Sex-specific mouse liver gene expression: genome-wide analysis of developmental changes from pre-pubertal period to young adulthood

Abstract

BackgroundEarly liver development and the transcriptional transitions during hepatogenesis are well characterized. However, gene expression changes during the late postnatal/pre-pubertal to young adulthood period are less well understood, especially with regards to sex-specific gene expression.MethodsMicroarray analysis of male and female mouse liver was carried out at 3, 4, and 8 wk of age to elucidate developmental changes in gene expression from the late postnatal/pre-pubertal period to young adulthood.ResultsA large number of sex-biased and sex-independent genes showed significant changes during this developmental period. Notably, sex-independent genes involved in cell cycle, chromosome condensation, and DNA replication were down regulated from 3 wk to 8 wk, while genes associated with metal ion binding, ion transport and kinase activity were up regulated. A majority of genes showing sex differential expression in adult liver did not display sex differences prior to puberty, at which time extensive changes in sex-specific gene expression were seen, primarily in males. Thus, in male liver, 76% of male-specific genes were up regulated and 47% of female-specific genes were down regulated from 3 to 8 wk of age, whereas in female liver 67% of sex-specific genes showed no significant change in expression. In both sexes, genes up regulated from 3 to 8 wk were significantly enriched (p < E-76) in the set of genes positively regulated by the liver transcription factor HNF4α, as determined in a liver-specific HNF4α knockout mouse model, while genes down regulated during this developmental period showed significant enrichment (p < E-65) for negative regulation by HNF4α. Significant enrichment of the developmentally regulated genes in the set of genes subject to positive and negative regulation by pituitary hormone was also observed. Five sex-specific transcriptional regulators showed sex-specific expression at 4 wk (male-specific Ihh; female-specific Cdx4, Cux2, Tox, and Trim24) and may contribute to the developmental changes that lead to global acquisition of liver sex-specificity by 8 wk of age.ConclusionsOverall, the observed changes in gene expression during postnatal liver development reflect the deceleration of liver growth and the induction of specialized liver functions, with widespread changes in sex-specific gene expression primarily occurring in male liver.

Impact of CUX2 on the Female Mouse Liver Transcriptome: Activation of Female-Biased Genes and Repression of Male-Biased Genes

“…Our findings suggest that CUX2 contributes to the large changes in expression of many sex-biased genes that occur in mouse liver at puberty (6). Genes showing male-biased expression in adult liver are proposed to be repressed by CUX2 in immature liver, where CUX2 expression is high in both males and females; they are then selectively derepressed in male liver at puberty, when CUX2 expression is extinguished.…”

“…Next, we examined whether genes altered by CUX2 overexpression are enriched for genes that show a developmental change in mouse liver between 3 and 8 weeks (6). Strikingly, 83% of the male-biased genes that were downregulated in adult male liver following adeno-CUX2 infection were upregulated in male liver from 3 to 8 weeks, consistent with CUX2 repressing these genes in prepubertal male liver (Fig.…”

“…This may reflect a differential availability of transcriptional cofactors of CUX2, leading to the observed sex-differential regulation of these genes, , and stringent sex-independent (C) genes altered by adeno-CUX2 treatment (5 days) to genes showing developmental changes between 3 weeks and 8 weeks in male (left) and female (right) mouse liver is shown. The developmental changes considered were upregulation, downregulation, and no change in expression from 3 weeks to 8 weeks at Խfold changeԽ Ͼ 1.5 and P Ͻ 0.0001, based on microarray studies reported elsewhere (6). Statistical analysis (two-tailed Fisher exact test): ***, ES P Ͻ 10 Ϫ5 for genes showing developmental upregulation from 3 to 8 weeks; ϩϩϩ, ES P Ͻ 10 Ϫ5 for genes showing development downregulation from 3 to 8 weeks.…”

“…The DAVID annotation tool (13,14) was used to analyze genes in hierarchical clusters to identify enrichment clusters deemed significant (minimum enrichment score [ES] of 1.3, which is equivalent to an uncorrected P value of 0.05). Enrichment of genes altered by CUX2 overexpression in mouse liver in gene sets that showed a development change from 3 to 8 weeks in a previous microarray study (6) was calculated using genes common to both microarray platforms (G4846A-026655 used in the developmental study [6] and G4122F-014868 used in the present adeno-CUX2 study). For sex-biased genes, only genes that showed sex bias in both studies were used when calculating the enrichment score.…”

“…These findings suggest that CUX2 contributes to the widespread changes in sex-biased gene expression that occur at puberty. Those changes primarily occur in male liver, where many male-biased genes are upregulated and female-biased genes are downregulated after 4 weeks of age (6). Given the transcriptional repressive activity of CUX2, we hypothesized that CUX2 binds to and represses a subset of male-biased genes in prepubertal male liver and that these genes are derepressed after 4 weeks of age, when CUX2 expression declines.…”