Genomic DNA is typically wound around clusters of protein known as histones, an arrangement that keeps the chromosomes compact but also helps to regulate the activity of local genes. To achieve this latter function, enzymes attach specific chemical modifications to histone proteins, and these in turn act as recruitment signals for activators or repressors. Ernesto Guccione at the A*STAR Institute of Molecular and Cellular Biology and National University of Singapore and colleagues have now revealed how subtle changes in these chemical marks can convey radically different messages.
The initial discovery was made serendipitously when Guccione and his team were studying an arginine amino acid in histone 3, which can be modified with two methyl groups in either a symmetrical (H3R2me2s) or asymmetrical pattern (H3R2me2a). The researchers were surprised to find that the two modifications appeared to exert opposite regulatory effects. “In science, you always have to be very open-minded,” says Guccione. “So rather than dismiss it, we decided to use that initial preliminary observation to build up a strong follow-up story.”
Their new study confirms these findings, demonstrating that although H3R2me2a suppresses local gene expression, H3R2me2s instead switches on transcription. Indeed, when they mapped H3R2me2s sites on the chromosomes in cultured human cells, they found that the histone modification frequently appeared near the transcriptional start sites of active genes. In many cases, H3R2me2s appeared adjacent to methylation at lysine 4 (H3K4), another histone modification associated with gene activation.
The researchers also observed H3R2me2s at so-called ‘enhancer’ positions farther away from transcription start sites, where it acts by recruiting the activator protein WDR5 (see image). This was especially surprising, as H3R2me2a physically blocks WDR5 binding. “A tiny variation in the position of the methyl moiety radically affects the binding of several proteins to histone H3,” says Guccione. Activator protein WDR5 in turn recruits additional factors that methylate H3K4, thereby stimulating the expression of genes associated with a particular enhancer region. “This provides a possible explanation for how enhancers get enriched with the histone mark H3K4me1.”
Having demonstrated the biological impact of the symmetric H3R2 modification, Guccione and his team are now exploring its role in different tissues and cell types by raising genetically modified mice that lack either or both enzymes for generating the H3R2me2s mark. At the same time, they are using mouse embryonic stem cells to examine the importance of this mode of gene regulation at the early stages of development.
The A*STAR-affiliated researchers contributing to this research are from the Institute of Molecular and Cellular Biology.