Whole methylomes reveal high-altitude-associated methylation at hypoxia and pigmentation genes in South American Indigenous populations

Towards the full spectrum of genes for human skin colour.

Measuring stress-induced DNA methylation in apomictic Dandelions

DNA methylation (DNAm) is one of the major epigenetic mechanisms in humans and is important in diverse cellular processes. The variation of DNAm in the human population is related to both genetic and environmental factors. However, the DNAm profiles have not been investigated in the Chinese population of diverse ethnicities. Here, we performed double-strand bisulfite sequencing (DSBS) for 32 Chinese individuals representing four major ethnic groups including Han Chinese, Tibetan, Zhuang, and Mongolian. We identified a total of 604,649 SNPs and quantified DNAm at more than 14 million CpGs in the population. We found global DNAm-based epigenetic structure is different from the genetic structure of the population, and ethnic difference only partially explains the variation of DNAm. Surprisingly, non-ethnic-specific DNAm variations showed stronger correlation with the global genetic divergence than these ethnic-specific DNAm. Differentially methylated regions (DMRs) among these ethnic groups were found around genes in diverse biological processes. Especially, these DMR-genes between Tibetan and non-Tibetans were enriched around high-altitude genes including EPAS1 and EGLN1, suggesting DNAm alteration plays an important role in high-altitude adaptation. Our results provide the first batch of epigenetic maps for Chinese populations and the first evidence of the association of epigenetic changes with Tibetans' high-altitude adaptation.

BackgroundDNA methylation, an important epigenetic mark, is well known for its regulatory role in gene expression, especially the negative correlation in the promoter region. However, its correlation with gene expression across genome at human population level has not been well studied. In particular, it is unclear if genome-wide DNA methylation profile of an individual can predict her/his gene expression profile. Previous studies were mostly limited to association analyses between single CpG site methylation and gene expression. It is not known whether DNA methylation of a gene has enough prediction power to serve as a surrogate for gene expression in existing human study cohorts with DNA samples other than RNA samples.ResultsWe examined DNA methylation in the gene region for predicting gene expression across individuals in non-cancer tissues of three human population datasets, adipose tissue of the Multiple Tissue Human Expression Resource Projects (MuTHER), peripheral blood mononuclear cell (PBMC) from Asthma and normal control study participates, and lymphoblastoid cell lines (LCL) from healthy individuals. Three prediction models were investigated, single linear regression, multiple linear regression, and least absolute shrinkage and selection operator (LASSO) penalized regression. Our results showed that LASSO regression has superior performance among these methods. However, the prediction power is generally low and varies across datasets. Only 30 and 42 genes were found to have cross-validation R2 greater than 0.3 in the PBMC and Adipose datasets, respectively. A substantially larger number of genes (258) were identified in the LCL dataset, which was generated from a more homogeneous cell line sample source. We also demonstrated that it gives better prediction power not to exclude any CpG probe due to cross hybridization or SNP effect.ConclusionIn our three population analyses DNA methylation of CpG sites at gene region have limited prediction power for gene expression across individuals with linear regression models. The prediction power potentially varies depending on tissue, cell type, and data sources. In our analyses, the combination of LASSO regression and all probes not excluding any probe on the methylation array provides the best prediction for gene expression.

Understanding natural epigenetic variation

In recent years, research has gradually uncovered the mechanisms of animal adaptation to hypoxic conditions in different altitude environments, particularly at the genomic level. However, past genomic studies on high-altitude adaptation have often not delved deeply into the differences between varying altitude levels. This study conducted whole-genome sequencing on 60 Tibetan sheep (Medium Altitude Group (MA): 20 Tao sheep (TS) at 2887 m, High Altitude Group (HA): 20 OuLa sheep (OL) at 3501 m, and Ultra-High Altitude Group (UA): 20 AWang sheep (AW) at 4643 m) from different regions of the Tibetan Plateau in China to assess their responses under varying conditions. Population genetic structure analysis revealed that the three groups are genetically independent, but the TS and OL groups have experienced gene flow with other northern Chinese sheep due to geographical factors. Selection signal analysis identified FGF10, MMP14, SLC25A51, NDUFB8, ALAS1, PRMT1, PRMT5, and HIF1AN as genes associated with ultra-high-altitude hypoxia adaptation, while HMOX2, SEMA4G, SLC16A2, SLC22A17, and BCL2L2 were linked to high-altitude hypoxia adaptation. Functional analysis showed that ultra-high-altitude adaptation genes tend to influence physiological mechanisms directly affecting oxygen uptake, such as lung development, angiogenesis, and red blood cell formation. In contrast, high-altitude adaptation genes are more inclined to regulate mitochondrial DNA replication, iron homeostasis, and calcium signaling pathways to maintain cellular function. Additionally, the functions of shared genes further support the adaptive capacity of Tibetan sheep across a broad geographic range, indicating that these genes offer significant selective advantages in coping with oxygen scarcity. In summary, this study not only reveals the genetic basis of Tibetan sheep adaptation to different altitudinal conditions but also highlights the differences in gene regulation between ultra-high- and high-altitude adaptations. These findings offer new insights into the adaptive evolution of animals in extreme environments and provide a reference for exploring adaptation mechanisms in other species under hypoxic conditions.

High-altitude environments (>2,500 m) provide scientists with a natural laboratory to study the physiological and genetic effects of low ambient oxygen tension on human populations. One approach to understanding how life at high altitude has affected human metabolism is to survey genome-wide datasets for signatures of natural selection. In this work, we report on a study to identify selection-nominated candidate genes involved in adaptation to hypoxia in one highland group, Andeans from the South American Altiplano. We analysed dense microarray genotype data using four test statistics that detect departures from neutrality. Using a candidate gene, single nucleotide polymorphism-based approach, we identified genes exhibiting preliminary evidence of recent genetic adaptation in this population. These included genes that are part of the hypoxia-inducible transcription factor (HIF) pathway, a biochemical pathway involved in oxygen homeostasis, as well as three other genomic regions previously not known to be associated with high-altitude phenotypes. In addition to identifying selection-nominated candidate genes, we also tested whether the HIF pathway shows evidence of natural selection. Our results indicate that the genes of this biochemical pathway as a group show no evidence of having evolved in response to hypoxia in Andeans. Results from particular HIF-targeted genes, however, suggest that genes in this pathway could play a role in Andean adaptation to high altitude, even if the pathway as a whole does not show higher relative rates of evolution. These data suggest a genetic role in high-altitude adaptation and provide a basis for genotype/phenotype association studies that are necessary to confirm the role of putative natural selection candidate genes and gene regions in adaptation to altitude.

Effects of DNA Methylation on Progression to Interstitial Fibrosis and Tubular Atrophy in Renal Allograft Biopsies: A Multi-Omics Approach.

The gut microbiota is a complex and essential system organ that plays an integrative role in balancing key vital functions in the host. Knowledge of the impact of altitude on the gut microbiota of European mouflon (Ovis orientalis musimon) and blue sheep (Pseudois nayaur) is currently limited. In this study, we compared the characteristics of gut microbiota in 5 mouflon at low altitude (K group), 4 mouflon at high altitude (L group), 4 blue sheep at low altitude (M group), and 4 blue sheep at high altitude (N group). The V3–V4 region of the 16S rRNA gene was analyzed using high-throughput sequencing. Analyses based on the operational taxonomic units showed significant changes in the gut microbial communities between groups at different altitudes. At the phylum level, groups at the high altitudes had a higher relative abundance of Firmicutes and a lower relative abundance of Bacteroidetes than those at the low altitudes. A higher Firmicutes:Bacteroidetes ratio is beneficial to animals in terms of the gut microbiota-mediated energy harvest. The relative abundance of Proteobacteria was significantly higher in the gut microbiota of mouflon sheep at high altitudes. At the genus level, the Bacteroides:Prevotella ratio was significantly higher in the low-altitude group (than the high-altitude group) of mouflon sheep and the ratio was significantly higher in the high-altitude group (than the low-altitude group) in blue sheep. In addition, the Ruminococcaceae_UCG-005 related to cellulose and starch digestion was the predominant genus in blue sheep and the relative abundance of the genus was significant higher in the high-altitude group than the low-altitude group of blue sheep (P < 0.01). In conclusion, our results suggested that the gut microbiota of high-altitude groups of sheep had stronger abilities related to energy metabolism and the decomposition of substances, e.g., fiber and cellulose, and that such abilities are associated with high-altitude adaptation.

Epigenetics in health and disease: heralding the EWAS era

High-altitude hypoxia (reduced inspired oxygen tension due to decreased barometric pressure) exerts severe physiological stress on the human body. Two high-altitude regions where humans have lived for millennia are the Andean Altiplano and the Tibetan Plateau. Populations living in these regions exhibit unique circulatory, respiratory, and hematological adaptations to life at high altitude. Although these responses have been well characterized physiologically, their underlying genetic basis remains unknown. We performed a genome scan to identify genes showing evidence of adaptation to hypoxia. We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes. In addition, groups of genes functioning in oxygen metabolism and sensing were examined to test the hypothesis that particular pathways have been involved in genetic adaptation to altitude. Applying four population genetic statistics commonly used for detecting signatures of natural selection, we identified selection-nominated candidate genes and gene regions in these two populations (Andeans and Tibetans) separately. The Tibetan and Andean patterns of genetic adaptation are largely distinct from one another, with both populations showing evidence of positive natural selection in different genes or gene regions. Interestingly, one gene previously known to be important in cellular oxygen sensing, EGLN1 (also known as PHD2), shows evidence of positive selection in both Tibetans and Andeans. However, the pattern of variation for this gene differs between the two populations. Our results indicate that several key HIF-regulatory and targeted genes are responsible for adaptation to high altitude in Andeans and Tibetans, and several different chromosomal regions are implicated in the putative response to selection. These data suggest a genetic role in high-altitude adaption and provide a basis for future genotype/phenotype association studies necessary to confirm the role of selection-nominated candidate genes and gene regions in adaptation to altitude.

BackgroundIn various neurodevelopmental disorders (NDDs), sets of differential methylation marks (referred to as DNA methylation signatures or episignatures) are syndrome-specific and useful in evaluating the pathogenicity of detected genetic variants. These signatures have generally been tested using methylation arrays, requiring additional experimental and evaluation costs. As an alternative, long-read sequencing can simultaneously and accurately evaluate genetic and epigenetic changes. In addition, genome-wide DNA methylation profiling with more complete sets of CpG using long-read sequencing (than methylation arrays) may provide alternative but more comprehensive DNA methylation signatures, which have yet to be adequately investigated.MethodsNine and seven cases of molecularly diagnosed Sotos syndrome and ATR-X syndrome, respectively, were sequenced using nanopore long-read sequencing, together with 22 controls. Genome-wide differential DNA methylation analysis was performed. Among these differential DNA methylation sites, a single-locus DNA methylation mark at part of the NSD1 CpG island (CpGi) was subsequently studied in an additional 22 cases with a NSD1 point mutation or a 5q35 submicroscopic deletion involving NSD1. To investigate the potential utility of a single-locus DNA methylation test at NSD1 CpGi for differential diagnosis, nine cases with NSD1-negative clinically overlapping overgrowth intellectual disability syndromes (OGIDs) were also tested.ResultsLong-read sequencing enabled the successful extraction of two sets of differential methylation marks unique to each of Sotos syndrome and ATR-X syndrome, referred to as long-read-based DNA methylation signatures (LR-DNAm signatures), as alternatives to reported DNA methylation signatures (obtained by methylation array). Additionally, we found that a part, but not all, of the NSD1 CpGi were hypomethylated compared with the level in controls in both cases harboring NSD1 point mutations and those with a 5q35 submicroscopic deletion. This difference in methylation is specific to Sotos syndrome and lacking in other OGIDs.ConclusionsSimultaneous evaluation of genetic and epigenetic alterations using long-read sequencing may improve the discovery of DNA methylation signatures, which may in turn increase the diagnostic yields. As an example of the outcomes of these analyses, we propose that a single-locus DNA methylation test at NSD1 CpGi may streamline the molecular diagnosis of Sotos syndrome, regardless of the type of NSD1 aberration.

Background:Smoking is a risk factor for many human diseases. DNA methylation has been related to smoking, but genome-wide methylation data for smoking in Chinese populations is limited.Objectives:We aimed to investigate epigenome-wide methylation in relation to smoking in a Chinese population.Methods:We measured the methylation levels at > 485,000 CpG sites (CpGs) in DNA from leukocytes using a methylation array and conducted a genome-wide meta-analysis of DNA methylation and smoking in a total of 596 Chinese participants. We further evaluated the associations of smoking-related CpGs with internal polycyclic aromatic hydrocarbon (PAH) biomarkers and their correlations with the expression of corresponding genes.Results:We identified 318 CpGs whose methylation levels were associated with smoking at a genome-wide significance level (false discovery rate < 0.05), among which 161 CpGs annotated to 123 genes were not associated with smoking in recent studies of Europeans and African Americans. Of these smoking-related CpGs, methylation levels at 80 CpGs showed significant correlations with the expression of corresponding genes (including RUNX3, IL6R, PTAFR, ANKRD11, CEP135 and CDH23), and methylation at 15 CpGs was significantly associated with urinary 2-hydroxynaphthalene, the most representative internal monohydroxy-PAH biomarker for smoking.Conclusion:We identified DNA methylation markers associated with smoking in a Chinese population, including some markers that were also correlated with gene expression. Exposure to naphthalene, a byproduct of tobacco smoke, may contribute to smoking-related methylation.Citation:Zhu X, Li J, Deng S, Yu K, Liu X, Deng Q, Sun H, Zhang X, He M, Guo H, Chen W, Yuan J, Zhang B, Kuang D, He X, Bai Y, Han X, Liu B, Li X, Yang L, Jiang H, Zhang Y, Hu J, Cheng L, Luo X, Mei W, Zhou Z, Sun S, Zhang L, Liu C, Guo Y, Zhang Z, Hu FB, Liang L, Wu T. 2016. Genome-wide analysis of DNA methylation and cigarette smoking in Chinese. Environ Health Perspect 124:966–973; http://dx.doi.org/10.1289/ehp.1509834

When our human ancestors began to migrate from the African savannahs across the Alps into Northern Europe and Asia between 200,000 and 60,000 years ago, they encountered a colder climate, different food sources and new predators. Inevitably, evolution began to work on those wandering tribes: their skin became lighter, their metabolism adapted to new food sources, and their immune system had to handle different pathogens. Modern Homo sapiens began to evolve into slightly different subspecies or, as they are referred to in the common vernacular, different races. This shallow notion of race—that differences in our appearance have deep‐seated consequences for who and what we are as human beings—is the root of racism, which has led to slavery, discrimination, murder and genocide throughout the millennia. With the emergence of modern genetics and genomics, scientists had hoped that a better understanding of genetic differences and similarities among humans would eventually help to overcome the controversial and toxic notion of race as having anything to do with a person's ability, intelligence or humanity. As J. Craig Venter, then head of the Celera Genomics Corporation in Rockville, MD, USA, put it in 2000, when the first draft of the human genome was published: “Race is a social concept, not a scientific one”. Since the publication of the human genome, further advances in genomic sequencing and statistical analysis are now yielding new insights into the link between past human migrations and today's variety of genetic differences that govern disease resistance, skin pigmentation, tolerance to cold, and ability to digest or metabolize various nutrients. Such findings are contributing to discussions around the delicate issues of race, ethnicity and identity, but they are also having a significant impact on biomedical research and personalized health care. Furthermore, genetic analysis is shedding light on the migrations themselves, along with …

Ultraviolet radiation (UVR) is a ubiquitous exposure which may contribute to decreased folate levels. Skin pigmentation mediates the biological effect of UVR exposure, but its relationship to folate levels is unexamined. Interactions may exist between UVR and pigmentation genes in determining folate status, which may, in turn, impact homocysteine levels, a potential risk factor for multiple chronic diseases. Therefore, independent and interactive influences of environmental UVR and genetic variants related to skin pigmentation (MC1R-rs1805007, IRF4-rs12203592 and HERC2-rs12913832) on folate (red blood cell (RBC) and serum) and homocysteine levels were examined in an elderly Australian cohort (n = 599). Genotypes were assessed by RT/RFLP-PCR, and UVR exposures were assessed as the accumulated erythemal dose rate accumulated over 4 months (4M-EDR). Multivariate analysis found significant negative associations between 4M-EDR and RBC folate (p < 0.001, β = −0.19), serum folate (p = 0.045, β = −0.08) and homocysteine levels (p < 0.001, β = −0.28). Significant associations between MC1R-rs1805007 and serum folate levels (p = 0.020), and IRF4-rs12203592 and homocysteine levels (p = 0.026) occurred but did not remain significant following corrections with confounders. No interactions between 4M-EDR and pigmentation variants in predicting folate/homocysteine levels were found. UVR levels and skin pigmentation-related variants are potential determinants of folate and homocysteine status, although, associations are mixed and complex, with further studies warranted.