Sex-specific parent-of-origin allelic expression in the mouse brain

Abstract

Genomic imprinting results in preferential gene expression from paternally versus maternally inherited chromosomes. We used a genome-wide approach to uncover sex-specific parent-of-origin allelic effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex. Moreover, analysis of the cortex and hypothalamus identified 347 autosomal genes with sex-specific imprinting features. In the hypothalamus, sex-specific imprinted genes were mostly found in females, which suggests parental influence over the hypothalamic function of daughters. We show that interleukin-18, a gene linked to diseases with sex-specific prevalence, is subject to complex, regional, and sex-specific parental effects in the brain. Parent-of-origin effects thus provide new avenues for investigation of sexual dimorphism in brain function and disease.

Fig. 1

Sex specific imprinting and preferential expression of the Xm in the female brain. (A) Total maternal and paternal X-linked reads for the adult female mPFC and POA in F1i and F1r crosses reveals a highly significant association between strain and cross (mPFC P<0.0001; POA: P<0.0001, two-tailed Fisher’s Exact Test). (B) Identification of a significant strain effect favoring CAST X-chromosome expression (χ² analysis). (C) Preferential expression of the Xm in the mPFC and POA (χ² analysis). ***P <0.001; *P<0.05.

Fig. 2

Preferential expression of Xm in female cortical regions indicated by Xm^egfpXp and XmXp^egfp transgenic mice. (A, B) The number of EGFP+ cells in different cortical (A) and hypothalamic (B) brain regions of Xm^egfpXp (red) versus XmXp^egfp (blue) 5 week old females. Cortical regions: medial prefrontal CTX mPFC, sensory CTX, piriform CTX, and CA1/2 regions and dentate gyrus (DG) of the hippocampus (HPC CA1). Hypothalamic regions: anteroperiventricular nucleus (AVPV), medial preoptic area (MPOA), periventricular nucleus (PVN), or arcuate nucleus (ARC). Two-tailed unpaired t-test; n=7; ***P< 0.001; **P< 0.01; *P< 0.05. Red bars, Xm^egfpXp; Blue bars, XmXp^egfp. Scale bar is 50 μm.

Fig. 3

Sex-specific imprinted autosomal genes were uncovered in the adult male and female POA and mPFC. (A and B) Scatterplots and Pearson’s correlation analysis (R) of the paternal expression bias exhibited by imprinted SNP sites identified in male versus female data. Note some SNP sites exhibit parental effects that are not reproduced (shaded regions). (C) Analysis of the proportion of sex specific PEGs and MEGs in the female versus male POA (χ² Analysis). ***P<0.001. Red, maternal expression; Blue, paternal expression.

Fig. 4

Sex specific imprinted expression of Mrpl48 and Il18 in the female brain. (A) Illumina read data for an imprinted SNP in the 3′ UTR of Mrpl48 (highlighted in blue in (A); SNP_ID: uc009inh.1_801) indicates preferential expression of the paternal allele in the female, but not male POA (χ² Analysis). Sequenom analysis confirmed the result (average allele frequency from 3 biological and 3 technical replicates). (B) Illumina read data for the imprinted SNP in ll18 (SNP_ID: uc009inh.1_801) indicates preferential expression of the maternal allele in the female mPFC, but not the male mPFC or the POA (χ² Analysis). (C) QPCR analysis of Il18 expression in maternal versus paternal deletion Il18 heterozygous mice on C57 background reveals reduced expression in the mPFC of female maternal deletion mice relative to paternal deletion mice (n= 10, two-tailed, unpaired t-test, P = 0.0086). No difference was observed in the male mPFC (n=5) or the hypothalamus (females: n=5, males: n = 6). ***P<0.001; **P<0.01; *P<0.05. Red, maternal expression; Blue, paternal expression.