DNA methylation status of cyp17-II gene correlated with its expression pattern and reproductive endocrinology during ovarian development stages of Japanese flounder (Paralichthys olivaceus)

DNA Methylation Analysis Reveals Potential Mechanism in Takifugu rubripes Against Cryptocaryon irritans Infection

Takifugu rubripes (T. rubripes) is a valuable commercial fish, and Cryptocaryon irritans (C. irritans) has a significant impact on its aquaculture productivity. DNA methylation is one of the earliest discovered ways of gene epigenetic modification and also an important form of modification, as well as an essential type of alteration that regulates gene expression, including immune response. To further explore the anti-infection mechanism of T. rubripes in inhibiting this disease, we determined genome-wide DNA methylation profiles in the gill of T. rubripes using whole-genome bisulfite sequencing (WGBS) and combined with RNA sequence (RNA-seq). A total of 4659 differentially methylated genes (DMGs) in the gene body and 1546 DMGs in the promoter between the infection and control group were identified. And we identified 2501 differentially expressed genes (DEGs), including 1100 upregulated and 1401 downregulated genes. After enrichment analysis, we identified DMGs and DEGs of immune-related pathways including MAPK, Wnt, ErbB, and VEGF signaling pathways, as well as node genes prkcb, myca, tp53, and map2k2a. Based on the RNA-Seq results, we plotted a network graph to demonstrate the relationship between immune pathways and functional related genes, in addition to gene methylation and expression levels. At the same time, we predicted the CpG island and transcription factor of four immune-related key genes prkcb and mapped the gene structure. These unique discoveries could be helpful in the understanding of C. irritans pathogenesis, and the candidate genes screened may serve as optimum methylation-based biomarkers that can be utilized for the correct diagnosis and therapy T. rubripes in the development of the ability to resist C. irritans infection.

Molecular and Epigenetic Control of Aldosterone Synthase, CYP11B2 and 11-Hydroxylase, CYP11B1

Aldosterone and cortisol serve important roles in the pathogenesis of cardiovascular diseases and metabolic disorders. Epigenetics is a mechanism to control enzyme expression by genes without changing the gene sequence. Steroid hormone synthase gene expression is regulated by transcription factors specific to each gene, and methylation has been reported to be involved in steroid hormone production and disease. Angiotensin II or potassium regulates the aldosterone synthase gene, CYP11B2. The adrenocorticotropic hormone controls the 11b-hydroxylase, CYP11B1. DNA methylation negatively controls the CYP11B2 and CYP11B1 expression and dynamically changes the expression responsive to continuous stimulation of the promoter gene. Hypomethylation status of the CYP11B2 promoter region is seen in aldosterone-producing adenomas. Methylation of recognition sites of transcription factors, including cyclic AMP responsive element binding protein 1 or nerve growth factor-induced clone B, diminish their DNA-binding activity. A methyl-CpG-binding protein 2 cooperates directly with the methylated CpG dinucleotides of CYP11B2. A low-salt diet, treatment with angiotensin II, and potassium increase the CYP11B2 mRNA levels and induce DNA hypomethylation in the adrenal gland. A close association between a low DNA methylation ratio and an increased CYP11B1 expression is seen in Cushing's adenoma and aldosterone-producing adenoma with autonomous cortisol secretion. Epigenetic control of CYP11B2 or CYP11B1 plays an important role in autonomic aldosterone or cortisol synthesis.

DNA methylation mediates gonadal development via regulating the expression levels of cyp19a1a in loach Misgurnus anguillicaudatus

DNA methylation-mediated transcriptional regulation has been considered to significantly impact some steroidogenic enzyme genes expression. To uncover the roles of DNA methylation on the regulation of aromatase gene expression during gametogenesis in Misgurnus anguillicaudatus, the expression profiles and cellular localization of cyp19a1a and cyp19a1b were analyzed, and the landscape of DNA methylation dynamics was investigated. We found that cyp19a1a was predominantly expressed in granulosa cells of oocytes, while cyp19a1b expression was enriched in radial glial cells of the forebrain. In ovary, cyp19a1a was highly expressed until the vitellogenesis stage. The average methylation levels, especially for two CpG sites within the cAMP response element, were negatively correlated with cyp19a1a expression levels, indicating that methylation could regulate cyp19a1a transcriptional activity by modulating the binding efficiency of cAMP to its response elements. Compared with in ovary, cyp19a1a showed lower expression in testis but was hypermethylated. Cyp19a1b in female brain weakly expressed before the vitellogenesis stage, but significantly elevated at the maturation stage. In both sexes, it maintained high methylation levels in brain despite the obvious fluctuation of the cyp19a1b expression. This study revealed that DNA methylation plays a key role in establishing cyp19a1a spatiotemporal expression patterns and thus mediates gonadal development in teleosts.

Multi-omics analysis reveals that natural hibernation is crucial for oocyte maturation in the female Chinese alligator

BACKGROUND

Hibernation in an appropriate environment not only is important for the survival of hibernators in winter, but also is crucial for breeding in the following season for many hibernating species. However, the genetic and epigenetic mechanism underlying this process remain unclear. In the current study, we performed an integrative multi-omics analysis of gonads collected from Chinese alligators that overwintered in wild cave and artificial warmroom to explore transcriptomic and epigenomic alternations in these organs.

RESULTS

The data revealed that in the breeding season, female alligators were more strongly affected in terms of gene expression than males by non-hibernation because of overwintering in a warm room, especially for genes related to oocyte maturation, and this effect commenced in winter with the downregulation of STAR, which is the rate limiting factor of steroid biosynthesis. Further, miRNAs were found to play essential roles in this negative effect of overwintering in the warm room on hibernation. The upregulated miRNAs likely were responsible for the suppression of oocyte maturation in the breeding season. Finally, DNA methylome changes, especially hypomethylation, were found to play an important role in the alterations in ovarian function-related gene expression induced by non-hibernation.

CONCLUSIONS

Our study revealed the crucial role of hibernation quality for oocyte maturation in the Chinese alligator and the underlying genetic and epigenetic mechanisms, and highlights the importance of habitat, and especially, the overwintering site, in the conservation of not only the Chinese alligator, but also other endangered hibernators.

Characterizing transcriptome in female scallop Chlamys farreri provides new insights into the molecular mechanisms of reproductive regulation during ovarian development and spawn

Bivalve mollusks are descendants of an early-Cambrian lineage and have successfully evolved unique strategies for reproduction. Nonetheless, the molecular mechanisms underlying reproductive regulation in mollusks remain to be elucidated. In this study, transcriptomes of ovary at four reproductive stages in female Chlamys farreri were characterized by RNA-Seq. Regarding signaling pathways, ECM-receptor interaction pathway, mTOR signaling pathway, Fanconi anemia pathway, FoxO signaling pathway, Wnt signaling pathway and Hedgehog signaling pathway were enriched during ovarian development processes. In addition, pathways related to energy metabolism such as Nitrogen metabolism and Arachidonic acid metabolism were enriched at spawn stage. Interestingly, Neuroactive ligand-receptor interaction was significantly enriched involved in ovarian development and spawn, and indicated the potential functions of nervous system on reproductive regulation in C. farreri. What's more, this study identified and characterized fourteen genes involved in "sex hormones synthesis and regulation", "ovarian development and spawn" and "maternal immunity" during the four reproductive stages in C. farreri. We determined that CYP17 uniquely affected gamete release by influencing the physiological balance among the steroid hormones and showed that receptors of the 5-HT and GABA neurotransmitters were tightly associated with ovarian maturation. Furthermore, to the best of our knowledge, this is the first study to report the maternal effect gene Zar1 in bivalve mollusks, likewise the maternal immunity genes displayed coordinated and cooperative expression during reproductive periods, which strengthened the environmental adaptation mechanisms of bivalves. Taken together, this study provides the first dynamic transcriptomic analysis of C. farreri at four key reproductive stages, which will assist in revealing the molecular mechanisms underlying bivalves on reproductive regulation in ovarian development and spawn.

Comparative analyses of the Sox9a-Amh-Cyp19a1a regulatory Cascade in Autotetraploid fish and its diploid parent

BACKGROUND

Autotetraploid Carassius auratus (4nRCC, 4n = 200, RRRR) was derived from the whole genome duplication of diploid red crucian carp (Carassius auratus red var.) (2nRCC, 2n = 100, RR). To investigate the genetic effects of tetraploidization, we analyzed DNA variation, epigenetic modification and gene expression changes in the Sox9a-Amh-Cyp19a1a regulatory cascade between 4nRCC and 2nRCC.

RESULTS

We found that the Sox9a gene contained two variants in 2nRCC and four variants in 4nRCC. Compared with that in 2nRCC, DNA methylation in the promoter regions of the Amh and Cyp19a1a genes in 4nRCC was altered by single nucleotide polymorphism (SNP) mutations, which resulted in the insertions and deletions of CpG sites, and the methylation levels of the Sox9a, Amh and Cyp19a1a genes increased after tetraploidization. The gene expression level of the Sox9a-Amh-Cyp19a1a regulatory cascade was downregulated in 4nRCC compared with that in 2nRCC.

CONCLUSION

The above results demonstrate that tetraploidization leads to significant changes in the genome, epigenetic modification and gene expression in the Sox9a-Amh-Cyp19a1a regulatory cascade; these findings increase the extant knowledge regarding the effects of polyploidization.

Methylation status and expression patterns of myomaker gene play important roles in postnatal development in the Japanese flounder (Paralichthys olivaceus)

Myomaker is a membrane protein that plays a crucial role in the fusion of myoblasts during muscle growth. DNA methylation, a significant factor, regulates gene expression. The aim of this study was to examine the methylation and mRNA expression patterns of the myomaker gene during 8 different postnatal developmental stages in the Japanese flounder (L: 7 days post hatch (dph); M1: 21 dph; M2: 28 dph; M3: 35 dph; J1: 90 dph; J2: 180 dph; A1: 24 months; A2: 36 months). Muscle tissue samples were taken from Japanese flounder at different postnatal development stages to measure the extent of DNA methylation and gene expression. Methylation level in the promoter and exon 1 of myomaker was measured using bisulfite sequencing, and the relative expression of myomaker during each developmental stage was measured by quantitative PCR. The relative expression levels of myomaker were up-regulated from stages L to M2, M3 to J2, and methylation of myomaker was negatively correlated with mRNA expression. Furthermore, the CpG site located at -26 bp in the promoter was the lowest methylated region in all developmental stages. These results offer a basis for understanding the mechanism by which myomaker regulates muscle formation during postnatal development.

Dynamic Expression and Regulation of Urotensin I and Corticotropin-Releasing Hormone Receptors in Ovary of Olive Flounder Paralichthys olivaceus

Urotensin I (UI), a fish corticotropin-releasing hormone (CRH) like peptide, has been found throughout vertebrate species that has great effects on adaptive physiology comprising stress-related responses, and osmotic regulation by binding with CRH type I receptor (CRHR1) and CRH type II receptor (CRHR2) in fish. Dynamic expression and regulation of UI and CRH receptors in the olive flounder ovarian follicle were studied so as to make further efforts to understand the role of UI in the development of teleost ovary. The results showed that stage-specific change in UI mRNA levels in ovarian follicles of olive flounder. UI and CRHR1 mRNA levels were higher in stage III follicles (300∼500 μm diameter) compared to stage II (90∼300 μm diameter) and IV (500∼800 μm diameter) follicles, however, the levels of CRHR2 mRNA were decreased in line with the ovarian development from stage II to stage IV. A strong signal of UI protein was observed in the follicular cells and oocyte in stage III and IV follicles by immunohistochemistry. In vitro treatment of olive flounder ovarian follicles with human chorionic gonadotropin (hCG) showed that the mRNA expression of UI increased significantly at low concentration and decreased at high concentration at 6 h, but the CRHR1 and CRHR2 mRNA did not change obviously. In addition, the results of incubation with 17α, 20β-dihydroxy-4-oregnen-3-one (DHP) show that UI and CRHR1 mRNA expression were elevated with increasing concentrations at 9 h. All above results indicated that UI and CRH receptors may have a vital effect on olive flounder ovarian development.

Uptake, depuration, dose estimation and effects in zebrafish exposed to Am-241 via dietary route

Zebrafish were chronically exposed to Am-241, an alpha-emitting radionuclide via daily consumption of an enriched artificial diet. Am-241 uptake was quantified in Danio rerio after 5 and 21 days of exposure via daily Am-spiked food ingestion and after 21 days of exposure followed by 5 days of depuration. Americium accumulates mostly in digestive tract, muscle, rest of the body but the accumulation levels and trophic transfer rate (0.033-0.013%) were low. Corresponding cumulative doses were calculated for the whole body (9 mGy) and for the digestive tract (42 mGy) with internal alpha radiation contributing to more than 99% of the total dose. Genotoxic effects (gamma-H2AX assay) and differential gene expressions of main biological functions were examined. Although fish were exposed to a low dose rate of 13 μGy h^-1, DNA integrity and gene expression linked to oxidative stress, hormonal signaling and spermatogenesis were altered after 21 days of Am-241 exposure. These results underline the higher toxicity of alpha emitter Am-241, as compared to other studies on gamma radiation exposure.

Primary males guide the femaleness through the regulation of testicular Dmrt1 and ovarian Cyp19a1a in protandrous black porgy

Controlling the development of the sexes is critically important for the broodstock management in aquaculture. Sex steroids are widely used for sex control of fish. However, hermaphroditic fish have a plastic sex, and a stable sex is difficult to maintain with sex steroids. We used the black porgy (Acanthopagrus schlegelii) as a model to understand the possible mechanism of sexual fate decision. Low exogenous estradiol (E2) induced male development. In contrast, high exogenous E2 induced the regression of the testis and the development of the ovary and resulted in an unstable expression of femaleness (passive femaleness, with ovaries containing only the primary oocytes). The removal of testicular tissue by surgery resulted in the early development of vitellogenic oocytes and active femaleness. Our data also demonstrated that the male-to-female sex change is blocked by the maintenance of male function with gonadotropin-induced dmrt1 expression in the testis. Furthermore, our data also indicated that ovarian cyp19a1a expression is regulated by the testis through epigenetic modifications. Therefore, the primary male guides the femaleness in the protandrous black porgy and the transition of sexual fate from male to female is determined by the status of the testicular tissue.

The DNA methylation status of MyoD and IGF-I genes are correlated with muscle growth during different developmental stages of Japanese flounder (Paralichthys olivaceus)

Many genes related to muscle growth modulate myoblast proliferation and differentiation and promote muscle hypertrophy. MyoD is a myogenic determinant that contributes to myoblast determination, and insulin-like growth factor 1 (IGF-I) interacts with MyoD to regulate muscle hypertrophy and muscle mass. In this study, we aimed to assess DNA methylation and mRNA expression patterns of MyoD and IGF-I during different developmental stages of Japanese flounder, and to examine the relationship between MyoD and IGF-I gene. DNA and RNA were extracted from muscles, and DNA methylation of MyoD and IGF-I promoter and exons was detected by bisulfite sequencing. The relative expression of MyoD and IGF-I was measured by quantitative polymerase chain reaction. IGF-I was measured by radioimmunoassay. Interestingly, the lowest expression of MyoD and IGF-I emerged at larva stage, and the mRNA expression was negatively associated with methylation. We hypothesized that many skeletal muscle were required to complete metamorphosis; thus, the expression levels of MyoD and IGF-I genes increased from larva stage and then decreased. The relative expression levels of MyoD and IGF-I exhibited similar patterns, suggesting that MyoD and IGF-I regulated muscle growth through combined effects. Changes in the concentrations of IGF-I hormone were similar to those of IGF-I gene expression. Our results the mechanism through which MyoD and IGF-I regulate muscle development and demonstrated that MyoD interacted with IGF-I to regulate muscle growth during different developmental stages.

Methylation of the genes ROD1, NLRC5, and HKR1 is associated with aging in Hainan centenarians

Background

Human aging is a hot topic in biology, and it has been associated with DNA methylation changes at specific genomic sites. We aimed to study the changes of DNA methylation at a single-CpG-site resolution using peripheral blood samples from centenarians.

Methods

Using Illumina 450 K Methylation BeadChip microarray assays, we carried out a pool-based, epigenome-wide investigation of DNA methylation of blood samples from 12 centenarians and 12 healthy controls. Differentially methylated cytosine-phosphate-guanosine (CpG) sites were selected for further pyrosequencing analysis of blood samples from 30 centenarians and 30 healthy controls.

Result

We identified a total of 31 high-confidence CpG sites with differential methylation profiles between the groups: 9 (29%) were hypermethylated and 22 (71%) were hypomethylated in centenarians. It was also found that hypermethylation of HKR1 and hypomethylation of ROD1 and NLRC5 genes strongly correlated with age in centenarians.

Conclusion

Our results indicate that the methylation profile combination of HKR1, ROD1, and NLRC5 could be a promising biomarker for aging in Hainan centenarians.

Electronic supplementary material

The online version of this article (10.1186/s12920-018-0334-1) contains supplementary material, which is available to authorized users.

Gonadal Transcriptome Analysis in Sterile Double Haploid Japanese Flounder

Sterility is a serious problem that can affect all bionts. In teleosts, double haploids (DHs) induced by mitogynogenesis are often sterile. This sterility severely restricts the further application of DHs for production of clones, genetic analysis, and breeding. However, sterile DH individuals are good source materials for investigation of the molecular mechanisms of gonad development, especially for studies into the role of genes that are indispensable for fish reproduction. Here, we used the Illumina sequencing platform to analyze the transcriptome of sterile female DH Japanese flounder in order to identify major genes that cause sterility and to provide a molecular basis for an intensive study of gonadal development in teleosts. Through sequencing, assembly, and annotation, we obtained 52,474 contigs and found that 60.7% of these shared homologies with existing sequences. A total of 1225 differentially expressed unigenes were found, including 492 upregulated and 733 downregulated genes. Gene Ontology and KEGG analyses showed that genes showing significant upregulation, such as CYP11A1, CYP11B2, CYP17, CYP21, HSD3β, bcl2l1, and PRLR, principally correlated with sterol metabolic process, steroid biosynthetic process, and the Jak-stat signaling pathway. The significantly downregulated genes were primarily associated with immune response, antigen processing and presentation, cytokine–cytokine receptor interaction, and protein digestion and absorption. Using a co-expression network analysis, we conducted a comprehensive comparison of gene expression in the gonads of fertile and sterile female DH Japanese flounder. Identification of genes showing significantly different expression will provide further insights into DH reproductive dysfunction and oocyte maturation processes in teleosts.

Steroids in teleost fishes: A functional point of view

Steroid hormones are involved in the regulation of a variety of processes like embryonic development, sex differentiation, metabolism, immune responses, circadian rhythms, stress response, and reproduction in vertebrates. Teleost fishes and humans show a remarkable conservation in many developmental and physiological aspects, including the endocrine system in general and the steroid hormone related processes in particular. This review provides an overview of the current knowledge about steroid hormone biosynthesis and the steroid hormone receptors in teleost fishes and compares the findings to the human system. The impact of the duplicated genome in teleost fishes on steroid hormone biosynthesis and perception is addressed. Additionally, important processes in fish physiology regulated by steroid hormones, which are most dissimilar to humans, are described. We also give a short overview on the influence of anthropogenic endocrine disrupting compounds on steroid hormone signaling and the resulting adverse physiological effects for teleost fishes. By this approach, we show that the steroidogenesis, hormone receptors, and function of the steroid hormones are reasonably well understood when summarizing the available data of all teleost species analyzed to date. However, on the level of a single species or a certain fish-specific aspect of physiology, further research is needed.

DNA methylation level of cyp19a1a and Foxl2 gene related to their expression patterns and reproduction traits during ovary development stages of Japanese flounder (Paralichthys olivaceus)

Foxl2 and cyp19a1a genes are crucial for the ovarian development, and Foxl2 could play a direct regulatory role on cyp19a1a transcription. In this study, we aimed to study DNA methylation status and mRNA expression patterns of Foxl2 and cyp19a1a genes during ovarian development of female Japanese flounder. The relative expression level of cyp19a1a and Foxl2 gene during the gonadal development stages was measured by quantitative PCR. Moreover, DNA methylation status in the promoter and coding regions of the two genes was detected by bisulfite sequencing. The estradiol-17β (E2) was measured by radioimmunoassay. The results showed low expression levels of cyp19a1a and Foxl2 genes in stages II and V, while the highest expression levels were detected in stage IV. The variation trend of the methylation level of all CpG sites in promoter and exon 1 of cyp19a1a gene and three CpG rich regions in coding region of Foxl2 gene was negatively associated with their expression levels during the ovarian development. In addition, two CpG sites in promoter and seven CpG sites in exon 1 of cyp19a1a were on the putative transcription factors binding sequence. Further studies showed that the forkhead domain, which is important for Foxl2 binding to cyp19a1a was located in the F1 and F2 region. These results provide a powerful theoretical basis for the regulatory mechanism on Foxl2 regulating cyp19a1a and promoting gonadal differentiation towards the female pathway, and further reveal that Foxl2 and cyp19a1a play a vital role in the female Japanese flounder gonad development.

Effects of atrazine and chlorpyrifos on DNA methylation in the liver, kidney and gill of the common carp (Cyprinus carpio L.)

Pesticide exposure has repeatedly been associated with cancers, although the molecular mechanisms behind this association are largely undetermined. Abnormal DNA methylation plays a key role in the process of some disease. However, little was known about the effect of pesticides on DNA methylation in the common carp. In this study, we investigated the mRNA levels of DNA methyltransferases (DNMTs) and methyl-CpG-binding protein DNA-binding domain protein 2 (MBD2) as well as the DNA methylation levels in the liver, kidney and gill of the common carp (Cyprinus carpio L.) after 40-d exposure to atrazine (ATR) and chlorpyrifos (CPF) alone or in combination, and a 40-d recovery period. Juvenile common carp were exposed to various concentrations of ATR (at concentrations of 4.28, 42.8 and 428μg/L), CPF (1.16, 11.6 and 116μg/L), and an ATR/CPF mixture (at concentrations of 1.13, 11.3 and 113μg/L). The results revealed that the levels of genomic DNA methylation decreased in all tissues after 40d of exposure to ATR and CPF either individually or in combination. Moreover, the mRNA expression of DNMTs was down-regulated in all treatment groups. In contrast, the mRNA expression of MBD2 was up-regulated. These results demonstrated that long-term exposure to ATR, CPF and ATR/CPF mixtures could disrupt genomic DNA. It might imply that DNA methylation is involved in the toxicity caused by ATR and CPF in the common carp.

Gonadal transcriptome analysis of male and female olive flounder (Paralichthys olivaceus)

Olive flounder (Paralichthys olivaceus) is an important commercially cultured marine flatfish in China, Korea, and Japan, of which female grows faster than male. In order to explore the molecular mechanism of flounder sex determination and development, we used RNA-seq technology to investigate transcriptomes of flounder gonads. This produced 22,253,217 and 19,777,841 qualified reads from ovary and testes, which were jointly assembled into 97,233 contigs. Among them, 23,223 contigs were mapped to known genes, of which 2,193 were predicted to be differentially expressed in ovary and 887 in testes. According to annotation information, several sex-related biological pathways including ovarian steroidogenesis and estrogen signaling pathways were firstly found in flounder. The dimorphic expression of overall sex-related genes provides further insights into sex determination and gonadal development. Our study also provides an archive for further studies of molecular mechanism of fish sex determination.

DNA methylation in the 5' flanking region of cytochrome P450 17 in adult rare minnow Gobiocypris rarus - tissue difference and effects of 17α-ethinylestradiol and 17α-methyltestoterone exposures

Cytochrome P450 17 (CYP17) plays a vital role in hormone production in the body. In our previous study, mRNA expression of cyp17a1 was regulated by endocrine disrupting chemicals in rare minnow Gobiocypris rarus. However, the mechanism underlying the regulation is unclear. In the present study, we aim to explore whether the differential expression of cyp17a1 in distinct tissues and the modulation of its expression upon 17α-ethinylestradiol (EE2) and 17α-methyltestoterone (MT) are related to the DNA methylation status in G. rarus. The 732-bp fragment of 5' flanking region of cyp17a1 gene was isolated in G. rarus. The bisulfite sequencing PCR result showed that DNA methylation levels in 5' flanking of cyp17a1 in the gonads were significantly lower than those in the brains, which is negatively related to its mRNA expression in the 2 tissues in the previous study. The 7-day EE2 exposure of 25 ng/L caused a significant increase of methylation levels of cyp17a1 gene and a significant decrease of its transcript in testis. While 100 ng/L MT exposure for 7 days caused a significant decrease of methylation levels of cyp17a1 gene and a significant increase of its transcript in the ovary. The present findings indicate that the methylation status of cyp17a1 gene is negatively correlated with its mRNA expression in response to EE2 and MT in G. rarus. We hypothesize that the regulation of cyp17a1 expression by EE2 and MT might attribute to the change of its DNA methylation status in G. rarus.

Gender-specific DNA methylome analysis of a Han Chinese longevity population

Human longevity is always a biological hotspot and so much effort has been devoted to identifying genes and genetic variations associated with longer lives. Most of the demographic studies have highlighted that females have a longer life span than males. The reasons for this are not entirely clear. In this study, we carried out a pool-based, epigenome-wide investigation of DNA methylation profiles in male and female nonagenarians/centenarians using the Illumina 450 K Methylation Beadchip assays. Although no significant difference was detected for the average methylation levels of examined CpGs (or probes) between male and female samples, a significant number of differentially methylated probes (DMPs) were identified, which appeared to be enriched in certain chromosome regions and certain parts of genes. Further analysis of DMP-containing genes (named DMGs) revealed that almost all of them are solely hypermethylated or hypomethylated. Functional enrichment analysis of these DMGs indicated that DNA hypermethylation and hypomethylation may regulate genes involved in different biological processes, such as hormone regulation, neuron projection, and disease-related pathways. This is the first effort to explore the gender-based methylome difference in nonagenarians/centenarians, which may provide new insights into the complex mechanism of longevity gender gap of human beings.