During multicellular development, cells must make fate decisions that reproducibly generate the correct cell type proportions. It is remarkable that in certain developmental scenarios, seemingly identical cells in a homogenous environment can achieve this. It is thought that this is possible because cell populations exhibit reproducible cell-cell variation in gene expression. How these differences are generated has been intensely studied over the past decade, with transcriptional bursting emerging as an important factor for driving variability between cells. Furthermore, it is thought that chromatin structure around gene promoters is a key regulator of transcriptional bursting. However, key questions remain. What factors regulate chromatin structure at the molecular level? Is the activity of chromatin regulators governed by random processes or entrained by one of many hidden factors such as cell cycle positioning, cell volume, metabolism? Are the proportions of cells exhibiting different bursting patterns regulated to ensure normal cell fate choice and proportioning? To address these questions, we have investigated whether different regulators of chromatin structure affect the pre-stalk/pre-spore fate decision in the social amoebae D. discoideum. We have identified that set1, a methyl-transferase responsible for generating methylation on histone 3 at position lysine 4 (H3K4me), plays a key role in controlling the balance of cell types in multicellular development as in its absence cells become autonomously primed towards a pre-stalk fate. Single cell RNA-sequencing has revealed that genes normally regulated by this modification represent a specific class of hyper-variable genes. We find that this variability is generated by specific set1 dependent repression at these loci, as upon deletion of this enzyme we see an active recruitment of more cells to an expressing state. Our data suggest that set1 activity itself is controlled by the external source of the cell cycle. This cell cycle dependent regulation robustly ensures the correct proportions of cells within the population contain levels of set1 activity that prime 25% of cells towards the pre-stalk lineage and the other 75% to the pre-spore fate. As such we believe our study reveals a novel mechanism linking specific regulation of transcriptional bursting through the activity of set1 to cell fate propensity.