Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway


Human inactive X chromosome (Xi) forms a compact structure called the Barr body, which is enriched in repressive histone modifications such as trimethylation of histone H3 Lys9 (H3K9me3) and Lys27 (H3K27me3). These two histone marks are distributed in distinct domains, and X-inactive specific transcript (XIST) preferentially colocalizes with H3K27me3 domains. Here we show that Xi compaction requires HBiX1, a heterochromatin protein 1 (HP1)–binding protein, and structural maintenance of chromosomes hinge domain–containing protein 1 (SMCHD1), both of which are enriched throughout the Xi chromosome. HBiX1 localization to H3K9me3 and XIST-associated H3K27me3 (XIST-H3K27me3) domains was mediated through interactions with HP1 and SMCHD1, respectively. Furthermore, HBiX1 was required for SMCHD1 localization to H3K9me3 domains. Depletion of HBiX1 or SMCHD1, but not Polycomb repressive complex 2 (PRC2), resulted in Xi decompaction, similarly to XIST depletion. Thus, the molecular network involving HBiX1 and SMCHD1 links the H3K9me3 and XIST-H3K27me3 domains to organize the compact Xi structure.

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Figure 1: HBiX1 interacts with HP1 and SMCHD1.
Figure 2: HBiX1 and SMCHD1 affect the distribution of H3K9me3 on Xi in interphase.
Figure 3: HBiX1 and SMCHD1 are involved in Xi chromosome compaction.
Figure 4: Localization of HBiX1 and SMCHD1 on Xi.
Figure 5: Localization of XIST on Xi.
Figure 6: Summary and model of the organization of the human Xi.

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We thank I. Hiratani, J. Nakayama and D.B. Goto for comments; Y. Hayashi-Takanaka (Osaka University) for the fluorescently labeled antibodies to histones; Y. Ohkubo for cloning the XIST gene; Y. Ohkawa for advice on ChIP-seq; and E. Ono and A. Tokushima for administrative assistance. R.-S.N. was supported by the Japan Society for the Promotion of Science (JSPS) Research Fellowships for Young Scientists (09J01447). This work was supported by the Japanese Ministry of Education, Culture, Sports, Science and Technology (20114006 to C.O. and K.N.), JSPS (24370071 to C.O. and 22710180 to K.N.) and Matrix Science KK (C.O.).

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R.-S.N. and K.-T.I. performed most of the experiments. K.N. performed the bioinformatics analysis. S.S. operated the Illumina GAIIx. N.S. performed MS. N.N. and H.K. raised antibodies. T.S. performed northern blotting and some RNA FISH experiments. C.O. conceived the study. C.O., K.N. and H.K. wrote the manuscript.

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Correspondence to Chikashi Obuse.

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Competing interests

N. Nozaki is a founder of the MAB Institute, Inc., which produces the antibodies to H3K9me3 and H3K27me3 used in this study.

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Nozawa, R., Nagao, K., Igami, K. et al. Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway. Nat Struct Mol Biol 20, 566–573 (2013).

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