Expanding the network of enzymes affecting methylation atH3K4 (histone 3 lysine 4) during Caenorhabditis elegansembryogenesis

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Abstract

Post translational modifications (PTMs) of histone tails are an important determinantof chromatin structure, and can act as key regulators of DNA-dependent processes.Methylation of histone 3 at lysine 4 (H3K4) is one of the most widely studied PTMsbecause of its correlation with transcription. Three methylation states exist at H3K4:mono-, di, and tri-methylation (H3K4me1, -me2, and -me3, respectively). Eachmethylation state occupies a distinct genomic position, supporting the view that theextent of methylation at H3K4 has a functional significance. However, the exactbiological function of these three marks are not well understood. H3K4 methylation iswritten by SET domain-containing enzymes that function within SET/COMPASS/MLLcomplexes. Our lab has previously identified the SET-16 enzyme as writing H3K4me3in C. elegans. The other well-characterised H3K4-specific methyltransferases in theworm is SET-2, an enzymes responsible for bulk H3K4me2/me3 levels. Usingtargeted RNAi screens, we have charecterised the full landscape of SET domainenzymes affecting all three methylation states at H3K4 during embryogenesis in C.elegans (Chapter 3). Unexpectedly, many previously uncharacterised enzymes wereidentified as preferentially affecting each of the methylation states, including SET-19that can deposit all three marks, and several candidates that preferentially affectH3K4me1: SET-30, SET-27, MES-2, and MES-4. During the project, Greer et al. 2014independently identified two enzymes with activities targeting H3K4, SET-17 andSET-30, which were also candidates from our RNAi screens. With a focus on enzymesacting on H3K4me1, we demonstrate that H3K4me1 candidates can show differentpatterns of temporal regulation and also have roles in regulating soma versusgermline cell-fate decisions (Chapter 4). Finally, we demonstrate a novel role for MES-2 (a methyltransferase enzyme with a highly conserved role in depositing repressiveH3K27 methylation) in acting alongside the SPR-5 H3K4me2 demethylase to regulatelevels of H3K4me1 during embryogenesis (Chapter 5).

Layman's Abstract

DNA carries all the instructions to create a living organism. This huge molecule is repeatedly wrapped around proteins called histones that ‘package’ and condense the information, enabling it to cram into a small compartment known as the nucleus. I am using a small, free-living worm to study how changing the way that DNA is packaged can alter the genetic information that is available in each of our cells. Generating a different set of instructions produces a different type of cell, for example a muscle cell, or a neuron. This 'identity' is very important, because every single cell contains an identical copy of our DNA. We must therefore be able to manipulate the information differently if we are to generate the myriad of different cell types, with very different identities, which are needed to carry out all the jobs that our bodies need to 'run smoothly'. We use the worm as a simple model to study biological processes that are more complex in humans. My project addresses how changing the packaging of DNA can produce a specific type of cell by turning on the information that this cell needs, and keeping other information switched off. We can study this question by removing a piece of the DNA packaging machinery in a mother, and observing the effect(s) in this worm’s offspring.

Keyword(s)

C. elegans; Chromatin; Embryogenesis ; Histones; Lysine ; Methylation

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