<i>Utx</i> mutant alleles.

<p>(A) Schematics of mouse mutations in <i>Utx</i>. Included are annotations and locations of where the protein would be mutated. Two <i>Utx</i> mutant alleles included a gene trap in intron 3 (X<i>^UtxGT1</i>) and a gene trap/floxed exon 3 (X<i>^UtxGT2fl</i>). A UTX protein annotation is illustrated at the top to indicate to positions of <i>Utx</i> alleles. A germline Cre recombinase deleted exon 3 in the X<i>^UtxGT2fl</i> background to create X<i>^UtxGT2Δ</i>. Additionally, the gene trap of X<i>^UtxGT2fl</i> was excised with Flp recombinase to create a standard floxed exon 3 (X<i>^Utxfl</i>) and Cre recombination created X<i>^UtxΔ</i>. (B) Western blotting of E18.5 liver demonstrates a complete loss of UTX in X<i>^UtxGT1</i> Y<i>^Uty+</i> lysates. RbBP5 was used as a loading control. (C) Western blotting of E10.5 whole embryo demonstrates a complete loss of UTX in X<i>^UtxΔ</i> Y<i>^Uty+</i> and X<i>^UtxΔ</i> X<i>^UtxΔ</i> lysates. RbBP5 was used as a loading control. (D) Western blotting of E12.5 primary MEFs demonstrates a reduction of UTX in X<i>^UtxGT2fl</i> Y<i>^Uty+</i> and X<i>^UtxGT2fl</i> X<i>^UtxGT2fl</i> lysates. RbBP5 was used as a loading control.</p

UTX and UTY have essential, redundant functions in embryonic development.

<p>(A) Schematic of mouse mutation in <i>Uty</i>. The <i>Uty</i> gene trap Y<i>^UtyGT</i> is located in intron 4. Protein annotation is illustrated at the top to denote the location of the gene trap within the <i>Uty</i> coding sequence. (B) Quantitative RT-PCR downstream of the gene trap (exon 15) from tail RNA of X⁺ Y^UtyGT mice demonstrates essentially no mutant RNA. (C) X<i>^UtxGT2Δ</i> Y<i>^UtyGT</i> males (C-iii, iv) have identical phenotypes to X<i>^UtxGT2Δ</i> X<i>^UtxGT2Δ</i> females (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002964#pgen-1002964-g003" target="_blank">Figure 3A-vi, vii</a>). Arrowheads denote open neural tube in the head, while white and red arrows denote moderate and more severe cardiac phenotypes.</p

UTX and UTY Demonstrate Histone Demethylase-Independent Function in Mouse Embryonic Development

<div><p>UTX (KDM6A) and UTY are homologous X and Y chromosome members of the Histone H3 Lysine 27 (H3K27) demethylase gene family. UTX can demethylate H3K27; however, <em>in vitro</em> assays suggest that human UTY has lost enzymatic activity due to sequence divergence. We produced mouse mutations in both <em>Utx</em> and <em>Uty</em>. Homozygous <em>Utx</em> mutant female embryos are mid-gestational lethal with defects in neural tube, yolk sac, and cardiac development. We demonstrate that mouse UTY is devoid of <em>in vivo</em> demethylase activity, so hemizygous X<em>^Utx−</em> Y<em>⁺</em> mutant male embryos should phenocopy homozygous X<em>^Utx−</em> X<em>^Utx−</em> females. However, X<em>^Utx−</em> Y<em>⁺</em> mutant male embryos develop to term; although runted, approximately 25% survive postnatally reaching adulthood. Hemizygous X<em>⁺</em> Y<em>^Uty−</em> mutant males are viable. In contrast, compound hemizygous X<em>^Utx−</em> Y<em>^Uty−</em> males phenocopy homozygous X<em>^Utx−</em> X<em>^Utx−</em> females. Therefore, despite divergence of UTX and UTY in catalyzing H3K27 demethylation, they maintain functional redundancy during embryonic development. Our data suggest that UTX and UTY are able to regulate gene activity through demethylase independent mechanisms. We conclude that UTX H3K27 demethylation is non-essential for embryonic viability.</p> </div

UTX and UTY redundancy is essential for progression of cardiac development.

<p>(A) Similar sized <i>Utx</i> heterozygous (i), <i>Utx</i> homozygous (ii), <i>Utx</i> hemizygous (iii), or <i>Utx/Uty</i> compound hemizygous (iv) embryos were analyzed in more detail for cardiac developmental abnormalities. Frontal views of the respective hearts of these embryos revealed that <i>Utx</i> homozygotes and <i>Utx/Uty</i> compound hemizygotes (A-vi, viii) have smaller hearts that have not completed looping relative to <i>Utx</i> heterozygotes (A-v) or hemizygotes (A-vii). A white dashed line was drawn at an identical angle in all panels to illustrate the failure of hearts to loop around in alignment with this appropriate plane. Only control and <i>Utx</i> hemizygous embryos (A-v, vii) have initiated the formation of the interventricular groove (white arrows), indicative of early interventricular septum development. (B) Transverse sections of E10.5 X<i>^UtxGT2Δ</i> X<i>^UtxGT2Δ</i> (B-ii) and X<i>^UtxGT2Δ</i> Y<i>^UtyGT</i> (B-iv) embryos reveal smaller heart size with defects in ventricular myocardial trabeculation and organization. The control and <i>Utx</i> hemizygous hearts initiated the formation of the interventricular septum (B-i, iii, IVS, black arrow), while other mutant combinations (B-ii, iv) have not (red asterisk). RA and LA = Right and Left Atrium, and RV and LV = Right and Left Ventricle. (C) More magnified images further illustrate the narrowing of the ventricular wall (red scale) and the lack of myocardial cells and structure in <i>Utx</i> homozygotes and <i>Utx/Uty</i> compound hemizygotes (Epi = epicardium, MC = myocardium, Endo = Endocardium).</p

UTX and UTY associate in common protein complexes and are capable of H3K27 demethylase independent gene regulation.

<p>(A) Co-transfection of HA-UTX with Flag-UTX or Flag-UTY demonstrates that HA-UTX can immunoprecipitate with both Flag-UTX and Flag-UTY. (B) Immunoprecipitation of Flag-UTX and Flag-UTY reveal interaction with RBBP5, a component of the H3K4 methyl-transferase complex. Flag vector transfection was used as a negative control for immunoprecipitation. (C) <i>Fnbp1</i>, a gene targeted directly by UTX, has intermediate downregulation in X<i>^Utx−</i> Y<i>^Uty+</i> MEFs (68% of WT, t-test p-value = 0.002), but was further compromised in X<i>^Utx−</i> X<i>^Utx−</i> (42% of WT, t-test p-value relative to X<i>^Utx−</i> Y<i>^Uty+</i> = 0.001) and X<i>^Utx−</i> Y<i>^Uty−</i> (48% of WT, t-test p-value relative to X<i>^Utx−</i> Y<i>^Uty+</i> = 0.02, N>4 independent MEF lines per genotype) MEFs. MEFs were generated from the X<i>^UtxGT2Δ</i> and Y<i>^UtyGT</i> alleles. (D) <i>Fnbp1</i> is similarly mis-expressed in X<i>^UtxGT2fl</i> allelic combinations of E12.5 MEFs. X<i>^Utx−</i> X<i>^Utx−</i> and X<i>^Utx−</i> Y<i>^Uty−</i> MEFs significantly differ from X<i>^Utx−</i> Y<i>^Uty+</i> MEFs (t-test p-value = 0.05 and 0.02 respectively, N>4 independent MEF lines per genotype). (E) H3K27me3 ChIP was performed on E12.5 X<i>^Utx+</i> Y<i>^Uty+</i> control (green) and X<i>^Utx−</i> X<i>^Utx−</i> (red) MEFs. An IgG antibody control is indicated in grey. Quantitative PCR for the ChIP was performed over a negative control region (an intergenic region) as well as a positive control (<i>HoxB1</i>). <i>Fnbp1</i> failed to accumulate H3K27me3 in X<i>^Utx−</i> X<i>^Utx−</i> MEFs (t-test p-value = 0.5, N = 4 independent MEF lines per genotype). (F) H3K4me3 ChIP was performed on E12.5 X<i>^Utx+</i> Y<i>^Uty+</i> control (green) and X<i>^Utx−</i> X<i>^Utx−</i> (red) MEFs. An IgG antibody control is indicated in grey. Quantitative PCR for the ChIP was performed over a negative control region (intergenic region) as well as a positive control (<i>Npm1</i>). The WT <i>Fnbp1</i> promoter exhibited significant H3K4me3 accumulation, which was reduced in X<i>^Utx−</i> X<i>^Utx−</i> MEFs (t-test p-value = 0.005, N = 3 independent MEF lines per genotype).</p

Human and mouse UTY have no H3K27 demethylase activity.

<p>(A) HEK293T cells were transfected with Flag-tagged C-terminal human (H) and mouse (M) UTX and UTY constructs. The C-terminal fragments span AA 880–1401 in human UTX (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002964#pgen.1002964.s006" target="_blank">Figure S6</a>) and include the corresponding regions in mouse UTX. Transfected cells (white arrows) over-expressing H-UTX and M-UTX (Flag immunofluorescence, green pseudo-color) exhibited global loss of H3K27me3 immunofluorescence (red pseudo-color). Cells transfected with H-UTY and M-UTY C-terminal constructs did not demethylate H3K27me3. (B) H3K27me3 demethylase assay of UTX and UTY mutant constructs. H-UTX H1146A contains a point mutation in a residue that was previously reported as defective in H3K27 demethylation. Cells expressing H-UTX H1146A had no loss of H3K27me3. Mouse UTY has a Y to C amino acid change that corresponds to position 1135 in human UTX. This UTX residue is predicted to regulate H3K27me3 binding and demethylation. Expression of H-UTX Y1135C failed to demethylate H3K27me3. Mouse UTY also has a T to I amino acid change that corresponds to position 1143 in human UTX that is predicted to regulate binding of ketoglutarate in the demethylase reaction. Expression of H-UTX T1143I failed to demethylate H3K27me3. Correction of these two altered residues in mouse Uty (M-UTY-C947Y, I955T) failed to recover H3K27me3 demethylase activity. (C) Alignment of the JmjC domains of human/mouse UTX human UTY, mouse UTY, and human/mouse JMJD3. UTY non-conservative substitutions are indicated by white boxes and residues of interest are labeled with red asterisks. The UTX mutations that were analyzed are listed above the alignment, while JMJD3 mutations are listed below the alignment. (D) HEK293T cells were transfected with C-terminal UTX and UTY constructs or full-length mouse JMJD3 constructs carrying various AA substitutions. Medium-high expressing cells (N≥100 cells scored for each experiment) were scored for any visible reduction in H3K27me3 levels relative to nearby untransfected cells. 100% of WT H-UTX, M-UTX and M-JMJD3 expressing cells had observable H3K27me3 demethylation. The negative controls of H-UTX H1146A, M-JMJD3 H1388A, and M-JMJD3 with deletion of the JmjC domain had no visible H3K27me3 demethylation (0% of cells). Wild type H-UTY and M-UTY had 0% of cells with detectable demethylation. Of the point mutations in UTY predicted to affect H3K27me3, only mutation of H-UTX Y1135C and T1143I with corresponding M-JMJD3 Y1377C and T1385I had no cells with any detectable H3K27 demethylation (0%). (E) Stereo view of the active site of human UTX (PDB ID: 3AVR). The corresponding residues in mouse UTY are also indicated in parentheses. The figure was prepared with the program Pymol (Schrodinger LLC).</p

Genotype frequencies of <i>Utx</i> and <i>Uty</i> mutant mice.

<p>Observed (Obs) and expected (Ex) frequencies of indicated genotypes (Geno) at embryonic (E) or postnatal (P) developmental stages with χ² p-values (p-value) for the corresponding crosses to obtain each genotype.</p

Homozygous female <i>Utx</i> mutant embryos have mid-gestational developmental delay.

<p>(A) Compared to controls (A-i and A-v), homozygous female E10.5 X<i>^UtxGT1</i> X<i>^UtxGT1</i> (A-ii) and X<i>^UtxGT2Δ</i> X<i>^UtxGT2Δ</i> (A-vi) embryos have some developmental delay including smaller size, underdeveloped hearts (white arrows), and open neural tube in the head (arrowheads). More severe embryos resemble the size and features of E9.5 embryos with cardiac abnormalities and peri-cardial edema (A-iii, vii, red arrows). Hemizygous male X<i>^UtxGT1</i> Y^Uty+ embryos appear phenotypically normal at this stage (A-iv). The X<i>^UtxGT1</i> and X<i>^UtxGT2Δ</i> alleles fail to complement as female X<i>^UtxGT1</i> X<i>^UtxGT2Δ</i> embryos have identical phenotypes to homozygotes (A-viii). (B) At E10.5, homozygous X<i>^UtxGT1</i> X<i>^UtxGT1</i> female embryos exhibit either normal yolk sac vasculature with a reduction in red blood cells (B-ii) or have a completely pale yolk sac with unremodeled vascular plexus (B-iii).</p

Hemizygous male <i>Utx</i> mutant mice are runted.

<p>(A) Hemizygous male <i>Utx</i> mutant mice are runted in size. Wild type male X<i>^Utx</i>⁺ Y⁺ mice are displayed next to hemizygous X<i>^UtxGT1</i> Y⁺ mice. (B) The hemizygous mice exhibit a smaller size throughout adulthood.</p