- Research article
- Open Access
Sexually dimorphic gene expression emerges with embryonic genome activation and is dynamic throughout development
© Lowe et al.; licensee BioMed Central. 2015
- Received: 28 July 2014
- Accepted: 30 March 2015
- Published: 14 April 2015
As sex determines mammalian development, understanding the nature and developmental dynamics of the sexually dimorphic transcriptome is important. To explore this, we generated 76 genome-wide RNA-seq profiles from mouse eight-cell embryos, late gestation and adult livers, together with 4 ground-state pluripotent embryonic (ES) cell lines from which we generated both RNA-seq and multiple ChIP-seq profiles. We complemented this with previously published data to yield 5 snap-shots of pre-implantation development, late-gestation placenta and somatic tissue and multiple adult tissues for integrative analysis.
We define a high-confidence sex-dimorphic signature of 69 genes in eight-cell embryos. Sex-chromosome-linked components of this signature are largely conserved throughout pre-implantation development and in ES cells, whilst the autosomal component is more dynamic. Sex-biased gene expression is reflected by enrichment for activating and repressive histone modifications. The eight-cell signature is largely non-overlapping with that defined from fetal liver, neither was it correlated with adult liver or other tissues analysed. The number of sex-dimorphic genes increases throughout development. We identified many more dimorphic genes in adult compared to fetal liver. However, approximately two thirds of the dimorphic genes identified in fetal liver were also dimorphic in adult liver. Sex-biased expression differences unique to adult liver were enriched for growth hormone-responsiveness. Sexually dimorphic gene expression in pre-implantation development is driven by sex-chromosome based transcription, whilst later development is characterised by sex dimorphic autosomal transcription.
This systematic study identifies three distinct phases of sex dimorphism throughout mouse development, and has significant implications for understanding the developmental origins of sex-specific phenotypes and disease in mammals.
- Sexual dimorphism
- Pre-implantation embryo
- Gene expression
Sex determines anatomical, physiological and behavioural development in mammals. This developmental divergence arises as a consequence of sex-chromosome complement and is largely, although, not exclusively mediated through the organisational and activational effects of sex-specific hormones . In adulthood, sex-specific gene expression is widespread in somatic tissues . Consequentially, sex influences a plethora of complex traits that do not directly relate to reproductive roles. Exemplifying this, many diseases exhibit sex bias in prevalence or severity , and association of genetic variants with disease states is sex-dependent [4,5].
The ‘Four Core Genotypes’ mouse model has been used to dissect the contribution of sex-chromosome complement and the organisational and activational effects of sex-specific hormones , revealing that both hormones and chromosomal complement exert independent and divergent effects over metabolic and behavioural phenotypes [7,8]. Furthermore, animal models of the Developmental Origins of Health and Disease hypothesis reveal differential outcomes of early environmental insults dependent on sex , suggesting that sex should be considered as third parameter in any gene-environment interactions. Despite this, the origin and nature of these sex based differences are largely unexplored.
There is evidence that sexually dimorphic gene expression arises prior to gonadal differentiation, even in pre-implantation blastocysts, with both sex-linked and autosomal genes affected [10,11]. This dimorphism could determine the effects of specific environmental factors on long term developmental outcomes. Indeed, embryo culture medium induces long-term effects on glucose homeostasis in a sexually dimorphic manner . Despite the relevance to human health and reproductive technologies, the origins and developmental dynamics of mammalian sexual dimorphism have not been characterized in detail. Here we report a high confidence signature of sexually dimorphic genes in the mouse coincident with embryonic genome activation using unmanipulated embryos, and from fetal and adult liver and performed comparative analyses using data from other sources. Our findings demonstrate that dimorphic expression emerges in the early cleavage embryo and is highly dynamic throughout development. Furthermore, we show that this is reflected in the chromatin structure. Through defining the nature and developmental origins of sexual dimorphism we provide a background for interpreting gene-environment interactions in directing developmental outcomes.
Sexually dimorphic gene expression emerges very early in development
Genes defined as sexually dimorphic from eight-cell embryos
Substantial variation between individual embryos is apparent (Figures 1A,B, Additional file 2: Figure S2), and may reflect small differences in the timing of embryonic genome activation. However, we validated sex-biased expression of these genes in another 12 eight-cell embryos isolated in an independent experiment (8 female, 4 male) (Figure 1C). Biological replicates showed a strong directional correlation (ρ = 0.95, p-value < 2.2x10−16), with all but one of the 69 genes showing the same sex-based expression bias, even though transcripts show average log(male/female) values small in magnitude. Three non-coding transcripts were included in the eight-cell signature, consistent with a role for non-coding RNAs in early embryo development . Two of these were involved in X inactivation, Xist and B230206F22Rik (also known as Ftx) [16,17]. The third, D7Ertd715e is located immediately 3′ to the Snrpn/Snurf imprinted cluster on chromosome 7, but its function is unknown. We performed KEGG analysis of X-linked genes, using detected X chromosome genes as background and separately for the autosomal genes, using all detected autosomal genes as background. Neither analysis revealed enrichment after Bonferroni correction (p < 0.05).
The dynamics of sexual dimorphism at different developmental stages
Sample characteristics and sources for comparative analyses
Number of males
Number of females
Single cell RNA-seq
Single cell RNA-seq
Single cell RNA-seq
8-cell embryos (discovery)
Whole embryo RNA-seq
8-cell embryos (replication)
Whole embryo RNA-seq
Single cell RNA-seq
2i ES cells
2i ES cells
Interestingly, the 15 autosomal genes that are sexually dimorphic in eight-cell embryos did not show consistent directional changes at other time-points in pre-implantation development. As these genes were expressed at comparable levels to the sex-chromosome encoded transcripts, it seems unlikely that an increased signal to noise ratio is responsible for this. Despite not showing dimorphism at other pre-implantation stages, 14/15 of these genes show biological validation at the eight-cell stage (Figure 1C), suggesting that this stage-specific autosomal sexual dimorphism is bona fide. The expression level of these genes seems to be very dynamic throughout pre-implantation development (Additional file 2: Figure S5). Similar pre-implantation stage-specific expression has also been shown for genes identified as dimorphic in bovine blastocysts . Indeed, global autosomal gene expression reaches a nadir at the eight-cell stage (Additional file 2: Figure S6). Collectively, we show that sex-chromosome genes show largely consistent sexual dimorphism throughout pre-implantation development and in ground state pluripotent stem cells, regardless of genetic background, but that dimorphism of autosomal genes is more temporally dynamic.
X-linked dimorphic genes escape paternal X inactivation in pre-implantation development
The emergence of sexually dimorphic expression of Xist at the four-cell stage coincides with the initiation of transcriptional inactivation of the paternal X chromosome in mice . Higher X-linked expression in females must therefore reflect either an up-regulation of these genes from the maternal X chromosome in females, or escape from paternal X chromosome inactivation in the pre-implantation stages. Consistent with the escape from silencing of the paternal X we find that the majority of X-linked sex dimorphic genes are located distally from the X inactivation centre (Additional file 2: Figure S7), confirming previous observations . Indeed, allelic data generated by Deng et al., confirms that 35/38 (~92%) genes that had adequate allele-specific information were expressed from both maternal and paternal X chromosomes at one or more developmental time-points (four-, sixteen- or early blastocyst) . Although there is some suggestion that inter-specific crosses may have altered X inactivation, reassuringly, two of the three transcripts solely of paternal origin are known to be involved in silencing the chromosome from which they are transcribed, Xist and B230206F22Rik (also known as Ftx) [16,17]. The other transcript (Gla) showed paternal-specific expression at the four-cell stage, with allelic data for later stages not available. Notably, silencing of paternal expression of this transcript has previously been shown to be initiated after the eight-cell and completed only by the blastocyst stage .
Sex-biased expression of most X chromosome genes that are dimorphic in eight-cell embryos, with the exception of Xist, and Eif2s3x is erased (−0.5 < logFC > 0.5) in fetal and adult liver (Figure 2A), but female-biased expression was retained for 5/51 X-linked genes in publically available gene expression array data from late gestation placenta , at log(male/female) < −0.5. As extra-embryonic tissues in the mouse demonstrate imprinted inactivation of the paternal X chromosome, we asked if dimorphic X-linked expression is more similar in general between these two tissues. Using a cut-off of log(male/female) < −0.5, we identified 79 X-linked genes showing female biased expression in placenta and found that there was a trend towards female-biased expression of these genes in the eight-cell embryos (t test, mean = −0.14, p-value = 0.046). Consistent with re-activation of the inactive paternal X chromosome in the epiblast-like 2i ES cells, the female bias in expression of the dimorphic X-linked genes identified from eight-cell embryos is maintained and expanded upon (Additional file 2: Figure S8). In fetal and adult somatic tissues, a different set of X chromosome genes are dimorphic.
Sex-biased expression is correlated with post-translational histone modifications
Specific post-translational histone modifications are associated with particular transcriptional states and genomic features. We sought to explore the relationship of sexually dimorphic expression in pre-implantation development with chromatin features. To address this, we generated genome-wide profiles for three post-translational histone modifications in our 2i ES cells using chromatin immunoprecipitation combined with deep sequencing (ChIP-seq). 12–20 million mapped reads were generated for each mark (Additional file 1: Table S1). Determining average profiles for the 2000 most high- or low-expressed genes confirmed the expected enrichment of H3K4me3 at active gene promoters, whilst H3K27me3 was depleted (Additional file 2: Figure S9). Both H3K27me3 and H3K9me3 were enriched at repetitive elements and H3K9me3 was associated with imprinted genes, confirming the distribution of these modifications is typical of ground state pluripotency . Genes located on the X chromosome conform to genome-wide distribution patterns.
A positive correlation between expression and H3K4me3 enrichment in the 3 kb surrounding the TSS of sex-dimorphic autosomal genes expressed in ES cells was found (Figure 4D; ρ = 0.57, p-value < 2.2x10−16). TSS H3K9me3 enrichment does not correlate with gene expression, although is enriched in males (Figure 4E; ρ = 0.0052, p-value = 0.89), whilst H3K27me3 is very weakly anti-correlated (Figure 4F; ρ = −0.077, p-value = 0.036). The autosomal genes identified in the eight-cell embryos were not called as significantly dimorphic in the ES cells, although they were still expressed. Furthermore, as there were so few sexually dimorphic autosomal genes in the eight-cell signature, we could not make correlations with the ESC histone marks. Our findings suggest that sex-biased gene expression associates with enrichment of H3K4me3 at the TSS in the sex that has higher expression. This relationship is true for both X-linked and autosomal genes.
Sexual dimorphism is more pronounced in adult compared to fetal liver
Sexually dimorphic expression of the eight-cell signature genes in liver at adult and fetal stages did not recapitulate that found in pre-implantation development (Figure 2). To investigate the inter-relationship of sex-biased gene expression at later developmental stages, we identified a signature of 1488 dimorphic genes within adult liver (genome-wide corrected P < 0.1, −0.5 < logFC > 0.5; Additional file 3: Table S2). Autosomal genes account for ~96% of the dimorphic genes, in contrast to what is observed at pre-implantation stages (Additional file 2: Figure S8). KEGG analyses identified many enriched pathways, with drug metabolism as most significant, consistent with previous findings (Additional file 4: Table S3) . Reassuringly, our data strongly correlated with previously published adult liver dimorphic differences, despite the different profiling platforms and genetic backgrounds between the two datasets (ρ = 0.82; p-value < 2.2x10−16) . On the premise of this, we established a cut off (−0.5 < logFC > 0.5) by which we could define a signature for the other tissues; adipose, muscle and brain, profiled by Yang et al. Consistent with previous analyses we found that there was not a significant correlation for sex-dimorphic expression across tissues (data not shown), whilst X-linked genes showed modest female-biased expression differences . Furthermore, the signature defined from eight-cell embryos did not show directional consistency in any of the adult tissues (data not shown).
Sex-based expression differences in adult liver are known to be largely dependent on differences in growth hormone regulation in response to sex-specific gonadal hormones [33,34]. To test if growth hormone responsiveness underlies the differences in dimorphic expression between fetal and adult liver, we asked if the dimorphic genes present in adult, but not fetal liver were enriched for previously identified growth hormone responsive transcripts . Indeed, adult-specific sex-dimorphic genes had a 5.4X enrichment (p < 0.001). Collectively, our results suggest that sex-biased expression of some genes in liver is intrinsic, but that sex differences in growth hormone induces dimorphism of additional genes. Our data suggests that this latter mechanism is not yet operational in late gestation.
We present a whole-genome view of in vivo sexually dimorphic gene expression throughout mouse development, revealing that sex-specific expression biases in the embryo, fetus and adult are largely distinct.
Our study of dimorphism in pre-implantation development provides advances on previous work, by sampling prior to any cellular differentiation and eliminating culture induced artifacts [11,36,37]. By defining a high-confidence signature from eight-cell embryos we could then use this signature to probe other pre-implantation developmental stages despite the data being underpowered for defining sex dimorphic signatures de novo. We find that pre-implantation development is characterised by conserved dimorphism of sex-chromosome-linked genes, predominantly from the X chromosome . Female-biased expression of some X-linked genes arises in two cell embryos, around the time embryonic genome activation is initiated in the mouse. Whether this is indicative of differences in the rate at which maternally inherited transcripts are degraded amongst sexes, or otherwise results from nascent transcription is unknown . However, at least in the case of Fthl17, an X-linked maternally imprinted gene, transcription from the paternally inherited chromosome in the early embryo is responsible for female only expression . Some of the X-linked genes in our eight-cell signature have been shown to escape paternal X inactivation in extra-embryonic tissues [39,40]. Allelic information suggests that for many of these genes, escape from paternal X silencing might also underlie their dimorphism in pre-implantation development. Consistent with previous findings, absolute paternal expression is either associated with the establishment of X inactivation (with the exception of Fthl17), whilst partial expression is more common amongst genes distal from the X inactivation centre  These genes also show a selective depletion of H3K27me3 in female ES cells, in contrast to sex-dimorphic X-linked genes that are not dimorphic in the eight cell embryos, even though the transcriptional behaviour between these subsets is similar in the ES cells. The difference between gene subsets escaping imprinted X inactivation in the pre-implantation embryo and placenta might be accounted for by progressive silencing of the paternal X chromosome throughout the pre-implantation period . Similar X-linked dimorphism may not be conserved in humans, however, as regulation of X-inactivation is substantially different between species .
Autosomal genes also show dimorphism in pre-implantation stages, but sex-specific expression of these genes seems to be temporally restricted. Although we did not see conservation of these differences at other pre-implantation stages, we demonstrate validation in two independent cohorts of eight-cell embryos. The identification of dimorphic autosomal genes in eight-cell embryos implies regulation by sex-specific trans acting factors. In epiblast-like ES cells, autosomal genes highly expressed in one sex had corresponding enrichment for H3K4me3 around the TSS, consistent with what has been observed for strongly sex-biased genes in mouse liver . Our eight-cell dimorphic signature included both X-linked transcription factors, e.g. YY2, and chromatin modifiers e.g. Kdm6a . Interestingly, Kdm6a, has been shown to regulate specific targets, such as the Rhox6/9 cluster in a sex-specific manner in ES cells , whilst its Y-encoded homolog (Uty), does not completely recapitulate its function [43,44]. Sex-chromosome complement might otherwise influence autosomal gene transcription through the inactive X chromosome influencing heterochromatic gene silencing in trans .
In line with previous findings, we found a large number of dimorphically expressed genes in adult liver that were not conserved across other adult tissues. Expanding on this, we also show that directionality was not conserved with the pre-implantation signature. We did, however, identify a subset of genes that show dimorphic expression in both fetal and adult liver. KEGG pathway analysis revealed dimorphism in common pathways relating to metabolism and stage-specific pathways relating to signal transduction in the liver at these two stages. Many additional genes were dimorphic in adults, possibly due to the activational effects of gonadal hormones. Consistent with this hypothesis we show that adult-specific liver dimorphic genes are enriched for growth hormone responsiveness . Although gonadal hormones are produced in late gestation, the regulation of pituitary growth hormone secretion by gonadal hormones is minimal prior to puberty in mice .
Our findings reveal that there are core transcriptional differences between the sexes that are consistent throughout pre-implantation development. Most of the genes identified in eight-cell embryos do not retain significantly dimorphic expression in fetal and adult tissues. Although sex-dimorphic expression is highly tissue-specific, a subset of genes is conserved across fetal and adult liver suggesting that sex-biased expression of this subset may be due to sex-chromosome complement, whilst differences are more likely driven by sex-specific physiology, which differs according to the stage of development. Although at a gene level we see a dramatic difference across pre-implantation, fetal and adult development, pathway level analysis reveals some conservation. By providing a genome-wide view of sex-dimorphic expression from post-fertilisation to adult, we hope to improve the understanding of the underlying molecular biology of sexually dimorphic phenotypes.
There is substantial evidence to suggest that sex-specific responses to environmental stimuli can occur prior to exposure to sex-specific hormones, and in some instances, even when the exposure is restricted to the previous generation . Sex-chromosome complement can drive dramatic effects, as exemplified by the epigenome-wide differences in male and female murine ES cells when cultured in the presence of serum or defined medium [22,48]. Such effects may have lasting impact on developmental trajectories and disease risk . Through characterising sexually dimorphic gene expression through a developmental trajectory, we reveal novel aspects of sex-specific biology and the inter-relationship of key phases across development. Our findings provide a platform for future work exploring the role of sex in moderating gene-environment interactions and highlight the importance of incorporating sex in studies of common disease and interventions [9,49].
Animal maintenance and tissue isolation
All animal procedures were conducted in accordance with the Home Office Animals (Scientific Procedures) Act 1986 (Project License number - 70/6693). C57BL/6 J mice were obtained from Charles River Laboratories, UK. All animals were maintained on standard laboratory chow and a 12 hr light/dark cycle. Male mice were housed with virgin females overnight. The detection of a vaginal plug the following morning was considered 0.5 dpc. Females were killed at 2.5 dpc and eight-cell embryos isolated from the fallopian tubes by flushing. Alternatively, females were killed at 17.5 dpc and embryonic liver was collected and snap frozen with liquid nitrogen. Adult animals were killed at 15–20 weeks of age and tissues collected and snap frozen. All animals were killed between 10 am and 12 pm.
Single cell isolation from 8 cell embryos
Single embryos were transferred to acidic Tyrode’s solution to remove the zona pellucida, then washed in PBS-BSA (1 mg/mL) and dissociated into single cells as described previously . All cells from a single embryo were used to generate a single RNA-seq library. For the discovery set, embryos of both sexes were derived from 4 independent litters, embryos used for biological replication were derived from an Additional 5 independent litters. The sires of the replicate litters were exposed to in utero protein restriction.
Derivation of embryonic stem (ES) cell lines
ES cells were derived from eight-cell embryos as previously described . Briefly, isolated eight-cell embryos were cultured in KSOM medium supplemented with (2i): mitogen-activated protein kinase inhibitor (PD0325901, 1 μM) and glycogen synthase kinase-3 inhibitor (CHIR99021, 3 μM). After two days, embryos were transferred to NDiff227 medium with 2i and LIF and allowed to develop into blastocysts. The trophectoderm was lysed by immunosurgery, and the ICM (inner cell mass) of each embryo plated in NDiff227 supplemented with 2i and LIF and for expansion to generate 2i ES cell lines.
Generation and sequencing of RNA-seq libraries
The eight-cell embryo RNA-seq libraries were generated using a single-cell protocol adapted from . Further details are provided in Supplementary Information.
Generation and sequencing of ChIP-seq libraries
The chromatin immunoprecipitation (ChIP) assay was performed according to previously published protocols with minor modifications . Chromatin was sonicated to get fragments of 100 to 700 bp and immunoprecipitated with the following antibodies anti-H3K27me3 (07–449, Millipore), anti-H3K4me3 (39159, Active Motif) and anti-H3K9me3 (ab8898, Abcam). ChIP-seq libraries were prepared using the Illumina ChIP-seq librarary prep kit, according to the manufacturers’ instructions.
All analysis was performed on UCSC reference genome mm10 and the gene annotation file downloaded from Tophat website (downloaded on September 25th 2013).
All RNA-Seq data was mapped using Tophat v2.0.4 with Bowtie 2 v2.1.0 and samtools v0.1.18 using default settings. The mean insert sizes and standard deviations were calculated in silico using Picard Tools v1.98 from 1,000,000 reads. Duplicates were filtered using Picard Tools and reads were assigned to a gene using HTSeq. Differential analysis was performed using DESeq2 v1.4.5 which uses a generalised linear model in which counts are modelled using a negative binomial distribution. Genome wide corrected p-values were calculated using Benjamini-Hochberg multiple testing adjustment procedure. Normalised variance stabilizing transformed counts were used for all plots and further analysis. Existing public data was extracted as raw counts and analysed with DESeq2 in the same manner as our data.
All ChiP-Seq data was mapped using Bowtie 2 v2.1.0 with default settings. Coverage across the genome was calculated using genomeCoverageBed from Bedtools v2.17.0 and converted to BigWig format using bedGraphToBigWig downloaded from the UCSC website. For correlation with RNA-Seq data the average coverage over +/−1.5 kbp of the TSS of each gene was calculated using bigWigAverageOverBed.
Chromosome dosage model
ChIP-seq data and RNA-seq data are available in the NCBI Gene Expression Omnibus (GSE59222), and will be made public upon acceptance of the manuscript for publication.
VKR is supported by grants from the Biotechnology and Biological Sciences Research Council, UK (BB/M012494/1), VKR and CG by (BB/G00711/X/1). MLH is supported by a Research Council UK Academic Fellowship. RL is supported by EU-FP7 BLUEPRINT. We thank King’s College London FWB Genomics Centre for performing high throughput sequencing.
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