YY1 tethers Xist RNA to the inactive X nucleation center

Abstract

The long noncoding Xist RNA inactivates one X chromosome in the female mammal. Current models posit that Xist induces silencing as it spreads along X and recruits Polycomb complexes. However, the mechanisms for Xist loading and spreading are currently unknown. Here, we define the nucleation center for Xist RNA and show that YY1 docks Xist particles onto the X chromosome. YY1 is a "bivalent" protein, capable of binding both RNA and DNA through different sequence motifs. Xist's exclusive attachment to the inactive X is determined by an epigenetically regulated trio of YY1 sites as well as allelic origin. Specific YY1-to-RNA and YY1-to-DNA contacts are required to load Xist particles onto X. YY1 interacts with Xist RNA through Repeat C. We propose that YY1 acts as adaptor between regulatory RNA and chromatin targets.

Figure 1. Newly introduced Xist transgenes squelch Xist RNA from Xi in MEFs

A. Map of Xist and transgenes. Restriction sites used for cloning: M, MluI; R, RsrII; N, NheI; P, PmlI. B. Xist RNA FISH (left) and H3K27me3 immunostaining (right) in X+P female clones. RNA FISH and immunostaining were followed by DNA FISH using a vector probe (Tg) to confirm transgenic origin of Xist or H3K27me3. Two representative clones shown before and after doxycycline induction (dox, 2μg/ml). Arrows, Xist squelching on Xi in progress. Number of cells with indicated Xist pattern/total cells shown. NOTE: MEF lines are tetraploid due to SV40 Large T-transformation. C. qRT-PCR of Xist in wildtype female MEF (WT) and two X+P clones. Transgenic RNA quantitated at uXist; total Xist at Exons 1–3. Xist levels normalized to WT (set arbitrarily to 1.0). Averages ± 1 standard deviation (SD) from three independent experiments shown. D. Serial Xist RNA/Tg DNA FISH in representative clones for four transgenic lines. Arrowheads, transgenic Xist locations. Arrows, Xist squelching in progress. Number of cells with indicated Xist pattern/total cells shown. E. Xist qRT-PCR measured at Exons 1–3. F. qRT-PCR of transgenic Xist for X-RF(7) and X-RARF(10). Levels at Dox 0h set to 1.0. G. qRT-PCR of endogenous (uRA) and total (exons 1–3) Xist in X-RA clones.

Figure 2. Autosomal transgenes attract Xist RNA way from Xi

A. Map of Xist, FISH probes, and transgenes. P, PasI. B. Serial Xist RNA/Tg DNA FISH in X-RA cells ± dox. Tg, transgene insertion site. Endogenous Xist, RA probe (RA); transgenic Xist, 5-Xist-riboprobe mix (5mix). Arrows, trans-migrated endogenous Xist to transgene site. C. H3K27me3 immunostaining followed by DNA FISH in X-RA cells. D. RNA FISH of female X+PE1 cells using probes E1 and E7 ± dox. Arrows, trans-migration of endogenous Xist to transgene site. E. qRT-PCR for total (uRA) and endogenous (dRE) Xist.

Figure 3. YY1 is required for Xist localization

A. Map of the proximal 2-kb region of Xist. One CTCF and three putative YY1 binding sites near Repeat F are shown. B. Western blot, qRT-PCR, and combined Xist RNA FISH/CTCF immunostain 48 hours after Ctcf knockdown using C1 or C3 siRNA. Averages ± SD of three independent experiments shown. C. YY1 Western blot and Yy1/Xist qRT-PCR after Yy1 knockdown using Y1 or Y2 siRNA. Averages ± SD from 7 independent experiments shown for qRT-PCR. One representative Western blot shown. D. Xist FISH after Yy1 knockdown. Cells with pinpoint (arrows) or no Xist were scored negative. Averages ± SD from 206–510 nuclei/sample from three independent experiments. E. H3K27me3 immunostaining (blue) followed by Xist RNA FISH in Yy1-knockdown cells. Two representative patterns shown. Histogram shows counts (n=62–138).

Figure 4. Mutating YY1-binding sites in DNA abolishes Xist RNA loading

A. Map of proximal Xist, YY1-binding sites, transgenes, and EMSA probe. Site-directed mutation of YY1 sites shown. B. Left panels: SDS-PAGE, Coomassie staining, and Western blot of purified recombinant His-YY1 protein. Right panel: EMSA using YY1 and a 280-bp uRF probe. WT, wildtype YY1 probe. Mut, mutated YY1 probe. Arrow, YY1-uRF shift. Asterisks, increasing Yy1 occupancy on uRF probe. C. Two-probe Xist RNA FISH of female X-RA^Yy1m clones, followed by DNA FISH to locate transgene (Tg) and Xs (X paint). Arrows, transgenic RNA and transgene position. Arrowheads, transmigrated mutated transgenic RNA onto the Xi that is closer. Asterisks, Xa located close to Tg. D. qRT-PCR of total (Exons 1–3) and endogenous (uRA) Xist in female X-RA^Yy1m cells. E. Two-probe Xist RNA FISH followed by DNA FISH in male X-RA^Yy1m cells. Asterisks, Xa located close to Tg.

Figure 5. YY1 binds specifically to Xi

A. Map of the Xist deletion (Csankovszki et al., 1999; Zhang et al., 2007), ChIP amplicons, and YY1 sites. B. YY1 ChIP analyses. At least three independent experiments performed for each cell line. Averages ± standard errors (SE) from ≥3 independent experiments shown. Statistical significance, P, determined by the Student t-test (asterisks). C. YY1 knockdown in differentiating female ES cells (Tsix^TST/+) via the indicated timeline. Cells were split into siRNA-treated and –untreated samples on day 6 (d6). Western blot showed good knockdown. Xist qRT-PCR showed constant steady state levels; averages ± SD from three independent knockdown experiments shown. D. Xist RNA FISH after YY1 knockdown in female ES cells. Percentage of Xist⁺ cells and sample sizes shown.

Figure 6. YY1 is an RNA-binding protein that bridges RNA and chromatin

A. Map of Xist, transgenes, and RT-PCR amplicons. B. UV-crosslink RIP of female MEFs, followed by qRT-PCR for Xist (dRC, Exons 1–3) or RNA controls (U1 snRNA, Gapdh). YY1 antibodies or IgG used. 1% input. -UV and -RT controls performed in parallel. Left panel, EtBr-stained gel. Right panel, RT-PCR quantitation. Averages ± SE of 3 independent experiments. C. RNA pulldown assay using purified His-YY1 or His-GFP (Western blot) and WT female ES RNA. qRT-PCR at 3 different Xist positions (uRF, uRA, dRE) and two controls (Gadph, α-tubulin). Averages of 5 independent experiments ± SE. D. RNA pulldown assay using RNAs from transgenic lines after dox induction. qRT-PCR performed at dRC. Averages ± SE for 3 independent experiments. E. RNA pulldown assay using equal molar amounts of in vitro-transcribed RNA fragments AF (2.5kb), BC (2.5kb), eE1 (2.5kb), B (1.2kb), and C (1.8kb) as illustrated in the map. Quantitated by qRT-PCR. 20% of input shown on the gel. P calculated using t-test. B, BamHI; E, EcoRI; Bs, BstBI; S, ScaI. Averages of 2 independent experiments ± SE. F. Bivalent function of YY1. YY1 contacts Xist RNA and DNA via different sequences. Asterisks, positions of blocking LNAs (Sarma et al., 2010).

Figure 7. Summary and Model

Events at the initiation of XCI. Co-transcriptional recruitment of PRC2 and docking onto the YY1-bound nucleation center account for the cis-acting nature of Xist RNA.