RNA and the epigenetic regulation of X chromosome inactivation.

The Xist RNA in female somatic cells appears as a cluster of particles that coats the Xi (Figure 4Figure 4; 2xClemson, C.M, McNeill, J.A, Willard, H.R, and Lawrence, J.B. J. Cell. Biol. 1996; 132: 1–17Crossref | PubMed | Scopus (455)See all References, 10xLee, J.T and Jaenisch, R. Nature. 1997; 386: 275–279Crossref | PubMed | Scopus (182)See all References). This distribution is not affected by DNase or RNase H treatment (Clemson et al. 1996xClemson, C.M, McNeill, J.A, Willard, H.R, and Lawrence, J.B. J. Cell. Biol. 1996; 132: 1–17Crossref | PubMed | Scopus (455)See all ReferencesClemson et al. 1996), suggesting that Xist does not contact DNA. These data are most consistent with the idea that RNA–protein interactions mediate the propagation and association of Xist RNA with a chromosome in cis. Xist RNA produced from a YAC transgene can spread and mediate silencing of linked autosomal sequences (Lee and Jaenisch 1997xLee, J.T and Jaenisch, R. Nature. 1997; 386: 275–279Crossref | PubMed | Scopus (182)See all ReferencesLee and Jaenisch 1997), indicating that X chromosome–specific elements are not required for the propagation of Xist RNA and heterochromatin.Figure 4The Particulate Nature of Xist RNA as It Coats the XiXist RNA (red) on a mouse Xi (blue) in mitosis. In humans XIST RNA does not coat metaphase chromosomes.View Large Image | View Hi-Res Image | Download PowerPoint SlidePropagation of Xist RNA precedes X chromosome silencing during imprinted and random X inactivation (8xKeohane, A.M, O'Neill, L.P, Belyaev, N.D, Lavender, J.S, and Turner, B.M. Dev. Biol. 1996; 180: 618–630Crossref | PubMed | Scopus (182)See all References, 19xSheardon, S.A, Duthie, S.M, Johnston, D.M, Newall, A.E.T, Formstone, E.J, Arkell, R.M, Nesterova, T.B, Alghisi, G.-C, Rastan, S, and Brockdorff, N. Cell. 1997; 91: 99–107Abstract | Full Text | Full Text PDF | PubMed | Scopus (201)See all References), suggesting that factors which act downstream of the stabilization and spread of Xist RNA are required to mediate silencing. Some clues as to the mechanism by which Xist RNA might mediate silencing come from conserved features of inactive X heterochromatin. In placental and marsupial mammals, the Xi replicates late in S phase and displays a decrease in abundance of acetylated isoforms of histone H4 (Graves 1996xGraves, J.A.M. Annu. Rev. Genet. 1996; 30: 233–260Crossref | PubMed | Scopus (112)See all ReferencesGraves 1996). Thus, the propagation of Xist RNA might delay initiation of replication from origins on the Xi and/or recruit modifiers of histone acetylation. In differentiating female embryonic stem cells, the appearance of a late-replicating X chromosome and stabilization of Xist transcripts coincide and precede the down-regulation of X-linked gene expression and the emergence of a hypoacetylated X chromosome (Keohane et al. 1996xKeohane, A.M, O'Neill, L.P, Belyaev, N.D, Lavender, J.S, and Turner, B.M. Dev. Biol. 1996; 180: 618–630Crossref | PubMed | Scopus (182)See all ReferencesKeohane et al. 1996). These results suggest that Xist RNA might function by causing replication origins on the Xi to fire late in S phase, which in turn results in the formation of heterochromatin on the late-replicating chromosome. It has been suggested that DNA replication timing may regulate chromatin formation through interactions between the origin recognition complex and heterochromatin proteins (Pak et al. 1997xPak, D.T.S, Pflumm, M, Chesnokov, I, Huang, D.W, Kellum, R, Marr, J, Romanowski, P, and Botchan, M.R. Cell. 1997; 91: 311–323Abstract | Full Text | Full Text PDF | PubMed | Scopus (321)See all ReferencesPak et al. 1997). Xist RNA might also function to modulate histone acetylation of the Xi, by obstructing histone acetyltransferases or recruiting deacetylases. It is worth noting that the Drosophila mof gene, which encodes a putative histone acetyltransferase, provides an example of a histone modifier that is required for dosage compensation and which acts as the result of the assembly of an RNA–protein complex on the X chromosome (Hilfiker et al. 1997xHilfiker, A, Hilfiker-Kleiner, D, Pannuti, A, and Lucchesi, J.C. EMBO J. 1997; 16: 2054–2060Crossref | PubMed | Scopus (314)See all ReferencesHilfiker et al. 1997).The Xi is maintained in a clonal and stable fashion. However, XIST is neither necessary nor sufficient to maintain X inactivation in somatic cell hybrids (1xBrown, C.J and Willard, H.F. Nature. 1994; 368: 154–156Crossref | PubMed | Scopus (149)See all References, 5xHansen, R.S, Canfield, T.K, Fjeld, A.D, and Gartler, S.M. Hum. Mol. Genet. 1996; 5: 1345–1353Crossref | PubMed | Scopus (71)See all References). Therefore, Xist RNA may function to mediate X inactivation during a precisely defined developmental window. X inactivation is most likely maintained by multiple redundant and self-perpetuating mechanisms that include late DNA replication and histone modifications. In the somatic lineage of placental mammals, CpG islands on the Xi are methylated. Methylation levels in marsupials and in the extraembryonic lineage of placental mammals are very low and X inactivation is less stable (Graves 1996xGraves, J.A.M. Annu. Rev. Genet. 1996; 30: 233–260Crossref | PubMed | Scopus (112)See all ReferencesGraves 1996), implicating DNA methylation in the stable maintenance of the inactive state.Despite an emerging understanding of the significance of XIST/Xist in X chromosome silencing, the molecular mechanisms by which cells initiate and propagate X inactivation still remain a mystery. The identification of the hypothetical blocking, stabilizing, and initiating factors will be important in understanding how Xist RNA assembles on one X chromosome and may provide insight into the biochemical mechanisms of X inactivation.‡Present address: Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.