Background

X inactivation is a developmentally regulated, epigenetic mechanism that results in monoallelic expression of X-linked genes in female mammals to achieve dosage equivalence between XX females and XY males [1]. Other examples of monoallelic expression include: (a) genomic imprinting where the parental origin of the alleles of specific genes or gene clusters are epigenetically marked during gametogenesis to be expressed exclusively from either the maternally or paternally inherited allele [2], (b) stochastic monoallelic expression, which includes allelic exclusion and is characteristic of multigene families (for example, genes encoding the olfactory [3] and pheromone receptors [4], interleukins [5], B and T cell receptors [6, 7], and natural killer cell receptors [8]), (c) the random combinatorial and differential monoallelic expression of the clustered protocadherins [9–11], and (d) the apparently random widespread monoallelic expression of possibly hundreds of individual genes spread throughout the genome [12, 13].

While the molecular mechanisms underlying the different forms of monoallelic expression have unique characteristics, they may be expected to share common elements. Some of the common epigenetic features identified to date include noncoding RNA (ncRNA) involvement [14–16], differential chromatin modification or DNA methylation [17–20], transchromosomal interactions [21–23], physical segregation of alleles in different nuclear compartments [24–26] and asynchronous replication [26–29].

Smchd1 (structural maintenance of chromosomes hinge domain containing 1) was identified as a semidominant suppressor of variegation in an N-ethyl-N-nitrosourea (ENU) mutagenesis screen for epigenetic modifiers [30]. The ENU derived mutant allele, named MommeD1, resulted from a nonsense mutation in the Smchd1 gene that lead to dramatically reduced Smchd1 transcript levels, probably the result of nonsense mediated mRNA decay [31]. Our breeding studies showed midgestation lethality of female but not male Smchd1MommeD1/MommeD1 embryos, suggestive of a failure of X inactivation in the female embryos. While the inactive X elect in female mutant embryos was decorated with Xist transcript and histone H3 trimethylated at lysine 27 (H3K27me3), many X-linked genes either failed to become inactivated or escaped X inactivation shortly after the initiation of silencing [31]. None of the genes tested showed the CpG island hypermethylation of the allele on the inactive X that is a normal characteristic of X inactivation [31]. Subsequently, it was shown that Smchd1 acts late in the epigenetic cascade driving X inactivation and that some X-linked genes undergo Smchd1-independent hypermethylation of the allele on the inactive X [32]. These findings demonstrated that Smchd1 function was critical for either the completion or maintenance, but not for the initiation, of X inactivation.

Several pieces of evidence suggest that Smchd1 has functions other than during X inactivation. The ENU mutagenesis screen in which Smchd1 was identified relied upon the detection of altered variegated expression from a green fluorescent protein (GFP) transgene array integrated into an autosomal location [30, 33]. Haploinsufficiency for Smchd1 also modified expression of the Agouti viable yellow (Avy) allele of the Agouti gene (A), which shows variegated expression due to varying CpG methylation of an intracisternal A particle inserted upstream of the gene’s promoter [30]. In addition, although some Smchd1MommeD1/MommeD1 males survived as fertile adults in the FVB/n background, when backcrossed onto the C57Bl6/J background all homozygous males displayed perinatal lethality [34]. Further, an independently generated Smchd1-null allele (Smchd1Gt(AD0165)Wtsi), which phenocopies the female Smchd1MommeD1/MommeD1 phenotype, also displays perinatal lethality of males on a mixed 129/C57 genetic background [31]. We hypothesized that Smchd1 does not function solely in X inactivation but probably also epigenetically modulates expression of autosomal genes in both males and females. In this study, we have used genome-wide approaches to identify autosomal genes that have deregulated expression in the absence of Smchd1 function.

Results

Genome-wide expression profiling of Smchd1 mutant embryos

We undertook genome-wide microarray expression profiling to screen for differences between Smchd1MommeD1/MommeD1 and Smchd1+/+, male and female embryos (n = 4 for each genotype and sex combination) at E9.5 (Figure 1, Additional files 1 and 2). Males and females were analyzed separately because the females are likely to have deregulated expression of autosomal genes as a secondary consequence of X inactivation failure in addition to autosomal genes whose expression is directly regulated by Smchd1. As expected, because the analysis involved comparison of Smchd1MommeD1/MommeD1 versus Smchd1+/+, the most significantly decreased transcript levels in all comparisons was Smchd1.

Figure 1
figure 1

Differential expression in Smchd1MommeD1/MommeD1versus Smchd1+/+embryos at E9.5. Heat maps for differentially expressed genes identified in the microarray analysis comparing the expression of ( A ) female and ( B ) male embryos. The lists of differentially expressed genes were sorted in order of level of significance with multiple testing correction and those showing a significant difference between the genotypes (adjusted P < 0.05) are displayed on the heat maps. For the female comparison, the top 20 genes are shown, while for the male comparison all genes that were significantly different are shown.

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After filtering out the genes represented by poor quality probes on the microarray, as determined by the Illumina BeadChip Probe Reannotation datasets [35], and counting genes represented by multiple probes only once, the list of unique genes showing significantly altered transcript levels in female Smchd1MommeD1/MommeD1 embryos (356 genes, adjusted P < 0.05, Figure 1A, Additional file 1) was much more extensive than that for males (9 genes, adjusted P < 0.05, Figure 1B, Additional file 2). The differentially expressed genes in females included 66 X-linked genes with increased transcript levels and no X-linked genes with decreased levels. Autosomal differentially expressed genes in females (290 genes in total) were distributed between those with increased transcript levels (157 genes) and those with decreased levels (133 genes) in Smchd1MommeD1/MommeD1 compared with Smchd1+/+ embryos.

The cell cycle related genes Ccng1 and Cdkn1a were high in the ranked list of significantly upregulated transcripts in female mutant embryos but not in male mutants. A likely explanation for the altered expression levels of these genes is that the female Smchd1MommeD1/MommeD1 embryos were beginning to fail at this stage of development despite looking normal at the macroscopic level. This was supported by gene set enrichment analysis of the autosomal gene classes altered in female mutants (Additional file 3). Gene categories associated with the apoptosis pathway were significantly altered, indicating that failure of X inactivation initiates cell death at this stage in at least a subset of embryo tissues. Gene categories involved in developmental processes normally active in this stage of development and biosynthetic categories were also significantly altered, consistent with failure of embryo growth and development. These results confirmed our previous study showing midgestation lethality due to failure of X inactivation in female Smchd1 mutants [31] and considerably extended the list of genes failing X inactivation (from 7 of 16 genes previously tested [31] to 66 genes in the current study, for a nonredundant list of 70 genes failing X inactivation). Most of the genes identified in this study were previously classified as dependent on Smchd1 function for methylation of their CpG island (48 of 66) [32], while three genes (Ebp, Magee1, and Ndufa1) were previously shown to have an intermediate level of methylation in Smchd1 mutants; the remaining 15 genes were not previously classified. Importantly, no X-linked genes showed significantly altered transcript levels in the male embryo comparison. The ability to detect statistically significant differential expression depends on several factors, including the signal intensity (A value) and intersample variability. Genes with tissue-specific expression, low absolute expression, or lower quality probes on the array are likely to produce false negatives, hence some X-linked differentially expressed genes could have been missed by this analysis. We therefore examined the observed fold change of all expressed X-linked genes (336 genes) compared with all expressed autosomal genes (9065 genes), where expressed genes were defined as having an A value > 7.0. The mean log2 fold change of expressed X-linked genes was significantly higher than zero (mean = 0.1730, n = 336, Wilcoxon signed rank test P value < 2.2x10−16, Additional file 4).

The nine genes showing significantly altered transcript levels in males were also altered to a similar degree (fold change and level of statistical significance) in females. Prominent within both male and female gene lists with increased transcript levels were Ndn and Mkrn3, two genes known to be subject to genomic imprinting, which are located in the Snrpn imprinted gene cluster on mouse chromosome 7 [15q11-13 in human beings] [36, 37]. The Snrpn imprinted gene cluster contains both paternally and maternally expressed imprinted genes (Figure 2A), with mutations within the cluster being responsible for Angelman [OMIM 105830] and Prader-Willi [OMIM 176270] syndromes in human beings.

Figure 2
figure 2

A subset of imprinted genes in the Snrpn cluster shows increased expression in Smchd1 mutants. ( A ) The Snrpn imprinted gene cluster, where those genes expressed from the paternal allele are shown in blue and those expressed from the maternal allele are in red. CpG islands are represented by circles on the line and where these represent an sDMR (small circles) or imprint control region (ICR) (large circle) the methylation status is indicated (M inside the filled circle for the methylated allele or unfilled circle for the unmethylated allele). Quantification of the expression levels of imprinted genes or transcripts within the Snrpn cluster by qRT-PCR measured using RNA derived from: ( B ) male and female E9.5 embryos, ( C ) mouse embryonic fibroblasts (MEF) derived from male E14.5 embryos, and ( D ) whole brain from adult male mice. The synthesis of first-strand cDNA from E9.5 embryo RNA was primed with oligo dT, but for the analysis of transcript levels in MEFs and brain the cDNA synthesis was primed with a cocktail of the reverse primers used for qRT-PCR. In each case the qRT-PCR signal was normalized relative to that of Rala and plotted relative to the corresponding Smchd1+/+ sample. The genotype, sex, and number of replicates are indicated in each case. Statistical analysis was performed using the t test. ** P < 0.01 and * P < 0.05 compared with wildtype. Error bars indicate standard error.

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Several of the clustered protocadherin genes had an altered expression. Pcdhβ22 was significantly differentially expressed in both males and females, with increased transcript levels in Smchd1 mutants. Pcdhβ3 and Pcdhβ16 also showed significantly altered expression, but only in the female list. Pcdhα, Pcdhβ, and Pcdhγ are located in a cluster on mouse chromosome 18 [38] and display an unusual form of monoallelic expression involving random and combinatorial expression with each individual neuron expressing a unique combination of the α, β and γ isoforms [9, 10, 39]. It has been proposed that this results in enormous combinatorial diversity of the protocadherins displayed on the surface of neurons and may confer a unique identity on each neuron [39]. To confirm the results obtained from the microarray analysis we performed qRT-PCR analysis for the top four deregulated genes in males using RNA derived from E9.5 embryos (Additional file 5). All genes tested displayed significantly increased transcript levels (P < 0.01 for Mkrn3, Pisd-ps1, and Pcdhβ22; P < 0.05 for Ndn) in both male and female Smchd1MommeD1/MommeD1 mutant embryos compared with Smchd1+/+ embryos.

Given the phenotypic variability displayed by male Smchd1 mutants on different genetic backgrounds, we subjected an independent set of male E9.5 embryos of a different genetic background to RNA-seq analysis (n = 3 for each genotype, Smchd1+/+ and Smchd1MommeD1/MommeD1). These embryos were generated from mice where the Smchd1MommeD1 mutation had been backcrossed to 129 T2/SvEms background for four generations. A partially overlapping, but still relatively short list of 24 genes showed significant differences in gene expression between the genotypes (Additional file 6). It is likely that the variation in gene expression differences detected using the microarray and RNA-seq analysis results from a combination of the different genetic background used in each study and the inherent sensitivity and selectivity differences of the two methods used to assay gene expression. The differentially expressed genes detected by both analyses again pointed to disruption of the Snrpn imprinted gene cluster, with Ndn (adjusted P = 0.0059) and Peg12/Frat3 (adjusted P = 0.0018) being significantly differently expressed approximately 2-fold in the RNA-seq analysis. The other gene detected by both analyses was Pisd-ps1, about which little is known.

What was evident in the RNA-seq analysis, and could not have been detected by the microarray, was a novel gene that flanked and spliced across Ndn, Magel2, and Mkrn3 (Additional file 7). This novel gene corresponded to [AK142799 Genbank], a 3478 bp mRNA identified in a RIKEN Mus musculus 15-day embryo head cDNA library. The mRNA encodes a hypothetical tyrosine-rich region profile/EGF-like domain-containing protein. Expression levels of this gene appeared to be increased in Smchd1MommeD1/MommeD1 compared with Smchd1+/+ embryos (although not to statistically significant levels, owing to relatively low sequence read count), similar to the imprinted genes Ndn, Magel2 and Mkrn3, which lie within its intron.

Specific analysis of the Snrpn cluster of imprinted genes

Since some genes within the Snrpn imprinted cluster showed statistically significant increased transcript levels in the absence of Smchd1 in both the microarray and the RNA-seq analyses, we used qRT-PCR to analyze further genes specifically from the Snrpn imprinted gene cluster in E9.5 embryos (Figure 2B). We found that Ndn, Mkrn3 and Peg12/Frat3 were significantly deregulated but Snrpn, Ube3a and Atp10a were not. Snrpn normally displays imprinted expression in all tissues [40], while Ube3a has imprinted expression only in the brain [41–43]. There are conflicting reports regarding the imprinted status of Atp10a in both human beings [44–46] and mice [47–49]. The inclusion of Smchd1MommeD1/+ female embryos in this analysis demonstrated that haploinsufficiency for Smchd1 was not sufficient to cause detectable disruption of expression for the affected genes. In addition, Magel2 transcript levels were not sufficient to allow reliable detection.

Similar results were obtained for Ndn, Mkrn3, Peg12/Frat3, Snrpn, Ube3a, and Atp10a in mouse embryonic fibroblast (MEF) cultures (Figure 2C) as for E9.5 embryo samples. Magel2 was more reliably detectable in MEFs but, while its transcript levels appeared to be increased in Smchd1MommeD1/MommeD1 MEFs, the difference was not statistically significant (P = 0.081012) for the four independently derived MEF cultures used.

While most genes within the Snrpn cluster have their highest expression levels in the brain (for example, Peg12/Frat3[50, 51]), some are only expressed in the brain (for example, snoRNAs[52, 53]) or are only expressed in an imprinted manner in the brain (for example, Ube3a[43]). In addition, a recent study [54] has identified transcripts uniquely expressed in the brain that originate from imprinted loci located between Snrpn and Ndn. These transcripts encode either ncRNAs or predicted miRNAs, and are normally expressed from only the paternal allele. Analysis using RNA isolated from the brains of adult Smchd1+/+ and Smchd1MommeD1/MommeD1 males (Figure 2D) also revealed similar results for Ndn, Mkrn3, Magel2, and Peg12/Frat3, with significantly increased transcript levels in the absence of Smchd1. A subset of the recently identified imprinted genes spread across the region between Ndn and Snrpn (that is, DOKist4, AK045535, and AK086712) were also tested and found to be significantly increased. The imprinted snoRNAs (SnoRD115 and SnoRD116) that lie between Snrpn and Ube3a were expressed equally in Smchd1+/+ and Smchd1MommeD1/MommeD1 brain.

Epigenetic signature and allelic expression of disrupted imprinted genes

We considered that the increased transcript levels seen in Smchd1 mutants (for example, Ndn, Magel2, Mkrn3, Peg12/Frat3, and the ncRNA transcripts originating from loci between Snrpn and Ndn) could result from loss of imprinting and the biallelic expression for these genes rather than an increased level of monoallelic expression. Imprinted genes can be identified by their overlapping permissive and nonpermissive epigenetic markings, where the expressed allele is marked by H3 dimethylated at lysine 4 (H3K4me2) and the nonexpressed allele by CpG methylation [55], or alternatively H3 trimethylated at lysine 4 (H3K4me3) and H3 trimethylated at lysine 9 (H3K9me3) [56], respectively. Thus, loss of imprinting and biallelic expression would result in easily detectable changes of these epigenetic signatures with increased levels of the permissive marks (that is, H3K4me2 or H3K4me3) and reduced levels of the nonpermissive marks (that is, CpG methylation or H3K9me3).

To analyze DNA methylation, we used methylated DNA immunoprecipitation (MeDIP) followed by qPCR to quantify the degree of enrichment. Differential methylation of the parental alleles of the imprint control region (ICR), associated with Snrpn[57], is the primary mechanism that directs imprinted expression within the cluster [58, 59]. It is the maternally inherited allele of the Snrpn ICR that is methylated, while the paternally inherited allele is not methylated (Figure 2A). A secondary (or somatic) differentially methylated region (sDMR) is associated with the CpG island of Ndn, Mkrn3, Magel2, and Peg12/Frat3[51, 60–62]. The sDMR becomes methylated on the maternally inherited allele at postzygotic stages, usually postimplantation, rather than being established in the gametes.

MeDIP analysis of DNA from E9.5 Smchd1+/+, Smchd1MommeD1/+, and Smchd1MommeD1/MommeD1 male and female embryos (Figure 3A) showed that the Snrpn ICR and the CpG island of Atp10a had no difference in DNA methylation levels between the genotypes. Recovery of MeDIP material indicated that in Smchd1MommeD1/MommeD1 embryos the sDMRs associated with Ndn, Magel2, Mkrn3, and Peg12/Frat3 were almost completely unmethylated compared with Smchd1+/+ embryos. The Smchd1MommeD1/+ embryos had a level of methylation intermediate between Smchd1+/+ and Smchd1MommeD1/MommeD1 embryos for Ndn, Magel2, Mkrn3, and Peg12/Frat3. This intermediate methylation level (Figure 3A) did not translate into a detectable effect on the expression of these genes (Figure 2A). This result was similar to that previously shown in Smchd1MommeD1/+ female embryos, where expression of many X-linked genes and X inactivation of an X-linked GFP transgene was similar to Smchd1+/+ embryos despite X-linked genes showing a level of CpG island methylation intermediate between Smchd1+/+ and Smchd1MommeD1/MommeD1 embryos [31]. While Ube3a displays imprinted expression in the brain, its CpG island is not strongly differentially methylated and remains unmethylated on both alleles [63]. The MeDIP result for Ube2a is consistent with this.

Figure 3
figure 3

The epigenetic signature of deregulated genes in the Snrpn cluster is consistent with biallelic expression. The relative level of DNA methylation was quantified by qPCR of MeDIP recovered DNA in samples from ( A ) male and female E9.5 embryos, and ( B ) MEFs isolated from male E14.5 embryos. ( C ) The relative level of H3K4me2 for each gene was quantified by qPCR of ChIP recovered material in chromatin derived from MEFs isolated from male E14.5 embryos. The qPCR signal was normalized relative to that of Rhox6/9 for MeDIP or relative to input for the H3K4me2 ChIP. Results are plotted relative to the corresponding Smchd1+/+ sample. The genotype, sex, and number of replicates are indicated in each case. Statistical analysis was performed using the t test. In ( A ) **P < 0.01 or *P < 0.05 for Smchd1MommeD1/MommeD1 compared with Smchd1+/+. Statistical significance not shown for the comparison of Smchd1+/+ compared with Smchd1MommeD1/+. In ( B ) and ( C ) ** P < 0.01 compared with wildtype. Error bars indicate standard error. ChIP, chromatin immunoprecipitation.

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These results indicated that in the absence of Smchd1 the levels of methylation of the Snrpn ICR were retained, but the sDMRs associated with Ndn, Magel2, Mkrn3, and Peg12/Frat3 were unmethylated. Similar results were obtained from MeDIP of MEF DNA (Figure 3B). The result was confirmed by bisulfite sequencing of MEF DNA (Additional file 8), which also confirmed that the differential methylation of the Snrpn ICR was retained in the absence of Smchd1. The imprinted loci lying between Snrpn and Ndn do not contain any annotated CpG islands in MM10 and were not analyzed.

In parallel, we used chromatin immunoprecipitation (ChIP) to analyze H3K4me2, marking the same region in MEFs. Similar ChIP in human cells shows that the CpG island of NDN and the Prader-Willi syndrome imprinting center (located in exon 1 of the SNRPN gene) carry H3K4me2 and H3K4me3 marks on the expressed paternal allele but not on the nonexpressed maternal allele [64, 65]. The results (Figure 3C) showed that levels of H3K4me2 were approximately doubled for each gene with deregulated expression and not different for genes whose expression level was indistinguishable in Smchd1MommeD1/MommeD1 compared with Smchd1+/+ controls. This is consistent with loss of imprinting for Ndn, Mkrn3, and Magel2, and both alleles being marked with this permissive histone modification in the absence of Smchd1. H3K4me2 levels on Peg12/Frat3 were not tested. No difference in H3K4me2 levels was seen at the Snrpn ICR, consistent with our finding that loss of Smchd1 did not affect the Snrpn expression.

In combination, these changes in epigenetic signature and gene expression in Smchd1 mutants are completely consistent with loss of imprinting resulting in biallelic expression of Ndn, Magel2, Mkrn3, and Peg12/Frat3 but with imprinting being maintained at the other imprinted genes within the cluster (that is, Snrpn and Ube3a). From our gene expression analysis DOKist4, AK045535, and AK086712 are also likely to be subject to loss of imprinting but not the imprinted snoRNAs (that is, SnoRD115 and SnoRD116). To definitively demonstrate the allelic expression of genes within the Snrpn imprinted gene cluster we used RNA-FISH on MEFs derived from E14.5 Smchd1+/+ compared with Smchd1MommeD1/MommeD1 embryos. We compared the number of signals in the nucleus resulting from FISH probes that detect Snrpn and either Ndn or Magel2 transcript (Figure 4A-D). In Smchd1+/+ MEFs Snrpn, Ndn, and Magel2 were expressed monoallelically in approximately 80% of nuclei (Figure 4E and F). In Smchd1MommeD1/MommeD1 MEFs, monoallelic expression of these genes was only seen in 12 to 23% of nuclei, with between 46% and 63% of nuclei showing biallelic expression of Ndn or Magel2 but monoallelic expression of Snrpn.

Figure 4
figure 4

RNA-FISH showing biallelic expression of deregulated genes in the Snrpn cluster. Snrpn (green) and Ndn (red) RNA-FISH signals on ( A ) Smchd1+/+ and ( B ) Smchd1MommeD1/MommeD1 MEFs. Snrpn (green) and Magel2 (red) RNA-FISH signals on ( C ) Smchd1+/+ and ( D ) Smchd1MommeD1/MommeD1 MEFs. Images representative of the predominant hybridizing pattern for each genotype and gene combination are shown. The number of RNA-FISH signals per nucleus for ( E ) Snrpn/Ndn and ( F ) Snrpn/Magel2 were counted (100 randomly selected nuclei counted in each case) and plotted for each line of MEFs (Smchd1+/+, Smchd1MommeD1/MommeD1#1, and Smchd1MommeD1/MommeD1#2). The genotypes are indicated in each case.

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Identification of other imprinted genes showing loss of imprinting in Smchd1 mutants

Lack of DNA methylation at the sDMR associated with Ndn, Magel2, Mkrn3, and Peg12 was the most obvious phenotype associated with homozygous mutation of Smchd1. The level of CpG methylation of the ICR associated with the Snrpn cluster showed no difference between Smchd1MommeD1/MommeD1 and Smchd1+/+ samples. We undertook qPCR MeDIP analysis of the ICR or sDMR associated with other imprinted genes using embryo- and male-MEF-derived DNA. In these analyses, only the sDMR associated with the Cdkn1c gene showed a significant decrease in CpG methylation levels in Smchd1Mommed1/MommeD1 samples; however, this was only observed in embryo-derived DNA (Additional file 9A), not in the DNA derived from MEFs (Additional file 9B). The degree of DNA methylation loss at Cdkn1c in the Smchd1Mommed1/MommeD1 samples was not as marked as for the sDMR associated with Ndn, Magel2, Mkrn3, and Frat3/Peg12. We were not able to demonstrate any significant loss of methylation at the ICR of any imprinted gene cluster that we tested.

The use of single nucleotide polymorphisms (SNPs) to determine the parental allele of origin of expressed alleles is the most widely accepted method for determining whether genes are subject to (or failing) genomic imprinting. We had previously backcrossed the Smchd1MommeD1 mutation from the FVB/n background (in which the ENU mutagenesis screen that identified Smchd1 was undertaken) onto the C57Bl6/J background for more than ten generations. While none of the genes in the Snrpn imprinted gene cluster carries SNPs between these genetic backgrounds, several other imprinted genes do. This is particularly the case for imprinted genes that are expressed in an imprinted manner uniquely in the placenta. To identify more imprinted genes with loss of imprinting in Smchd1 mutants, we analyzed the placentas of F1 (C57Bl6/J × FVB/n) E14.5 male embryos (n = 5 for each genotype, Smchd1+/+ and Smchd1MommeD1/MommeD1). To ensure that we were able to dissect out the embryonic portion of the placenta free from contamination by maternal tissue, we also included a ubiquitously expressed GFP transgene (UBI-GFP) [66] in the sires. The genotypes of the mice set up in the cross were as follows: (C57Bl6/J; Smchd1MommeD1/+, UBI-GFPT/+) sire crossed to (FVB/n; Smchd1MommeD1/+) dam. Only the brightly GFP fluorescent embryonic portion of the placenta was used for RNA-seq analysis. Very few genes showed differential levels of expression between the genotypes (Additional file 10), with only four RefSeq genes reaching statistical significance Smchd1, Mmp12, Cyp1a1, and Apoa1 (adjusted P < 0.05).

Using SNP analysis, we identified the Igf2r imprinted cluster as being disrupted in Smchd1 mutants. The cluster includes the imprinted genes Igf2r, Slc22a2, and Slc22a3, which are preferentially expressed from the maternally inherited allele, and the Airn ncRNA, which is preferentially expressed from the paternally inherited allele (Figure 5A). Igf2r and Airn are imprinted in all tissues, but Slc22a2 and Slc22a3 are imprinted only in the placenta, with Slc22a3 becoming biallelically expressed from E15.5 onwards [67]. In Smchd1 mutant placenta, the allelic pattern of Igf2r expression is identical to that in wildtype placenta with expression predominantly from the maternal allele, but the Slc22a3 gene showed biallelic expression rather than the predominant maternal allele shown by wildtype placenta of the same age (Figure 5B, Additional file 11). This finding was confirmed by analysis of placentas derived from a reciprocal cross: a (FVB/n; Smchd1MommeD1/+) sire crossed to a (C57Bl6/J; Smchd1MommeD1/+) dam (Figure 5C). This formally demonstrates loss of imprinting in the absence of Smchd1. No other imprinted genes that were amenable to analysis in this experiment (that is, showing imprinted expression in the placenta and carrying suitable SNPs) showed similar statistically significant loss of imprinting (Additional file 11). Bisulfite analysis confirmed that Smchd1 loss did not alter the differential methylation of the ICR that lies within exon 2 of Igf2r and that controls imprinting of the Igf2r imprinted cluster of genes (Additional file 12).

Figure 5
figure 5

Loss of imprinting at the Igf2r imprinted gene cluster in placenta in the absence of Smchd1 . ( A ) The Igf2r imprinted gene cluster shows imprinting in the placenta, where genes expressed from the paternal allele are shown in blue and those expressed from the maternal allele are in red. CpG islands are represented by circles on the line and where these represent an ICR (large circle) the methylation status is indicated (M inside the filled circle for the methylated allele or unfilled circle for the unmethylated allele). ( B ) In Smchd1+/+ F1 (C57Bl6/J sire × FVB/n dam) placental expression of both Igf2r and Slc22a3 is predominantly from the maternal FVB/n allele with only a minor proportion from the paternal C57Bl6/J allele, but in Smchd1MommeD1/MommeD1 placentas, expression of Slc22a3 becomes biallelic while expression of Igf2r remains imprinted with predominant expression of the maternal allele. ( C ) The same result is seen in the reciprocal cross F1 (FVB/n sire × C57Bl6/J dam) except here the maternal allele is derived from the C57Bl6/J dam. The genotype and number of replicates are indicated in each case. Statistical analysis was performed using the t test. ** P < 0.01 compared with wildtype. Error bars indicate standard error.

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The SNP analysis also revealed exclusive expression of the FVB/n alleles of genes within a region of chromosome 17 surrounding Smchd1 (that is, from Tgif1 at position [Chr17:70844412 MM10] to Ttc27 at [Chr17:74770280 MM10]. This resulted from FVB/n alleles of genes linked to the mutant Smchd1MommeD1 allele being retained in the backcross to C57Bl/6 J. While this finding was not relevant to the genomic imprinting data for the Igf2r imprinted cluster, it indicated that we were successful in obtaining clean embryonic placental tissue for the analysis and defined the region of the FVB/n chromosome surrounding the Smchd1MommeD1 that was retained in our backcrossed animals.

The clustered protocadherin genes show altered expression in Smchd1 mutants

Previously, we had shown that expression of members of the clustered protocadherin family was deregulated in Smchd1 mutant MEFs (normal and transformed) [34]. Since Pcdhβ22 also showed significantly altered transcript levels in the microarray analysis of E9.5 embryos, we considered the possibility that Smchd1 might function in the mechanism controlling the random combinatorial monoallelic expression of the clustered protocadherins (Figure 6A). We screened the full transcript set from all three types of clustered protocadherin gene for deregulated expression levels in the adult male brain and found that all three clusters showed altered expression in Smchd1 mutants (Figure 6B). The strongest changes occurred in the Pcdhα cluster, where Pcdhα1 was increased 22-fold and Pcdhα8 was increased approximately 7.5-fold. Three Pcdhα transcripts (Pcdhα9, PcdhαC1, and PcdhαC2) were significantly decreased. Almost all members of the Pcdhβ cluster (Pcdhβ1-6, 8, 10, 11, 14, 17 to 22) displayed increased transcript levels ranging from 2 to 4-fold, while the Pcdhγ cluster was least affected both in terms of fold change and number of alternative transcripts displaying some alteration.

Figure 6
figure 6

The clustered protocadherin genes show altered expression levels in Smchd1 mutants. ( A ) The clustered protocadherin genes (Pcdhα, Pcdhβ, and Pcdhγ) lie in a cluster on mouse Chr:18 and are expressed in a unique manner. Transcripts from the Pcdhα and Pcdhγ genes show alternative first exons that are monoallelically expressed in a random combinatorial manner and spliced to downstream exons that are biallelically expressed. The Pcdhβ genes exist as individual genes. ( B ) The expression levels of the protocadherin genes (Pcdhα, Pcdhβ, and Pcdhγ) were quantified by qRT-PCR using RNA derived from whole adult male mouse brains. The synthesis of first-strand cDNA was primed with a cocktail of the reverse primers used for qRT-PCR. In each case, the qRT-PCR signal was normalized relative to that of Rala and plotted relative to the corresponding Smchd1+/+ sample. Statistical analysis was performed using the t test. ** P < 0.01 and * P < 0.05 compared with wildtype. Error bars indicate standard error.

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Discussion

We initially identified Smchd1 as an epigenetic modifier in an ENU mutagenesis screen [30] and demonstrated a critical role for Smchd1 in either the completion or maintenance, but not the initiation, of X inactivation [31]. This study considerably extends the known genes failing X inactivation in Smchd1 mutants (7 previously published, 66 in the current study, for a nonredundant total list of 70 genes). While it is clear that some genes do not fail X inactivation in Smchd1 mutants [32], we believe that the current set of genes does not reflect the full extent of genes failing X inactivation since it is likely that many X-linked genes would not be expressed at sufficient levels at this developmental stage to be detected.

Our main aim was to identify autosomal genes whose correct expression was directly dependent upon Smchd1 function. We had reasoned that there would be many autosomal genes in female Smchd1 mutants that would display deregulated expression that was secondary to failure of X inactivation. To ensure that we could identify autosomal genes that were directly regulated by Smchd1, we analyzed males separately from females and concentrated on genes whose expression was altered to a similar degree in both males and females. Our analysis revealed a relatively short list of nine genes showing statistically significant altered expression in Smchd1 mutant males; all of these genes were similarly deregulated in females.

Amongst this list were two genes (Ndn and Mkrn3) from the Snrpn imprinted gene cluster with increased levels of expression. Specific analysis revealed further genes from the cluster (Magel2, Peg12/Frat3, DOKist4, AK045535, and AK086712) showing increased expression in Smchd1 mutants. The deregulated genes displayed epigenetic signatures consistent with biallelic expression and loss of imprinting. RNA-FISH showed that Ndn and Magel2 displayed biallelic expression but Snrpn retained monoallelic expression. From this result it is clear that the Snrpn imprinted cluster has two distinct parts in terms of its imprinting mechanism; (a) the region distal to the Snrpn start site containing genes, whose imprinted expression was dependent upon Smchd1, and (b) the region proximal to and including Snrpn, where genomic imprinting was maintained. This division of the cluster agrees with a previous model for the control of imprinting at the locus where genes from group (a) were controlled by DNA methylation and those from group (b) were regulated by the paternally expressed RNA transcript that initiated from the ICR [68]. To our knowledge, no other animal model has disassociated imprinting of the genes distal to Snrpn from the remainder of the cluster. The Snrpn cluster produces a poorly understood set of ncRNA transcript variants that are implicated in directing the imprinted expression of other genes within the cluster. Usually, these are expressed from the paternal allele and include the U-exon/Snrpn/Ube3a-ATS that has been proposed to control imprinted expression of Ube3a in the brain [69]. Recent reports have, however, identified yet other alternative Snrpn ncRNA transcripts emanating from upstream promoters and including upstream exons that are expressed from the maternal allele and required for silencing of genes on the maternal allele [70, 71]. Our finding that Smchd1 is essential for some of the activities associated with the imprinting of the Snrpn cluster (that is, silencing the maternal allele of Ndn/Magel2/Mkrn3 and Peg12/Frat3), but apparently not others (that is, silencing Ube3a on the paternal allele in the brain), adds further complexity to the regulation of this imprinted locus. Another new feature that has been identified in this study is the identification of a gene flanking Ndn, Magel2, and Mkrn3, which is likely to be imprinted and encodes a hypothetical novel tyrosine-rich region profile/EGF-like domain-containing protein.

Our SNP analysis of placental RNA-seq data also showed that the Igf2r imprinted gene cluster was disrupted in Smchd1 mutants, with the Slc22a3 gene showing loss of imprinting resulting in biallelic expression but imprinted Igf2r expression being unaffected. Imprinting of this cluster is governed by an ICR within exon 2 of Igf2r, which coincides with the transcriptional start site of the Airn ncRNA. It has recently been demonstrated that it is the transcriptional overlap of the Airn ncRNA and not the ncRNA transcript itself that induces the imprinting of Igf2r[72]. This is not the case for Slc22a3, whose imprinting is driven by the Airn ncRNA transcript itself, which targets G9a in cis to the allele of Slc22a3 that is silenced [73]. Thus, we conclude that Smchd1 functions as part of the mechanism by which Airn ncRNA induces facultative heterochromatin of linked genes in the Igf2r imprinted gene cluster.

We specifically demonstrated that the differential DNA methylation marking the ICR associated with the Snrpn imprinted gene cluster was maintained. The sDMRs associated with the disrupted genes in this cluster were, however, almost completely unmethylated. Differential methylation of the ICR controlling the Igf2r imprinted cluster was also not altered in Smchd1 mutants. The CpG island associated with Slc22a3 gene does not appear to carry a differential methylation mark in the placenta [67] and was not assessed in this study.

It is possible that Smchd1 is involved in regulating the expression of further imprinted genes not identified in this study. A complete analysis would involve crossing the Smchd1 mutant allele onto a suitable mouse strain carrying many SNPs in imprinted genes for determining allelic expression and analysis of suitable tissues where their expression is imprinted. If the imprinting of other genes involves Smchd1, we would predict that they would be situated within clusters of imprinted genes where the imprinting was regulated by the expression of an imprinted ncRNA similar to the situation for the Snrpn and Igf2r clusters. Our finding that in some Smchd1MommeD1/MommeD1 tissues the sDMR associated with Cdkn1c had altered levels of methylation may support this assertion, since regulation of the Kcnq1 imprinted gene cluster involves the imprinted Kcnq1ot1 ncRNA.

Our analysis has also highlighted altered expression of the clustered protocadherins in brain. These genes display an unusual form of random combinatorial monoallelic expression where each neuron expresses a unique combination of the protocadherin isoforms. This is proposed to confer individual neurons with a unique cell surface identity that may be important for neural circuit assembly [74]. The regulatory mechanism underlying the form of monoallelic expression displayed by protocadherins is poorly characterized but believed to involve the interaction of CTCF [75] with multiple enhancers and promoters [11, 76]. We found that expression levels of some of the protocadherins, in particular that of Pcdhα1, was strongly deregulated in the Smchd1 mutant brains (approximately 22-fold upregulated compared with wildtype). This is considerably more than the approximately 2-fold seen for the genes in the Snrpn imprinted gene cluster showing loss of imprinting, but this is possibly due to the unique form of random combinatorial monoallelic expression displayed by the clustered protocadherins, where Pcdhα chooses between 12 different alternative first exons to be utilized in each cell.

The exact molecular mechanism by which the Smchd1 protein functions in these roles remains unknown. Smchd1 was named because the predicted encoded protein contains the hinge domain characteristic of SMC proteins [77]. The SMC proteins usually act as heterodimers (that is, SMC1 and 3 in cohesin, SMC2 and 4 in condensin, SMC5 and 6 in an unnamed complex involved in DNA repair) that interact through their hinge domains. The hinge domain of SMC proteins is also where the protein folds back on itself to bring together two nucleotide binding domains lying at the amino- and carboxy-terminuses of SMC proteins to form an ATPase domain, which hydrolyses ATP to provide the energy needed to manipulate chromosome-size molecules. The predicted Smchd1 protein also contains an ATPase domain, but it varies from the ABC-type ATPase contained in the SMC proteins and is similar to the ATPase domain from the GHKL phosphotransferase superfamily of type II DNA topoisomerases, Hsp90, and MutL, and bacterial and mitochondrial protein kinases [78]. From this, one would predict that Smchd1 might function as part of a protein complex that manipulates chromatin ultrastructure in an ATP-dependent manner. It is possible that Smchd1 is involved in physically sequestering the chromosomal region containing the allele being silenced to a nuclear territory that is remote from the active allele and where it can be stably maintained in its silent state. Such a function is consistent with the essential role we have previously shown for Smchd1 in X inactivation and with our current findings in the Snrpn and Igf2r imprinted gene clusters, and the clustered protocadherins.

Conclusions

This work extends the involvement of Smchd1 from X inactivation to two other forms of monoallelic expression. Since the Killer cell lectin-like receptors (Klra), which are also subject to monoallelic expression, have previously also been reported to be deregulated in transformed MEFs and tumors that are mutant for Smchd1 [34], it will be interesting to determine whether Smchd1 can be implicated in other forms of monoallelic expression (that is, the olfactory receptors, T cell receptors). Moreover, SMCHD1 mutation has recently been shown to contribute to an inherited muscular weakness syndrome, FSHD2, which requires digenic inheritance of a heterozygous SMCHD1 mutation and a ‘permissive’ D4Z4 microsatellite array haplotype [79]. Heterozygous mutation of SMCHD1 results in hypomethylation of the D4Z4 microsatellite array and, consequently, the DUX4 retrogene embedded in the array becomes expressed in skeletal muscle tissue in a variegated manner. A seemingly distinct role for Smchd1 has also been suggested with the identification GMI1 as the likely Arabidopsis ortholog of Smchd1[80]. GMI1 encodes a γ-radiation inducible protein that is proposed to be involved in homologous recombination. If Smchd1 also proves to function in this role in mammals, its diversity of function may rival that of the SMC proteins.

Methods

Mice and genotyping

All experimental animals were treated in accordance with the Australian Government National Health and Medical Research Council guidelines for the care of experimental animals and the work was approved by the animal ethics committees of the Queensland Institute of Medical Research and the Walter and Eliza Hall Institute. Mice carrying the mutant Smchd1MommeD1 allele were genotyped by allelic discrimination using a custom Taqman assay [31] (primers and Taqman probes are listed in Additional file 13). Mice carrying the ubiquitously expressed GFP transgene (UBI-GFP) were genotyped by observing GFP fluorescence.

Embryos and cell cultures

All embryos were produced by natural matings between heterozygous (Smchd1MommeD1/+) males and females to produce wildtype, heterozygous, and homozygous Smchd1 mutant embryos. Embryos for microarray analysis were dissected at E9.5, with the yolk sacs of each embryo used for genotyping. Embryos for generation of MEFs were dissected at E14.5 and a small section of the tail was removed for Smchd1 genotyping. The remaining carcass of each embryo was individually treated for preparation of MEFs [81].

Microarray analysis

Total RNA was extracted from Smchd1MommeD1/MommeD1 and Smchd1+/+ E9.5 embryos with RNA yields quantified using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Australia, Scoresby, Vic, Australia) and RNA integrity assessed using a Bioanalyzer (Agilent 2100, Agilent Laboratories, Santa Clara, CA, USA). Only samples with an RNA integrity number [82] greater than eight were used.

Illumina Mouse Ref-8 Expression BeadChips, v2.0 were hybridized with biotinylated cRNA prepared using Illumina TotalPrep RNA Amplification Kits (Applied Biosystems, Carlsbad, CA, USA). Probe annotation was enhanced using the Illumina BeadChip Probe Reannotation datasets [35]. Microarray data was analyzed in R using the Beadarray and Limma Bioconductor packages [83–85]. Gene set testing was performed separately for up- and downregulated genes on autosomal genes only, using DAVID [86].

RNA-seq analysis

Total RNA was prepared from E9.5 embryos or the embryonic portion of placentas from F1 (C57Bl/6 J sire cross FVB/n dam) E14.5 male embryos dissected with the aid of a paternally inherited ubiquitin-GFP transgene [66]. RNA yields and integrity were assessed as for the microarrays. RNA-seq was performed by the Australian Genome Research Facility. The sequence reads were mapped to MM10 using TopHat 2 and expression differences between genotypes analyzed by Cufflinks/Cuffdiff v 2.0.2. For allele-specific expression, SNPs were identified in the RNA-seq sequence reads and allelic expression ratios quantified bioinformatically: SNPs were called in the RNA-seq data using the Samtools/BCFtools programs mpileup, bcftools and vcfutils, and mapped to the mouse RefSeq genes. For each called SNP and each sample, the ratio of reads supporting either the variant or reference was calculated. Significantly different allelic expression was identified by testing whether the means of these ratios were different in the Smchd1+/+ or Smchd1MommeD1/MommeD1 male embryos (using a two-tailed t test).

To confirm allelic bias, the placentas from reciprocal cross F1 mice (FVB/n sire cross C57Bl/6 J dam) were dissected and total RNA purified. RT-PCR was used to amplify the specific portions of transcripts containing the SNPs to be analyzed and PCR product used to generate barcoded libraries, which were pooled for Ion Torrent sequencing (Life Technologies, Grand Island, NY, USA). Allelic expression ratios were then determined from the mapped reads.

qPCR and qRT-PCR

Quantitative PCR (qPCR and qRT-PCR) was performed using Platinum SYBR Green qPCR SuperMix-UDG (Life Technologies, Grand Island, NY, USA). Primers were designed using Primer3 and levels of specific PCR amplicons determined relative to a standard curve. For qRT-PCR, first-strand cDNA synthesis was primed either by oligo dT or by a cocktail of specific reverse primers. The sequences of all primers used are listed in Additional file 13.

MeDIP analysis

MeDIP was performed using a protocol adapted from a published method [87]. Genomic DNA was sheared by sonication (Bioruptor, Diagenode, Liège, Belgium) to between 300 and 500 bp. DNA (1 μg) was then denatured and MeDIP performed with 1 μg of anti-5MeC monoclonal antibody clone 33D3 (ab10805, Abcam, Cambridge, UK) plus 0.5 mg of Dynabeads Protein G (Life Technologies, Grand Island, NY, USA). MeDIP material was purified by magnetic separation, phenol extraction, and precipitation. The recovery of specific genomic regions was measured by qPCR relative to Rhox6/9, as we had previously shown that CpG methylation at these loci was not affected by Smchd1 loss [31].

ChIP analysis

ChIP for H3K4me2 was performed using an adaptation of a published protocol [88]. Chromatin was prepared from isolated nuclei of formaldehyde cross-linked MEFs and sonically sheared to between 200 and 500 bp. Sheared chromatin was immunoprecipitated with anti-H3K4me2 Ab (ab11946, Abcam, Cambridge, UK) plus 0.5 mg of Dynabeads ProteinG (Life Technologies, Grand Island, NY, USA). ChIP material was purified, as for MeDIP, and recovery of specific genomic regions in the ChIP samples was measured by qPCR relative to input DNA.

Bisulfite sequencing

Nested primers for amplification of bisulfite converted DNA (Additional file 13) were designed using MethPrimer [89] and the sequencing data analyzed using BiQ analyzer [90]. Genomic DNA (1 μg) was bisulfite treated using the Qiagen EpiTect Bisulfite Kit (Qiagen, Hilden, Germany). After PCR, the product was purified (Qiagen PCR cleanup kit), cloned into pGemT (Promega, Madison, WI, USA) and colonies picked for PCR amplification with SP6 and T7 primers. The PCR product was sequenced with either SP6 or T7 primer.

RNA-FISH

RNA-FISH was carried out as previously described [91] on Smchd1+/+ and Smchd1MommeD1/MommeD1 MEFs grown on gelatin-coated glass coverslips fixed with 3% paraformaldehyde. The probe for Snrpn was a BAC (RP23-97I5, RPCI-23 Female (C57BL/6 J) Mouse BAC Library), while the probes for Ndn and Magel2 consisted of most of each gene PCR amplified from mouse genomic DNA (Additional file 12) and cloned into pGemT. The probes were labeled with Orange or Green dUTP (Abbott Molecular, Abbott Park, Illinois, USA) by nick translation and cell nuclei were counterstained with DAPI (1 μg/ml) before visualization on Zeiss Axioplan epifluorescence microscope equipped with a SPOT RT3 CCD camera. For quantification, 100 randomly selected nuclei were scored for the signal from each gene (that is, Snrpn and Ndn or Magel2).

Data access

Microarray and RNA-seq data reported in this study have been submitted to the NCBI Gene Expression Omnibus under the accession numbers GSE44958 and GSE44669, respectively.