Stable X chromosome inactivation involves the PRC1 Polycomb complex and requires histone MACROH2A1 and the CULLIN3/SPOP ubiquitin E3 ligase

doi:10.1073/pnas.0408918102

Stable X chromosome inactivation involves the PRC1 Polycomb complex and requires histone MACROH2A1 and the CULLIN3/SPOP ubiquitin E3 ligase

^*Division of Molecular Genetics, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands; ^‡Biotech Research and Innovation Centre, Symbion Science Park, 2100 Copenhagen, Denmark; ^§Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143-2200; and ^¶Department of Human Genetics, University of California, Los Angeles, CA 90095

Edited by Rudolf Jaenisch, Massachusetts Institute of Technology, Cambridge, MA, and approved April 14, 2005 (received for review December 1, 2004)

Abstract

X inactivation involves the stable silencing of one of the two X chromosomes in XX female mammals. Initiation of this process occurs during early development and involves Xist (X-inactive-specific transcript) RNA coating and the recruitment of Polycomb repressive complex (PRC) 2 and PRC1 proteins. This recruitment results in an inactive state that is initially labile but is further locked in by epigenetic marks such as DNA methylation, histone hypoacetylation, and MACROH2A deposition. Here, we report that the E3 ubiquitin ligase consisting of SPOP and CULLIN3 is able to ubiquitinate the Polycomb group protein BMI1 and the variant histone MACROH2A. We find that in addition to MACROH2A, PRC1 is recruited to the inactivated X chromosome in somatic cells in a highly dynamic, cell cycle-regulated manner. Importantly, RNAi-mediated knock-down of CULLIN3 or SPOP results in loss of MACROH2A1 from the inactivated X chromosome (Xi), leading to reactivation of the Xi in the presence of inhibitors of DNA methylation and histone deacetylation. Likewise, Xi reactivation is also seen on MacroH2A1 RNAi under these conditions. Hence, we propose that the PRC1 complex is involved in the maintenance of X chromosome inactivation in somatic cells. We further demonstrate that MACROH2A1 deposition is regulated by the CULLIN3/SPOP ligase complex and is actively involved in stable X inactivation, likely through the formation of an additional layer of epigenetic silencing.

Footnotes

↵ ∥ To whom correspondence should be addressed. E-mail: m.v.lohuizen{at}nki.nl.
↵ † I.H.-M., A.H.L., and P.v.d.S. contributed equally to this work.
Author contributions: I.H.-M., A.H.L., and M.v.L. designed research; I.H.-M., A.H.L., P.v.d.S., E.B., I.M., and E.V. performed research; I.M., D.A.N., B.P., and Y.M. contributed new reagents/analytic tools; I.H.-M., A.H.L., P.v.d.S., E.B., I.M., E.V., and M.v.L. analyzed data; and I.H.-M., A.H.L., P.v.d.S., and M.v.L. wrote the paper.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: PcG, Polycomb group; PRC, Polycomb repressive complex; Xi, inactivated X chromosome; Xist, X-inactive-specific transcript; 5-Aza-dC, 5-aza-2′-deoxycytidine; TSA, trichostatin A; HA, hemagglutinin.