Phyloepigenetic comparison of apes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA127641 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR057754.fastq.gz | Fastqsanger.gz | |||
| SRR057755.fastq.gz | Fastqsanger.gz | |||
| SRR057756.fastq.gz | Fastqsanger.gz | |||
| SRR057757.fastq.gz | Fastqsanger.gz | |||
| SRR057758.fastq.gz | Fastqsanger.gz |
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Project description:We have determined methylation state differences in the epigenomes of neutrophils purified from human and chimpanzee. We used deep sequencing of ends generated by digestion with a methylation-sensitive restriction enzyme, followed by analysis with the MetMap computational pipeline to infer methylation states from the sequencing data. Using the orangutan as an outgroup, analysis of DNA sequence substitutions in CG-dense regions that are either methylated or unmethylated in all three species indicates that methylation states in the neutrophil reflect methylation states in the germline. Differences in methylation states were not correlated with differences in the local genomic sequences, indicating that they can be determined independently of local DNA sequence. Methylation differences were not distributed randomly among the individuals we analyzed, but recapitulated the known phylogenetic relationships of the three species in a pattern consistent with their stable inheritance. This data provide the first comprehensive dataset indicating that epigenetic states are maintained as independent characters that are predictably transmitted within species. Heritable epigenetic differences such as those we have identified could readily have functional and adaptive consequences, and contribute to the phenotypic divergence of human and chimpanzee. Comparison of methylation states in a single, uncultered cell type from human and chimpanzee
2011-09-09 | E-GEOD-22376 | biostudies-arrayexpress
Project description:Small apes (family Hylobatidae), encompassing gibbons and siamangs, occupy a pivotal evolutionary position within the hominoid lineage, bridging the gap between great apes and catarrhine monkeys. Although they possess distinctive genomic and phenotypic features—such as rapid chromosomal rearrangements and adaptations for brachiation—functional genomic studies on small apes have been hindered by the limited availability of biological samples and developmental models. Here, we address this gap by successfully reprogramming primary skin fibroblasts from three small ape species: lar gibbons (Hylobates lar), Abbott’s gray gibbons (Hylobates abbotti), and siamangs (Symphalangus syndactylus). Using Sendai virus-based stealth RNA vectors, we generated 31 reprogrammed cell lines, five of which were developed into transgene-free induced pluripotent stem cells (iPSCs). These iPSCs displayed canonical features of primed pluripotency, both morphologically and molecularly, consistent with other primate iPSCs. Directed differentiation experiments confirmed the capacity of small ape iPSCs to generate cells representing all three germ layers. Particularly, the successful differentiation into limb bud mesoderm cells underscores their utility in investigating the molecular and developmental mechanisms unique to small ape forelimb evolution. Transcriptomic profiling of small ape iPSCs revealed significant upregulation of pluripotency-associated genes, alongside elevated expression of transposable elements. Remarkably, LAVA retrotransposons—a class of elements specific to small apes—exhibited particularly high expression levels in these cells. Comparative transcriptomic analyses with iPSCs from humans, great apes, and macaques identified evolutionary trends and clade-specific gene expression signatures. These signatures highlighted processes linked to genomic stability and cell death, providing insights into small ape-specific adaptations. This study positions small ape iPSCs as a transformative tool for advancing functional genomics and evolutionary developmental biology. By facilitating detailed investigations into hominoid genome evolution and phenotypic diversification, this system bridges critical gaps in comparative research, enabling deeper exploration of the genetic and cellular underpinnings of small ape-specific traits.
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Project description:MHC class II alleles in Great Apes
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Project description:DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex diseases. These changes can be inherited through generations and likely have played an important role during human evolution. We performed a comparative analysis of CpG methylation patterns between humans and all great apes (chimpanzee, bonobo, gorilla and orangutan) on a total of 32 individuals.Our analysis identified ~1,000 genes with significantly altered methylation patterns among the great apes, including ~200 with a methylation pattern unique to humans. Analysis of genes with human-specific epigenetic patterns identified enrichments for several functional categories that are key for human-specific traits, such as advanced facial expressions or equilibrium related to bipedalism. We also found a highly significant positive correlation between the genomic distance genome-wide and the methylation levels. In a pairwise comparison, we observed that ~9% (~30,000) of CpGs assayed show significant methylation differences between human and chimpanzee, including promoter regions of 879 genes (11.9% of those tested), suggesting that epigenetic changes have occurred at high frequency during recent primate evolution and represent an important substrate for adaptive modification of genome function. Epigenetic changes among primates are highly enriched for sites showing intermediate DNA methylation levels might be related to regulatory elements, and we observed a significant relationship between changes in DNA methylation and gene expression across multiple different tissues. We also identified a significant positive relationship between the rate of coding variation within genes and alterations of promoter methylation, suggesting concerted evolution between protein sequence and gene regulation. Contrastingly, our analysis also identified scores of genes that are perfectly conserved at the amino acid level between human and chimp, yet which show significant epigenetic difference between these two species. We conclude that epigenetic alterations represent an important force during primate evolution and has been systematically under explored in evolutionary comparative genomics.
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Project description:We have determined methylation state differences in the epigenomes of neutrophils purified from human and chimpanzee. We used deep sequencing of ends generated by digestion with a methylation-sensitive restriction enzyme, followed by analysis with the MetMap computational pipeline to infer methylation states from the sequencing data. Using the orangutan as an outgroup, analysis of DNA sequence substitutions in CG-dense regions that are either methylated or unmethylated in all three species indicates that methylation states in the neutrophil reflect methylation states in the germline. Differences in methylation states were not correlated with differences in the local genomic sequences, indicating that they can be determined independently of local DNA sequence. Methylation differences were not distributed randomly among the individuals we analyzed, but recapitulated the known phylogenetic relationships of the three species in a pattern consistent with their stable inheritance. This data provide the first comprehensive dataset indicating that epigenetic states are maintained as independent characters that are predictably transmitted within species. Heritable epigenetic differences such as those we have identified could readily have functional and adaptive consequences, and contribute to the phenotypic divergence of human and chimpanzee.
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Project description:DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex diseases. These changes can be inherited through generations and likely have played an important role during human evolution. We performed a comparative analysis of CpG methylation patterns between humans and all great apes (chimpanzee, bonobo, gorilla and orangutan) on a total of 32 individuals.Our analysis identified ~1,000 genes with significantly altered methylation patterns among the great apes, including ~200 with a methylation pattern unique to humans. Analysis of genes with human-specific epigenetic patterns identified enrichments for several functional categories that are key for human-specific traits, such as advanced facial expressions or equilibrium related to bipedalism. We also found a highly significant positive correlation between the genomic distance genome-wide and the methylation levels. In a pairwise comparison, we observed that ~9% (~30,000) of CpGs assayed show significant methylation differences between human and chimpanzee, including promoter regions of 879 genes (11.9% of those tested), suggesting that epigenetic changes have occurred at high frequency during recent primate evolution and represent an important substrate for adaptive modification of genome function. Epigenetic changes among primates are highly enriched for sites showing intermediate DNA methylation levels might be related to regulatory elements, and we observed a significant relationship between changes in DNA methylation and gene expression across multiple different tissues. We also identified a significant positive relationship between the rate of coding variation within genes and alterations of promoter methylation, suggesting concerted evolution between protein sequence and gene regulation. Contrastingly, our analysis also identified scores of genes that are perfectly conserved at the amino acid level between human and chimp, yet which show significant epigenetic difference between these two species. We conclude that epigenetic alterations represent an important force during primate evolution and has been systematically under explored in evolutionary comparative genomics. 32 samples analyzed in total: 9 humans, 5 chimpanzees, 6 bonobos, 6 gorillas and 6 orangutans. Blood-derived DNA methylation levels were assessed using Illumina Infinium HumanMethylation450 BeadChip. We performed a strict filtering step to remove divergent probes based on the number and location of mismatches with their target site in each species genome assembly tested, this resulted in the retention of 133,908 shared across all the species.
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