A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced

Abstract

During early mammalian female development, one of the two X chromosomes becomes inactivated. Although X-chromosome coating by Xist RNA is essential for the initiation of X inactivation, little is known about how this signal is transformed into transcriptional silencing. Here we show that exclusion of RNA Polymerase II and transcription factors from the Xist RNA-coated X chromosome represents the earliest event following Xist RNA accumulation described so far in differentiating embryonic stem (ES) cells. Paradoxically, exclusion of the transcription machinery occurs before gene silencing is complete. However, examination of the three-dimensional organization of X-linked genes reveals that, when transcribed, they are always located at the periphery of, or outside, the Xist RNA domain, in contact with the transcription machinery. Upon silencing, genes shift to a more internal location, within the Xist RNA compartment devoid of transcription factors. Surprisingly, the appearance of this compartment is not dependent on the A-repeats of the Xist transcript, which are essential for gene silencing. However, the A-repeats are required for the relocation of genes into the Xist RNA silent domain. We propose that Xist RNA has multiple functions: A-repeat-independent creation of a transcriptionally silent nuclear compartment; and A-repeat-dependent induction of gene repression, which is associated with their translocation into this silent domain.[Keywords: X inactivation; Xist RNA; transcriptional silencing; 3D nuclear organization; histone modifications; differentiation] Supplemental material is available at http://www.genesdev.org.

Host genome surveillance for retrotransposons by transposon-derived proteins

“…This mass action requirement for silencing might reflect a high concentration of specific transposable-element-binding proteins similar to CENP-Bs capable of recruiting chromatin modifiers. The formation of Tf bodies could have parallels in mammalian X-chromosome inactivation, in which transposable elements might facilitate the assembly of a silent nuclear compartment [45][46][47] . Recent evidence suggests that whereas RNAi has a prominent role in silencing transposable elements in germ cells in higher eukaryotes 7 , there are probably alternative mechanisms, possibly similar to that of S. pombe CENP-B-based surveillance, for regulating transposable elements in somatic cells.…”

Advances in understanding chromosome silencing by the long non-coding RNA Xist

“…A-repeat deficient RNA is also able to recruit macroH2A, SAF-A and Ash2L [45]. Either these proteins interact with regions of Xist RNA other than the A-repeats or their recruitment is secondary to the establishment of a transcriptionally silent domain that occurs using A-repeat deficient transgenes [58]. As discussed earlier, it has been suggested that the silent domain corresponds to common repeat sequences on the X chromosome and it follows that these could also be the site of recruitment of other factors.…”

“…DNA-FISH using X-linked sequences showed that while repetitive sequences on the X chromosome are included in the domain of Xist RNA lacking the A-repeat, genic regions are often found outside or at the periphery of the domain [58]. These findings raise the idea that one role of Xist RNA is to create a transcriptionally silent domain that represses repetitive sequences by recruiting PRCs and by excluding rstb.royalsocietypublishing.org Phil Trans R Soc B 368: 20110325 RNAPII in a manner independent of A-repeat function, and a second role is to incorporate genic regions on the X chromosome from outside or at the periphery of the Xist RNA domain into the interior in a manner dependent on the A-repeat.…”

Mechanistic concepts in X inactivation underlying dosage compensation in mammals

“…A conserved sequence on the 5 0 of Xist, which has been termed repeat A, is required for gene silencing (Wutz et al, 2002). Expression of Xist lacking repeat A does not cause gene repression but results in localization of Xist and recruitment of most chromatin modifications to the Xi (Chaumeil et al, 2006). The repeat A RNA motif is predicted to fold into a stem loop structure, which could function as a binding site for silencing factors (Wutz et al, 2002).…”

“…In mice, Xist RNA forms a domain over the non-genic chromatin of the core of the X chromosome territory (Chaumeil et al, 2006). Also on the human Xi XIST seems to overlap the central region of the chromosome territory, which contains mostly genomic repeats (Clemson et al, 2006).…”