Epigenetic regulation of mammalian sex determination

Sex differences in the intergenerational link between maternal and neonatal whole blood DNA methylation: a genome-wide analysis in 2 birth cohorts

BACKGROUND

The mother-child inheritance of DNA methylation (DNAm) variations could contribute to the inheritance of disease susceptibility across generations. However, no study has investigated patterns of mother-child associations in DNAm at the genome-wide scale. It remains unknown whether there are sex differences in mother-child DNAm associations.

RESULTS

Using genome-wide DNAm profiling data (721,331 DNAm sites, including 704,552 on autosomes and 16,779 on the X chromosome) of 396 mother-newborn pairs (54.5% male) from the Boston Birth Cohort, we found significant sex differences in mother-newborn correlations in genome-wide DNAm patterns (Spearman's rho = 0.91-0.98; p = 4.0 × 10-8), with female newborns having stronger correlations. Sex differences in correlations were attenuated but remained significant after excluding X-chromosomal DNAm sites (Spearman's rho = 0.91-0.98; p = 0.035). Moreover, 89,267 DNAm sites (12.4% of all analyzed, including 88,051 [12.5% of analyzed] autosomal and 1,216 [7.2% of analyzed] X-chromosomal sites) showed significant mother-newborn associations in methylation levels, and the top autosomal DNAm sites had high heritability than the genome-wide background (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.92). Additionally, significant interactions between newborn sex and methylation levels were observed for 11 X-chromosomal and 4 autosomal DNAm sites that were mapped to genes that have been associated with sex-specific disease/traits or early development (e.g., EFHC2, NXY, ADCYAP1R1, and BMP4). Finally, 18,769 DNAm sites (14,482 [77.2%] on the X chromosome) showed mother-newborn differences in methylation levels that were significantly associated with newborn sex, and the top autosomal DNAm sites had relatively small heritability (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.23). These DNAm sites were mapped to 2,532 autosomal genes and 978 X-chromosomal genes with significant enrichment in pathways involved in neurodegenerative and psychological diseases, development, neurophysiological process, immune response, and sex-specific cancers. Replication analysis in the Isle of Wight birth cohort yielded consistent results.

CONCLUSION

In two independent birth cohorts, we demonstrated strong mother-newborn correlations in whole blood DNAm on both autosomes and ChrX, and such correlations vary substantially by sex. Future studies are needed to examine to what extent our findings contribute to developmental origins of pediatric and adult diseases with well-observed sex differences.

Epigenetic Studies for Evaluation of NPS Toxicity: Focus on Synthetic Cannabinoids and Cathinones

In the recent decade, numerous new psychoactive substances (NPSs) have been added to the illicit drug market. These are synthetized to mimic the effects of classic drugs of abuse (i.e., cannabis, cocaine, etc.), with the purpose of bypassing substance legislations and increasing the pharmacotoxicological effects. To date, research into the acute pharmacological effects of new NPSs is ongoing and necessary in order to provide an appropriate contribution to public health. In fact, multiple examples of NPS-related acute intoxication and mortality have been recorded in the literature. Accordingly, several in vitro and in vivo studies have investigated the pharmacotoxicological profiles of these compounds, revealing that they can cause adverse effects involving various organ systems (i.e., cardiovascular, respiratory effects) and highlighting their potential increased consumption risks. In this sense, NPSs should be regarded as a complex issue that requires continuous monitoring. Moreover, knowledge of long-term NPS effects is lacking. Because genetic and environmental variables may impact NPS responses, epigenetics may aid in understanding the processes behind the harmful events induced by long-term NPS usage. Taken together, “pharmacoepigenomics” may provide a new field of combined study on genetic differences and epigenetic changes in drug reactions that might be predictive in forensic implications.

DNA Methylation Difference between Female and Male Ussuri Catfish (Pseudobagrus ussuriensis) in Brain and Gonad Tissues

DNA methylation has been found to be involved in sex determination and differentiation in many aquaculture species. The Ussuri catfish (Pseudobagrus ussuriensis) is a popular aquaculture fish in China with high economic value in which male-biased sex dimorphism was observed in terms of body size and body weight. In this study, DNA methylation-sensitive RAD sequencing (Methyl-RAD) was used to explore the epigenetic difference between adult male and female samples in brain and gonad tissues. In brain tissues, 5,442,496 methylated cytosine sites were found and 9.94% of these sites were from symmetric CCGG or CCWGG sites. Among these sites, 321 differential DNA methylation sites (DMSs) in 171 genes were identified, while in gonad tissues, 4,043,053 methylated cytosines sites were found in total and 11.70% of them were from CCGG or CCWGG. Among these sites, 78 differential DNA methylation sites were found which were located in 64 genes. We also found several sex-determination genes among these differential methylated genes, such as amh, gsdf and hsd11b2 in brain tissues and slco3a1, socs2 and trim47 in gonad tissues. These results provided evidence for understanding the function of DNA methylation in the sex differentiation in Pseudobagrus ussuriensis, which further deepens the relationship between gene regulation and epigenetics.

Characterization, expression and CpG methylation analysis of Dmrt1 and its response to steroid hormone in blotched snakehead (Channa maculata)

Dmrt1 is an important transcriptional regulator that plays critical role in male gonadogenesis, testicular differentiation and development. In this study, Dmrt1 was cloned from blotched snakehead (Channa maculata), which is designated as CmDmrt1. CmDmrt1 encoded a putative protein with 293 amino acids and presented an extremely conserved DM domain. It was nearly expressed in the gonads, and the expression was more than 15 times higher in the testis than in the ovary. 1851 bp promoter sequence of CmDmrt1 was characterized and the methylation levels of the CpG sites were analyzed to detect sex-related differences. A significant negative correlation between CmDmrt1 expression and CpG methylation level of its promoter was found in the testis and ovary. During gonadal development, CmDmrt1 transcription displayed strong male-biased expression patterns, increased with the maturation of testis and reached the peak at 195 days after hatching (dah), which indicates a significant role of Dmrt1 in spermatogenesis. Steroid treatment could influence CmDmrt1 expression, and long-term 17β-estradiol (E2) treatment could induce the male-to-female secondary sex reversal (SSR), which resulted in the differentiated testis transformed to ovary or ovotestis. Meanwhile, CmDmrt1 expression was down-regulated to fairly low level in the ovary of the SSR XY fish, which was similar to that in normal XX females ovary. Our research illustrates that Dmrt1 is linked to testis differentiation and spermatogenesis in blotched snakehead, providing information for functional studies on sex differentiation and gonadal development of C. maculata, and scientific basis for the production practice of all-male snakehead breeding.

Testis Development

Production of sperm and androgens is the main function of the testis. This depends on normal development of both testicular somatic cells and germ cells. A genetic program initiated from the Y chromosome gene sex-determining region Y (SRY) directs somatic cell specification to Sertoli cells that orchestrate further development. They first guide fetal germ cell differentiation toward spermatogenic destiny and then take care of the full service to spermatogenic cells during spermatogenesis. The number of Sertoli cells sets the limits of sperm production. Leydig cells secrete androgens that determine masculine development. Testis development does not depend on germ cells; that is, testicular somatic cells also develop in the absence of germ cells, and the testis can produce testosterone normally to induce full masculinization in these men. In contrast, spermatogenic cell development is totally dependent on somatic cells. We herein review germ cell differentiation from primordial germ cells to spermatogonia and development of the supporting somatic cells. Testicular descent to scrota is necessary for normal spermatogenesis, and cryptorchidism is the most common male birth defect. This is a mild form of a disorder of sex differentiation. Multiple genetic reasons for more severe forms of disorders of sex differentiation have been revealed during the last decades, and these are described along with the description of molecular regulation of testis development.

Characterization of deoxyribonucleic methylation and transcript abundance of sex-related genes during tempera ture-dependent sex determination in Mauremys reevesii†

A number of genes relevant for sex determination have been found in species with temperature-dependent sex determination. Epigenetics play a key role in sex determination, but characterization of deoxyribonucleic acid methylation of sex-related genes on temperature-dependent sex determination remains unclear. Mauremys reevesii is a typical species with temperature-dependent sex determination. In this study, we analyzed the Cytosine Guanine (CpG) methylation status of the proximal promoters, the messenger ribonucleic acid expression patterns and the correlation between methylation and expression levels of Aromatase, Forkhead box protein L2, Doublesex and mab3-related transcription factor 1, sex-determining region on Y chromosome-box 9, and anti-Müllerian hormone, which are key genes in sex determination in other species. We also analyzed the expression level of genes that encode enzymes involved in methylation and demethylation. The expression levels of Aromatase and Forkhead box protein L2 at the female producing temperature were higher than those at the male producing temperature; the expression levels of Doublesex and mab3-related transcription factor 1, sex-determining region on Y chromosome-box 9, and anti-Müllerian hormone were higher at MPT. The expression of some genes involved in methylation and demethylation is significantly different between male producing temperature and female producing temperature. The expression of messenger ribonucleic acid of genes involved in deoxyribonucleic acid methylation and demethylation affected by temperature, together with other factors, may change the methylation level of the regulatory regions of sex-related genes, which may further lead to temperature-specific expression of sex-related genes, and eventually affect the differentiation of the gonads.

Forensic Epigenetic Analysis: The Path Ahead

Unlike DNA fingerprinting, which scores for differences in the genome that are phenotype neutral, epigenetic variations are gaining importance in forensic investigations. Methylation of DNA has a broad range of effects on the lifestyle, health status, and physical appearance of individuals. DNA methylation profiling of forensic samples is useful in determination of the cell or tissue type of the DNA source and also for estimation of age. The quality and quantity of the biosample available from the crime scene limits the possible number of DNA methylation tests and the selection of the technology that can be used. Several techniques have been used for DNA methylation analysis for epigenetic investigations of forensic biological samples. However, novel techniques are needed for multiplex analysis of epigenetic markers as the techniques that are currently available require a large amount of high-quality DNA and are also limited in their multiplexing capacities that are often insufficient to fully resolve a forensic query of interest.

Molecular identification of dmrt1 and its promoter CpG methylation in correlation with gene expression during gonad development in Culter alburnus

Dmrt1, a member of the Dmrt family, is an important transcription regulator of gender determination. To study the biological function of dmrt1 in sexual differentiation and its potential implication in breeding technology, we obtained the full-length cDNA and proximal promoter sequence of dmrt1 in Culter alburnus, and analyzed the impact of promoter CpG methylation on the gene expression pattern of dmrt1 during gonad development. Dmrt1 was 922 bp in length and consisted a 150 bp 5'-UTR, a 28 bp 3'-UTR, and a 744 bp open reading frame (ORF). Based on the coding sequence of the dmrt1 gene, the deduced amino acid sequence was detected, and the protein structure of this gene was predicted in C. alburnus. The results indicate that the structure and function of dmrt1 were highly conservative compared to other vertebrates. The expression level of dmrt1 mRNA in different tissues was explored by qRT-PCR, which was only highly expressed in the testes and almost undetectable in other tissues. The CpG methylation pattern of the dmrt1 promoter was studied using DNA sequencing of sodium bisulfite in adult testes and ovaries, and it was found that dmrt1 promoter CpGs were not methylated in the testes, whereas hypermethylated in the ovaries. These findings demonstrate that DNA methylation can regulate sexual dimorphic expression of dmrt1, and therefore epigenetic modifications may play a critical role in the gonad differentiation of C. alburnus.

At the Crossroads of Fate-Somatic Cell Lineage Specification in the Fetal Gonad

The reproductive endocrine systems are vastly different between males and females. This sexual dimorphism of the endocrine milieu originates from sex-specific differentiation of the somatic cells in the gonads during fetal life. Most gonadal somatic cells arise from the adrenogonadal primordium. After separation of the adrenal and gonadal primordia, the gonadal somatic cells initiate sex-specific differentiation during gonadal sex determination with the specification of the supporting cell lineages: Sertoli cells in the testis vs granulosa cells in the ovary. The supporting cell lineages then facilitate the differentiation of the steroidogenic cell lineages, Leydig cells in the testis and theca cells in the ovary. Proper differentiation of these cell types defines the somatic cell environment that is essential for germ cell development, hormone production, and establishment of the reproductive tracts. Impairment of lineage specification and function of gonadal somatic cells can lead to disorders of sexual development (DSDs) in humans. Human DSDs and processes for gonadal development have been successfully modeled using genetically modified mouse models. In this review, we focus on the fate decision processes from the initial stage of formation of the adrenogonadal primordium in the embryo to the maintenance of the somatic cell identities in the gonads when they become fully differentiated in adulthood.

Dmrt1 induces the male pathway in a turtle species with temperature-dependent sex determination

The molecular mechanism underlying temperature-dependent sex determination (TSD) has been a long-standing mystery; in particular, the thermosensitive genetic triggers for gonadal sex differentiation are largely unknown. Here, we have characterized a conserved DM domain gene, Dmrt1, in the red-eared slider turtle Trachemys scripta (T. scripta), which exhibits TSD. We found that Dmrt1 has a temperature-dependent, sexually dimorphic expression pattern, preceding gonadal sex differentiation, and is capable of responding rapidly to temperature shifts and aromatase inhibitor treatment. Most importantly, loss- and gain-of-function analyses provide solid evidence that Dmrt1 is both necessary and sufficient to initiate male development in T. scripta Furthermore, the DNA methylation dynamics of the Dmrt1 promoter are tightly correlated with temperature and could mediate the impact of temperature on sex determination. Collectively, our findings demonstrate that Dmrt1 is a candidate master male sex-determining gene in this TSD species, consistent with the idea that DM domain genes are conserved during the evolution of sex determination mechanisms.