Mouse Polycomb Proteins Bind Differentially to Methylated Histone H3 and RNA and Are Enriched in Facultative Heterochromatin

Abstract

The chromodomain (CD) of the Drosophila Polycomb protein exhibits preferential binding affinity for histone H3 when trimethylated at lysine 27. Here we have investigated the five mouse Polycomb homologs known as Cbx2, Cbx4, Cbx6, Cbx7, and Cbx8. Despite a high degree of conservation, the Cbx chromodomains display significant differences in binding preferences. Not all CDs bind preferentially to K27me3; rather, some display affinity towards both histone H3 trimethylated at K9 and H3K27me3, and one CD prefers K9me3. Cbx7, in particular, displays strong affinity for both H3K9me3 and H3K27me3 and is developmentally regulated in its association with chromatin. Cbx7 associates with facultative heterochromatin and, more specifically, is enriched on the inactive X chromosome. Finally, we find that, in vitro, the chromodomain of Cbx7 can bind RNA and that, in vivo, the interaction of Cbx7 with chromatin, and the inactive X chromosome in particular, depends partly on its association with RNA. We propose that the capacity of this mouse Polycomb homolog to associate with the inactive X chromosome, or any other region of chromatin, depends not only on its chromodomain but also on the combination of histone modifications and RNA molecules present at its target sites.

We are grateful to members of the Allis laboratory for helpful discussions, in particular, W. Fischle and S. Hake. We greatly appreciate W. Fischle for purified HP1 and Pc proteins, Y. Wang for the initial work on this project, R. Diaz for help with peptide purification, and L. Cooper for assistance with protein purification. We thank W. Herr, M. Narita, A. Otte, A. E. L. Marjou, D. Reinberg and A. Smith for reagents and C. Maison for helpful discussions.

This work is funded by the Centre National de la Recherche Scientifique (ATIPE), the Curie Institute (PIC program), the “Epigenome” European Network of Excellence, and the Human Frontier Science Program to E.H., as well as the MRC (J.G.), the NSF (E.B.), and NIH grant GM53512 (C.D.A.).