Regulation of chromatin structure by site-specific histone H3 methyltransferases


The organization of chromatin into higher-order structures influences chromosome function and epigenetic gene regulation. Higher-order chromatin has been proposed to be nucleated by the covalent modification of histone tails and the subsequent establishment of chromosomal subdomains by non-histone modifier factors. Here we show that human SUV39H1 and murine Suv39h1—mammalian homologues of Drosophila Su(var)3-9 and of Schizosaccharomyces pombe clr4—encode histone H3-specific methyltransferases that selectively methylate lysine 9 of the amino terminus of histone H3 in vitro. We mapped the catalytic motif to the evolutionarily conserved SET domain, which requires adjacent cysteine-rich regions to confer histone methyltransferase activity. Methylation of lysine 9 interferes with phosphorylation of serine 10, but is also influenced by pre-existing modifications in the amino terminus of H3. In vivo, deregulated SUV39H1 or disrupted Suv39h activity modulate H3 serine 10 phosphorylation in native chromatin and induce aberrant mitotic divisions. Our data reveal a functional interdependence of site-specific H3 tail modifications and suggest a dynamic mechanism for the regulation of higher-order chromatin.

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Figure 1: Sequence similarity of SET domains with plant methyltransferases.
Figure 2: Histone methyltransferase activity of transfected and recombinant SUV39H1 and Suv39h1 proteins.
Figure 3: Specific HMTase activity of SU(VAR)3-9 related proteins.
Figure 4: Lysine 9 of the H3 N terminus is the principal site for in vitro methylation by recombinant Suv39h1.
Figure 5: Interdependence of Lys 9 methylation and Ser 10 phosphorylation in the H3 N terminus.
Figure 6: Suv39h-dependent modification of the H3 N terminus in native chromatin.


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We would like to thank M. Cleary for providing a partial HRX cDNA, R. Allshire for the Clr4 cDNA, I. Gorny for peptide synthesis and R. G. Cook for automated sequencing of the H3 N-terminal peptide. During the course of this work, E. V. Koonin and L. Aravind have independently discovered homology of the SET domain with plant methyltransferases. We acknowledge M. Doyle for the contribution to the Suv39HZ knockout and thank K. Nasmyth and M. Busslinger for helpful comments and critical reading of the manuscript. Research in the laboratory of C.D.A. is funded by grants from the NIH to C.D.A. and B.D.S. Z.-W.S. is supported by a postdoctoral cancer training grant from the University of Virginia Cancer center. Research in the laboratory of T.J. is supported by the IMP, the Austrian Research Promotion Fund and the Vienna Business Agency.

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Rea, S., Eisenhaber, F., O'Carroll, D. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases . Nature 406, 593–599 (2000).

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