scholarly journals Genetic factors contributing to extensive variability of sex-specific hepatic gene expression in Diversity Outbred mice

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0242665
Author(s):  
Tisha Melia ◽  
David J. Waxman
Keyword(s):  
Gene Expression ◽  
Growth Hormone ◽  
Sex Differences ◽  
Genetic Factors ◽  
Individual Variability ◽  
Specific Gene ◽  
Open Chromatin ◽  
Diversity Outbred ◽  
Outbred Mice ◽  
The Individual

Sex-specific transcription characterizes hundreds of genes in mouse liver, many implicated in sex-differential drug and lipid metabolism and disease susceptibility. While the regulation of liver sex differences by growth hormone-activated STAT5 is well established, little is known about autosomal genetic factors regulating the sex-specific liver transcriptome. Here we show, using genotyping and expression data from a large population of Diversity Outbred mice, that genetic factors work in tandem with growth hormone to control the individual variability of hundreds of sex-biased genes, including many long non-coding RNA genes. Significant associations between single nucleotide polymorphisms and sex-specific gene expression were identified as expression quantitative trait loci (eQTLs), many of which showed strong sex-dependent associations. Remarkably, autosomal genetic modifiers of sex-specific genes were found to account for more than 200 instances of gain or loss of sex-specificity across eight Diversity Outbred mouse founder strains. Sex-biased STAT5 binding sites and open chromatin regions with strain-specific variants were significantly enriched at eQTL regions regulating correspondingly sex-specific genes, supporting the proposed functional regulatory nature of the eQTL regions identified. Binding of the male-biased, growth hormone-regulated repressor BCL6 was most highly enriched at trans-eQTL regions controlling female-specific genes. Co-regulated gene clusters defined by overlapping eQTLs included sets of highly correlated genes from different chromosomes, further supporting trans-eQTL action. These findings elucidate how an unexpectedly large number of autosomal factors work in tandem with growth hormone signaling pathways to regulate the individual variability associated with sex differences in liver metabolism and disease.

scholarly journals Genetic factors contributing to extensive variability of sex-specific hepatic gene expression in Diversity Outbred mice

2020 ◽  
Author(s):  
Tisha Melia ◽  
David J. Waxman
Keyword(s):  
Gene Expression ◽  
Growth Hormone ◽  
Sex Differences ◽  
Genetic Variants ◽  
Genetic Factors ◽  
Disease Susceptibility ◽  
Gene Clusters ◽  
Individual Variability ◽  
Diversity Outbred ◽  
The Individual

AbstractSex-specific transcription characterizes hundreds of genes in mouse liver, many implicated in sex-differential drug and lipid metabolism and disease susceptibility. While the regulation of liver sex differences by growth hormone-activated STAT5 is well established, little is known about autosomal genetic factors regulating the sex-specific liver transcriptome. Here we show, using genotyping and expression data from a large population of Diversity Outbred mice, that genetic factors work in tandem with growth hormone to control the individual variability of hundreds of sex-biased genes, including many lncRNA genes. Significant associations between single nucleotide polymorphisms and sex-specific gene expression were identified as expression quantitative trait loci (eQTLs), many of which showed strong sex-dependent associations. Remarkably, autosomal genetic modifiers of sex-specific genes were found to account for more than 200 instances of gain or loss of sex-specificity across eight Diversity Outbred mouse founder strains. Sex-biased STAT5 binding sites and open chromatin regions with strain-specific variants were significantly enriched at eQTL regions regulating correspondingly sex-specific genes, supporting the proposed functional regulatory nature of the eQTL regions identified. Binding of the male-biased, growth hormone-regulated repressor BCL6 was most highly enriched at trans-eQTL regions controlling female-specific genes. Co-regulated gene clusters defined by overlapping eQTLs included sets of highly correlated genes from different chromosomes, further supporting trans-eQTL action. These findings elucidate how an unexpectedly large number of autosomal factors work in tandem with growth hormone signaling pathways to regulate the individual variability associated with sex differences in liver metabolism and disease.Author summaryMale-female differences in liver gene expression confer sex differences in many biological processes relevant to health and disease, including lipid and drug metabolism and liver disease susceptibility. While the role of hormonal factors, most notably growth hormone, in regulating hepatic sex differences is well established, little is known about how autosomal genetic factors impact sex differences on an individual basis. Here, we harness the power of mouse genetics provided by the Diversity Outbred mouse model to discover significant genome-wide associations between genetic variants and sex-specific liver gene expression. Remarkably, we found that autosomal expression quantitative trait loci with a strong sex-bias account for the loss or gain of sex-specific expression of more than 200 autosomal genes seen across eight founder mice strains. Genetic associations with sex-specific genes were enriched for sex-biased and growth hormone-dependent regulatory regions harboring strain-specific genetic variants. Co-regulated gene clusters identified by overlapping regulatory regions included highly correlated genes from different chromosomes. These findings reveal the extensive regulatory role played by autosomal genetic variants, working in tandem with growth hormone signaling pathways, in the transcriptional control of sex-biased genes, many of which have been implicated in sex differential outcomes in liver metabolism and disease susceptibility.

scholarly journals Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model

2021 ◽  
Author(s):  
Bryan J. Matthews ◽  
David J Waxman
Keyword(s):  
Gene Expression ◽  
Growth Hormone ◽  
Sex Differences ◽  
Genetic Variants ◽  
Mouse Liver ◽  
Regulatory Elements ◽  
Individual Variability ◽  
Sex Bias ◽  
Mouse Strains ◽  
Strain Dependent

Sex differences in gene expression are widespread in the liver, where a large number of autosomal factors act in tandem with growth hormone signaling to regulate individual variability of sex differences in liver metabolism and disease. Here, we compare hepatic transcriptomic and epigenetic profiles of mouse strains C57Bl/6J and CAST/EiJ, representing two subspecies separated by 0.5-1 million years of evolution, to elucidate the actions of genetic factors regulating liver sex differences. We identify 144 protein coding genes and 78 lncRNAs showing strain-conserved sex bias; many have gene ontologies relevant to liver function, are more highly liver-specific and show greater sex bias, and are more proximally regulated than genes whose sex bias is strain-dependent. The strain-conserved genes include key growth hormone-dependent transcriptional regulators of liver sex bias; however, three other transcription factors, Trim24 , Tox , and Zfp809, lose sex-biased expression in CAST/EiJ mouse liver. To elucidate these strain specificities in expression, we characterized the strain-dependence of sex-biased chromatin opening and enhancer marks at cis regulatory elements (CREs) within expression quantitative trait loci (eQTL) regulating liver sex-biased genes. Strikingly, 208 of 286 eQTLs with strain-specific, sex-differential effects on expression were associated with a complete gain, loss, or reversal of expression sex differences between strains. Moreover, 166 of the 286 eQTLs were linked to the strain-specific gain or loss of localized sex-biased CREs. Remarkably, a subset of these CREs lacked strain-specific genetic variants yet showed coordinated, strain-dependent sex-biased epigenetic regulation. Thus, we directly link hundreds of strain-specific genetic variants to the high variability in CRE activity and expression of sex-biased genes, and uncover underlying genetically-determined epigenetic states controlling liver sex bias in genetically diverse mouse populations.

scholarly journals Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model

PLoS Genetics ◽  
2021 ◽  
Vol 17 (11) ◽  
pp. e1009588
Author(s):  
Bryan J. Matthews ◽  
Tisha Melia ◽  
David J. Waxman
Keyword(s):  
Gene Expression ◽  
Growth Hormone ◽  
Sex Differences ◽  
Genetic Variants ◽  
Mouse Liver ◽  
Regulatory Elements ◽  
Individual Variability ◽  
Sex Bias ◽  
Mouse Strains ◽  
Strain Dependent

Sex differences in gene expression are widespread in the liver, where many autosomal factors act in tandem with growth hormone signaling to regulate individual variability of sex differences in liver metabolism and disease. Here, we compare hepatic transcriptomic and epigenetic profiles of mouse strains C57BL/6J and CAST/EiJ, representing two subspecies separated by 0.5–1 million years of evolution, to elucidate the actions of genetic factors regulating liver sex differences. We identify 144 protein coding genes and 78 lncRNAs showing strain-conserved sex bias; many have gene ontologies relevant to liver function, are more highly liver-specific and show greater sex bias, and are more proximally regulated than genes whose sex bias is strain-dependent. The strain-conserved genes include key growth hormone-dependent transcriptional regulators of liver sex bias; however, three other transcription factors, Trim24, Tox, and Zfp809, lose their sex-biased expression in CAST/EiJ mouse liver. To elucidate the observed strain specificities in expression, we characterized the strain-dependence of sex-biased chromatin opening and enhancer marks at cis regulatory elements (CREs) within expression quantitative trait loci (eQTL) regulating liver sex-biased genes. Strikingly, 208 of 286 eQTLs with strain-specific, sex-differential effects on expression were associated with a complete gain, loss, or reversal of the sex differences in expression between strains. Moreover, 166 of the 286 eQTLs were linked to the strain-dependent gain or loss of localized sex-biased CREs. Remarkably, a subset of these CREs apparently lacked strain-specific genetic variants yet showed coordinated, strain-dependent sex-biased epigenetic regulation. Thus, we directly link hundreds of strain-specific genetic variants to the high variability in CRE activity and expression of sex-biased genes and uncover underlying genetically-determined epigenetic states controlling liver sex bias in genetically diverse mouse populations.

scholarly journals E2f3a and E2f3b Contribute to the Control of Cell Proliferation and Mouse Development

2008 ◽  
Vol 29 (2) ◽  
pp. 414-424 ◽  
Author(s):  
Jean-Leon Chong ◽  
Shih-Yin Tsai ◽  
Nidhi Sharma ◽  
Rene Opavsky ◽  
Richard Price ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Cell Proliferation ◽  
Cell Cycle Progression ◽  
Specific Gene ◽  
Mouse Development ◽  
Double Knockout ◽  
Proliferation And Apoptosis ◽  
The Individual ◽  
Redundant Functions

ABSTRACT The E2f3 locus encodes two Rb-binding gene products, E2F3a and E2F3b, which are differentially regulated during the cell cycle and are thought to be critical for cell cycle progression. We targeted the individual inactivation of E2f3a or E2f3b in mice and examined their contributions to cell proliferation and development. Chromatin immunoprecipitation and gene expression experiments using mouse embryo fibroblasts deficient in each isoform showed that E2F3a and E2F3b contribute to G1/S-specific gene expression and cell proliferation. Expression of E2f3a or E2f3b was sufficient to support E2F target gene expression and cell proliferation in the absence of other E2F activators, E2f1 and E2f2, suggesting that these isoforms have redundant functions. Consistent with this notion, E2f3a −/− and E2f3b −/− embryos developed normally, whereas embryos lacking both isoforms (E2f3 −/−) died in utero. We also find that E2f3a and E2f3b have redundant and nonredundant roles in the context of Rb mutation. Analysis of double-knockout embryos suggests that the ectopic proliferation and apoptosis in Rb −/− embryos is mainly mediated by E2f3a in the placenta and nervous system and by both E2f3a and E2f3b in lens fiber cells. Together, we conclude that the contributions of E2F3a and E2F3b in cell proliferation and development are context dependent.

scholarly journals Starvation resistance and tissue-specific gene expression of stress-related genes in a naturally inbred ant population

2016 ◽  
Vol 3 (4) ◽  
pp. 160062 ◽  
Author(s):  
Nick Bos ◽  
Unni Pulliainen ◽  
Liselotte Sundström ◽  
Dalial Freitak
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
Specific Gene ◽  
Starvation Resistance ◽  
Specific Expression ◽  
Tissue Specific ◽  
Trade Offs ◽  
Stress Related Genes ◽  
The Individual ◽  
Different Tissues

Starvation is one of the most common and severe stressors in nature. Not only does it lead to death if not alleviated, it also forces the starved individual to allocate resources only to the most essential processes. This creates energetic trade-offs which can lead to many secondary challenges for the individual. These energetic trade-offs could be exacerbated in inbred individuals, which have been suggested to have a less efficient metabolism. Here, we studied the effect of inbreeding on starvation resistance in a natural population of Formica exsecta ants, with a focus on survival and tissue-specific expression of stress, metabolism and immunity-related genes. Starvation led to large tissue-specific changes in gene expression, but inbreeding had little effect on most of the genes studied. Our results illustrate the importance of studying stress responses in different tissues instead of entire organisms.

scholarly journals Recovering genomes and phenotypes using allele-specific gene expression

2020 ◽  
Author(s):  
Gamze Gürsoy ◽  
Nancy Lu ◽  
Sarah Wagner ◽  
Mark Gerstein
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Recent Increase ◽  
Variant Information ◽  
Allele Specific ◽  
The Individual

AbstractWith the recent increase in RNA sequencing efforts using large cohorts of individuals, studying allele-specific gene expression is becoming increasingly important. Here, we report that, despite not containing explicit variant information, a list of allele-specific gene names of an individual is enough to recover key variants and link the individual back to their genome or phenotype. This creates a privacy conundrum.

Genomic editing of intronic enhancers unveils their role in fine-tuning tissue-specific gene expression in Arabidopsis thaliana

2021 ◽  
Author(s):  
Fanli Meng ◽  
Hainan Zhao ◽  
Bo Zhu ◽  
Tao Zhang ◽  
Mingyu Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transcriptional Repression ◽  
Regulation Of Gene Expression ◽  
Fine Tuning ◽  
Specific Gene ◽  
Open Chromatin ◽  
Floral Tissue ◽  
Deletion Lines ◽  
A Genome

Abstract Enhancers located in introns are abundant and play a major role in the regulation of gene expression in mammalian species. By contrast, the functions of intronic enhancers in plants have largely been unexplored and only a handful of plant intronic enhancers have been reported. We performed a genome-wide prediction of intronic enhancers in Arabidopsis thaliana using open chromatin signatures based on DNase I sequencing. We identified 941 candidate intronic enhancers associated with 806 genes in seedling tissue and 1,271 intronic enhancers associated with 1,069 genes in floral tissue. We validated the function of 15 of 21 (71%) of the predicted intronic enhancers in transgenic assays using a reporter gene. We also created deletion lines of three intronic enhancers associated with two different genes using CRISPR/Cas. Deletion of these enhancers, which span key transcription factor binding sites, did not abolish gene expression but caused varying levels of transcriptional repression of their cognate genes. Remarkably, the transcriptional repression of the deletion lines occurred at specific developmental stages and resulted in distinct phenotypic effects on plant morphology and development. Clearly, these three intronic enhancers are important in fine-tuning tissue- and development-specific expression of their cognate genes.

Increased Thrombosis in Male Versus Female Mice Is Mediated by Pulsatile Growth Hormone Secretion Possibly through Inhibition of TFPI Expression in the Vasculature.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 266-266
Author(s):  
Joshua H. Wong ◽  
Robert E. Levy ◽  
Jonathan Dukes ◽  
Sara A. Mason ◽  
Brandon Sos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Growth Hormone ◽  
Sex Differences ◽  
Median Survival ◽  
Growth Hormone Secretion ◽  
Gene Copy ◽  
Sexually Dimorphic ◽  
Liver Protein ◽  
Gh Secretion ◽  
Liver Gene

Abstract Clinical reports suggest significant sex differences in risk for thrombosis-related diseases such as myocardial infarction, stroke, and venous thromboembolism. However, little is known about mechanism for such differences. There is a well-described sexual dimorphism in liver protein synthesis that is growth hormone (GH) dependent. GH secretion from the pituitary is itself highly sexually dimorphic with males (M) secreting in a pulsatile (P) and females (F) a continuous (C) fashion. These patterns induce M- and F-specific signatures of liver gene expression. In the past, we and others have observed significant sex differences in murine thrombosis models. Given that most coagulation proteases and inhibitors are synthesized or modified in the liver, we aimed to test whether sex-specific GH secretion patterns contribute to the observed sex differences in thrombosis. We measured whole blood clotting times (WCT), thrombosis susceptibility in the thromboplastin-mediated pulmonary embolism (PE) model, and hemostasis in the tail bleeding time (BT) model in M and F control (WT) and GH-deficient “little” (LIT) mice. We observed that WT Fs had longer WCTs (mean time 61.38 vs. 56.72 sec) and were significantly protected in the PE model (median survival 232.5 vs 165 sec) as compared to M. There were no differences in the BT model across all experiments. Interestingly, F and M LIT animals both had significantly prolonged WCTs (67.56 and 67.30 sec, respectively) and were substantially protected in the PE model (median survival 900 and 1200 sec) as compared to WT. Next, LIT animals were injected twice daily with GH to simulate the P pattern of GH secretion (LIT+). This resulted in a significant shortening of the F and M WCTs back to WT M levels (53.16 and 50.97 sec). A group of F WT animals were also injected with M pattern GH (WT+). This too resulted in significant shortening of the F WCTs (54.10 sec). To explore for possible mechanisms underlying these differences, we measured activity of coagulation factors II, V, VII, VIII, IX, X, and XI. The average of all factor activity levels was significantly higher in WT M vs F (100 vs. 81.99%), significantly lower and in both M and F LIT (60.85 and 57.97%), and increased to WT M levels in M and F LIT+ animals (106.6 and 99%). To determine whether these changes were mediated by changes in liver gene expression, we measured a panel of 30 coagulation protease and inhibitor genes in liver and vascular tissue by Taqman®. Surprisingly, we found no significant differences in coagulation factor expression, but found that expression of TFPI was significantly increased in F vs M WT vasculature (9431 vs. 7678 gene copy number (GCN)). Expression was increased in M and F LIT animals (10350 and 11710 GCN) and fell to below WT levels in M and F LIT+ animals (4534 and 4194 GCN). These results indicate that sex differences in thrombosis in mice are at least in part mediated by sex differences in GH secretion with F mice relatively protected as compared to M. M and F GH-deficient LIT mice are similarly protected as compared to WT M. Repletion of GH in a P pattern reverts M and F LIT and F WT mice to WT M levels. Finally, P GH secretion may promote increased thrombosis through inhibition of TFPI in the vasculature. This represents a novel mechanism underlying these sex-differences in thrombosis mediated by sexually dimorphic GH secretion and its effect on regulation of TFPI in the vasculature.

scholarly journals Testosterone-mediated regulation of mouse renal cytochrome P-450 isoenzymes

1990 ◽  
Vol 266 (3) ◽  
pp. 675-681 ◽  
Author(s):  
C J Henderson ◽  
A R Scott ◽  
C S Yang ◽  
C R Wolf
Keyword(s):  
Gene Expression ◽  
Growth Hormone ◽  
Sex Differences ◽  
Metabolic Activation ◽  
Gene Families ◽  
Mouse Kidney ◽  
Environmental Chemicals ◽  
Carcinogenic Effects ◽  
Cytochrome P 450 ◽  
Androgen Levels

We have studied the extent to which mouse renal cytochrome P-450 isoenzymes are sexually differentiated, and the factor(s) regulating this dimorphism. Intriguingly, sex differences were not seen in the expression of a single cytochrome P-450 enzyme, but were observed in the expression of all P-450 isoenzymes detectable, encoded by six gene families or sub-families. This effect was mediated by testosterone, which had the capacity to both induce and repress P-450 gene expression, and which was independent of growth hormone. The changes in protein content were mirrored in all but one case by changes in the levels of mRNA, indicating that these genes contain hormone-responsive elements. These findings are consistent with numerous reports of sex differences in the susceptibility of the mouse kidney to the toxic and carcinogenic effects of drugs and environmental chemicals, many of which are metabolized to cytotoxic products by the cytochrome P-450-dependent mono-oxygenases. These data imply that circulating androgen levels will be an important factor in susceptibility of the kidney to toxic or carcinogenic compounds which require metabolic activation.

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