previously uncharacterized isoform of SET1B as a putative candidate for this methyltransferase activity. Taken together, my findings indicate that SET1/MLL complexes collaborate extensively to deposit H3K4 methylation, and that a previously uncharacterized isoform of SET1B may have a major role in H3K4 methylation.

Authors: Au, HYA

• DOI: 10.5287/ora-zboqqek5x
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: SET1/MLL complexes; H3K4 methylation
• Subjects: Chromatin