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Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive

Abstract

Eukaryotic genomes are organized into active (euchromatic) and inactive (heterochromatic) chromatin domains. Post-translational modifications of histones (or ‘marks’) are key in defining these functional states, particularly in promoter regions1,2. Mutual regulatory interactions between these marks—and the enzymes that catalyse them—contribute to the shaping of this epigenetic landscape, in a manner that remains to be fully elucidated1,2. We previously observed that asymmetric di-methylation of histone H3 arginine 2 (H3R2me2a) counter-correlates with di- and tri- methylation of H3 lysine 4 (H3K4me2, H3K4me3) on human promoters3. Here we show that the arginine methyltransferase PRMT6 catalyses H3R2 di-methylation in vitro and controls global levels of H3R2me2a in vivo. H3R2 methylation by PRMT6 was prevented by the presence of H3K4me3 on the H3 tail. Conversely, the H3R2me2a mark prevented methylation of H3K4 as well as binding to the H3 tail by an ASH2/WDR5/MLL-family methyltransferase complex4,5,6,7. Chromatin immunoprecipitation showed that H3R2me2a was distributed within the body and at the 3′ end of human genes, regardless of their transcriptional state, whereas it was selectively and locally depleted from active promoters, coincident with the presence of H3K4me3. Hence, the mutual antagonism between H3R2 and H3K4 methylation, together with the association of MLL-family complexes with the basal transcription machinery8, may contribute to the localized patterns of H3K4 tri-methylation characteristic of transcriptionally poised or active promoters in mammalian genomes1,2,3,9,10.

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Figure 1: H3R2me2a is present on inactive promoters, and within genes independently from the expression status.
Figure 2: H3R2 methylation by PRMT6 is prevented by H3K4me3.
Figure 3: H3R2me2a excludes binding of WDR5 to the H3 tail.
Figure 4: H3R2me2a and MLL complex subunits are counter-correlated on chromatin.

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Acknowledgements

We thank G. Natoli, G. I. Dellino and all the members of our group for discussions; T. Kouzarides for PRMT4/CARM1 expression vectors and for communicating unpublished data; S. Richard, M. Wainberg and C. Invernizzi for PRMT6 vectors; D. Reinberg and P. Trojer for the Flag–ASH2 vector; and P. G. Pelicci for continuous support. This work was supported by a fellowship from the Italian Federation for Cancer Research (FIRC) to E.G., by grants from the Italian Association for Cancer Research (AIRC) to B.A. and by a grant from the Deutsche Forschungsgemeinschaft (DFG) to B.L.

Author Contributions E.G. and B.A. conceived the work and designed the experiments. B.A. supervised the project and wrote the manuscript. E.G. and F.M. performed ChIP, E.G. and C.B. performed biochemical experiments, and F.C. constructed expression vectors. M.C. performed the statistical analysis of ChIP data. H.S. and B.L. purified the TAP–ASH2 complex.

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The file contains Supplementary Table 1 with genomic coordinates and primers used in this work. (XLS 146 kb)

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Guccione, E., Bassi, C., Casadio, F. et al. Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive. Nature 449, 933–937 (2007). https://doi.org/10.1038/nature06166

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