Unbiased, Genome-Wide In Vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-Specific Liver Gene Expression

Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA.
Molecular and Cellular Biology (Impact Factor: 4.78). 09/2010; 30(23):5531-44. DOI: 10.1128/MCB.00601-10
Source: PubMed


We have used a simple and efficient method to identify condition-specific transcriptional regulatory sites in vivo to help elucidate the molecular basis of sex-related differences in transcription, which are widespread in mammalian tissues
and affect normal physiology, drug response, inflammation, and disease. To systematically uncover transcriptional regulators
responsible for these differences, we used DNase hypersensitivity analysis coupled with high-throughput sequencing to produce
condition-specific maps of regulatory sites in male and female mouse livers and in livers of male mice feminized by continuous
infusion of growth hormone (GH). We identified 71,264 hypersensitive sites, with 1,284 showing robust sex-related differences.
Continuous GH infusion suppressed the vast majority of male-specific sites and induced a subset of female-specific sites in
male livers. We also identified broad genomic regions (up to ∼100 kb) showing sex-dependent hypersensitivity and similar patterns
of GH responses. We found a strong association of sex-specific sites with sex-specific transcription; however, a majority
of sex-specific sites were >100 kb from sex-specific genes. By analyzing sequence motifs within regulatory regions, we identified
two known regulators of liver sexual dimorphism and several new candidates for further investigation. This approach can readily
be applied to mapping condition-specific regulatory sites in mammalian tissues under a wide variety of physiological conditions.

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    • "Furthermore, bioinformatic analyses of the DNA sequence of all activated or repressed enhancers allows for prediction of which sequence-specific transcription factors might be involved in mediating the response. This is a powerful approach that has been used in a number of studies to predict the major regulators involved (Siersbaek et al. 2011; Carroll et al. 2005; Lin et al. 2010; Yanez-Cuna et al. 2012; Ling et al. 2010; Steger et al. 2010; Mikkelsen et al. 2010). Bioinformatic limitations for these predictions are the fact that large families of transcription factors bind to very similar DNA sequences and that only TFs for which there is a priori knowledge of the binding motif can be predicted. "
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    ABSTRACT: Mammals have at least 210 histologically diverse cell types (Alberts, Molecular biology of the cell. Garland Science, New York, 2008) and the number would be even higher if functional differences are taken into account. The genome in each of these cell types is differentially programmed to express the specific set of genes needed to fulfill the phenotypical requirements of the cell. Furthermore, in each of these cell types, the gene program can be differentially modulated by exposure to external signals such as hormones or nutrients. The basis for the distinct gene programs relies on cell type-selective activation of transcriptional enhancers, which in turn are particularly sensitive to modulation. Until recently we had only fragmented insight into the regulation of a few of these enhancers; however, the recent advances in high-throughput sequencing technologies have enabled the development of a large number of technologies that can be used to obtain genome-wide insight into how genomes are reprogrammed during development and in response to specific external signals. By applying such technologies, we have begun to reveal the cross-talk between metabolism and the genome, i.e., how genomes are reprogrammed in response to metabolites, and how the regulation of metabolic networks is coordinated at the genomic level.
    Full-text · Article · Apr 2015 · Handbook of experimental pharmacology
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    • "It could relate to the location of genes on the sex chromosomes, as well as to epigenetic marks associated with the genes. Sex-specific DNA hypersensitive sites [41] and differences in DNA methylation [23] and in histone marks [22],[42] have been reported between males and females. Whether these mechanisms function equally in different organs and are globally regulated or mediated at a gene-specific level needs to be further investigated. "
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    ABSTRACT: Background There is increasing appreciation for sexually dimorphic effects, but the molecular mechanisms underlying these effects are only partially understood. In the present study, we explored transcriptomics and epigenetic differences in the small intestine and colon of prepubescent male and female mice. In addition, the microbiota composition of the colonic luminal content has been examined. Methods At postnatal day 14, male and female C57BL/6 mice were sacrificed and the small intestine, colon and content of luminal colon were isolated. Gene expression of both segments of the intestine was analysed by microarray analysis. DNA methylation of the promoter regions of selected sexually dimorphic genes was examined by pyrosequencing. Composition of the microbiota was explored by deep sequencing. Results Sexually dimorphic genes were observed in both segments of the intestine of 2-week-old mouse pups, with a stronger effect in the small intestine. Amongst the total of 349 genes displaying a sexually dimorphic effect in the small intestine and/or colon, several candidates exhibited a previously established function in the intestine (i.e. Nts, Nucb2, Alox5ap and Retnlγ). In addition, differential expression of genes linked to intestinal bowel disease (i.e. Ccr3, Ccl11 and Tnfr) and colorectal cancer development (i.e. Wt1 and Mmp25) was observed between males and females. Amongst the genes displaying significant sexually dimorphic expression, nine genes were histone-modifying enzymes, suggesting that epigenetic mechanisms might be a potential underlying regulatory mechanism. However, our results reveal no significant changes in DNA methylation of analysed CpGs within the selected differentially expressed genes. With respect to the bacterial community composition in the colon, a dominant effect of litter origin was found but no significant sex effect was detected. However, a sex effect on the dominance of specific taxa was observed. Conclusions This study reveals molecular dissimilarities between males and females in the small intestine and colon of prepubescent mice, which might underlie differences in physiological functioning and in disease predisposition in the two sexes.
    Full-text · Article · Aug 2014 · Biology of Sex Differences
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    • "The few unshared genes located on the Y chromosome are exclusively expressed in the testes, or are housekeeping genes with X-chromosome homologues that escape X-inactivation [8]. However, genome regulation seems highly sex-specific at secondary epigenetic levels such as DNA methylation [9], DNase hypersensitivity [10], chromatin structure [11] and gene expression [12,13]. Thus, a characterization of sex differences in genome regulation by gene expression will contribute to the understanding of the molecular basis of sexual dimorphism. "
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    ABSTRACT: Genomes of men and women differ in only a limited number of genes located on the sex chromosomes, whereas the transcriptome is far more sex-specific. Identification of sex-biased gene expression will contribute to understanding the molecular basis of sex-differences in complex traits and common diseases. Sex differences in the human peripheral blood transcriptome were characterized using microarrays in 5,241 subjects, accounting for menopause status and hormonal contraceptive use. Sex-specific expression was observed for 582 autosomal genes, of which 57.7% was upregulated in women (female-biased genes). Female-biased genes were enriched for several immune system GO categories, genes linked to rheumatoid arthritis (16%) and genes regulated by estrogen (18%). Male-biased genes were enriched for genes linked to renal cancer (9%). Sex-differences in gene expression were smaller in postmenopausal women, larger in women using hormonal contraceptives and not caused by sex-specific eQTLs, confirming the role of estrogen in regulating sex-biased genes. This study indicates that sex-bias in gene expression is extensive and may underlie sex-differences in the prevalence of common diseases.
    Full-text · Article · Jan 2014 · BMC Genomics
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