Identification of Spen as a Crucial Factor for Xist Function through Forward Genetic Screening in Haploid Embryonic Stem Cells

Abstract

In mammals, the noncoding Xist RNA triggers transcriptional silencing of one of the two X chromosomes in female cells. Here, we report a genetic screen for silencing factors in X chromosome inactivation using haploid mouse embryonic stem cells (ESCs) that carry an engineered selectable reporter system. This system was able to identify several candidate factors that are genetically required for chromosomal repression by Xist. Among the list of candidates, we identify the RNA-binding protein Spen, the homolog of split ends. Independent validation through gene deletion in ESCs confirms that Spen is required for gene repression by Xist. However, Spen is not required for Xist RNA localization and the recruitment of chromatin modifications, including Polycomb protein Ezh2. The identification of Spen opens avenues for further investigation into the gene-silencing pathway of Xist and shows the usefulness of haploid ESCs for genetic screening of epigenetic pathways.

Graphical abstract

Figure 1

Characterization of Xist-Inducible Mouse Haploid ESCs (A) Structure of the Xist inducible system. (B) Chromosome spread of haploid HATX ESCs. (C) Xist induction (+ dox) leads to loss of cells compared to growth in absence of doxycycline (no dox). (D) Xist RNA FISH in HATX3 ESCs grown with and without doxycycline. (E) Immunofluorescence image showing focal Ezh2 and H3K27me3 staining in HATX3 ESCs after Xist induction. (F) qRT-PCR analysis showing induction of Xist and repression of X-linked genes in HATX3 ESCs after doxycycline addition. The autosomal β-actin gene is shown as a control. NT, nontreated. (G) Flow cytometry profile of HATX3 ESCs before (red) and after (green) infection with gene trap viruses. DNA content (left) and GFP fluorescence (right) of a gene trap encoded reporter are shown. A mixed haploid/diploid DNA content profile is shown for reference in gray.

Figure 2

Mutation of Spen in ESCs (A) Schematic representation of viral gene trap insertions in Xist and Spen locus (not to scale, gene size is indicated). Chr, chromosome. (B) Schematic representation of the Spen gene locus showing the location of CRISPR/Cas9 guide RNAs (gRNAs) used for engineering a deletion and genotyping PCR primers. (C) Genomic PCR confirming the absence of wild-type Spen fragment in Spen mutant ESCs. (D) Quantitative expression analysis of Spen using primer sets spanning exons as indicated. ΔSpen ESCs lack transcript from the deleted region. Error bars represent SD (n = 3). (E) Cell survival of control HATX3 ESCs and derived ΔSpen ESCs clone 2 (top; n = 2) and clone 3 (bottom; n = 3) after Xist induction (+ dox). Survival was calculated relative to uninduced cells. Error bars represent SD. See also Figure S1.

Figure 3

Spen Is Required for Xist Function in ESCs and Binds Xist A-Repeat Sequences In Vitro (A and B) qRT-PCR analysis of the X-linked genes (A) and the autosomal control genes (B) as indicated in HATX and Spen mutant ESCs. Error bars represent SD (n = 3). The locations of the genes tested on the X chromosome (chr) is shown at the left. q represents the region of the chromosome. +dox, Xist induction; NT, nontreated. (C) Electrophoretic mobility shift analysis of Spen RRM domains using a ³²P-labeled synthetic XCR RNA probe and cold XCR, SRA, and tRNA competitors as indicated. Asterisk and black triangle indicate position of the RNA-protein complex and free probe, respectively. (D) Competition with cold XS1 and XNX competitors as in (C). See also Figure S2.

Figure 4

Mutation of Spen Reduces Recruitment of Polycomb Proteins (A, C, E, and F) Combined Xist RNA FISH and Ezh2 (A), Ring1b (C), acetylated histone H4 (E), and RNA polymerase II (F) immunofluorescence analysis of Spen mutant and control ESCs after 24 hr of induction with doxycycline. Scale bar, 5 μm. (B and D) Quantification of focal recruitment of Ezh2 (B) and Ring1b (D) by Xist expression in 2i-cultured (2i) and 24-hr-differentiated (retinoic acid; RA) ESCs (n = 100). cl 2 and cl 3 represent clones 2 and 3, respectively. See also Figures S3 and S4.