Differential LINE-1 retrotransposition in induced pluripotent stem cells between humans and great apes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA206563 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR873616_1.fastq.gz | Fastqsanger.gz | |||
| SRR873616_2.fastq.gz | Fastqsanger.gz | |||
| SRR873617_1.fastq.gz | Fastqsanger.gz | |||
| SRR873617_2.fastq.gz | Fastqsanger.gz | |||
| SRR873618_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 34 |
Similar Datasets
Project description:Understanding cellular and molecular differences between human and non-human primates (NHPs) is essential to the basic comprehension of the evolution and diversity of our own species. Until now, preserved tissues have been the main source of most comparative studies between humans, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). However, these tissue samples do not fairly represent the distinctive traits of live cell behavior, are not amenable to genetic manipulation and do not allow translation of observed differences into phenotypical divergence. We hypothesized that induced pluripotent stem cells (iPSCs) could provide a unique biological resource to elucidate relevant phenotypical differences between human and the great apes and that those differences could have potential adaptation and speciation value. Here, we describe the generation and initial characterization of iPSCs from chimpanzees and bonobos as novel tools to explore our most recent evolution. Comparative gene expression analysis of human and NHP iPSCs revealed differences in regulation of Long Interspersed Nuclear Element (LINE-1 or L1) transposons. A force of change in mammalian evolution, L1 elements are retrotransposons that have remained active during primate evolution. We observed decreased levels of L1 restricting factors APOBEC3B (A3B)7 and PIWIL28 in NHP iPSCs which was correlated with increased human and chimpanzee L1 mobility and endogenous L1 mRNA levels. Moreover, results from manipulation of A3B and PIWIL2 levels in iPSCs suggested a causal inverse relationship between levels of these proteins and L1 activity. Finally, we found increased copy numbers of species-specific L1 elements in the genome of chimpanzees compared to humans, supporting the idea that increased L1 mobility in NHPs is not limited to iPSCs in culture and may have also occurred in the germline during primate evolution. We propose that differences in L1 mobility may have differentially shaped the genomes of humans and NHPs and could have had an adaptive significance.
2013-10-23 | GSE47626 | GEO
Project description:Understanding cellular and molecular differences between human and non-human primates (NHPs) is essential to the basic comprehension of the evolution and diversity of our own species. Until now, preserved tissues have been the main source of most comparative studies between humans, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). However, these tissue samples do not fairly represent the distinctive traits of live cell behavior, are not amenable to genetic manipulation and do not allow translation of observed differences into phenotypical divergence. We hypothesized that induced pluripotent stem cells (iPSCs) could provide a unique biological resource to elucidate relevant phenotypical differences between human and the great apes and that those differences could have potential adaptation and speciation value. Here, we describe the generation and initial characterization of iPSCs from chimpanzees and bonobos as novel tools to explore our most recent evolution. Comparative gene expression analysis of human and NHP iPSCs revealed differences in regulation of Long Interspersed Nuclear Element (LINE-1 or L1) transposons. A force of change in mammalian evolution, L1 elements are retrotransposons that have remained active during primate evolution. We observed decreased levels of L1 restricting factors APOBEC3B (A3B)7 and PIWIL28 in NHP iPSCs which was correlated with increased human and chimpanzee L1 mobility and endogenous L1 mRNA levels. Moreover, results from manipulation of A3B and PIWIL2 levels in iPSCs suggested a causal inverse relationship between levels of these proteins and L1 activity. Finally, we found increased copy numbers of species-specific L1 elements in the genome of chimpanzees compared to humans, supporting the idea that increased L1 mobility in NHPs is not limited to iPSCs in culture and may have also occurred in the germline during primate evolution. We propose that differences in L1 mobility may have differentially shaped the genomes of humans and NHPs and could have had an adaptive significance. polyA RNA-Seq profiling of iPS cells from human, chimpanzee, and bonobo, and small RNA-Seq profiling of human iPS cells.
2013-10-23 | E-GEOD-47626 | biostudies-arrayexpress
Project description:Diversity of Entamoeba spp. in African Great Apes and Humans
| PRJEB23126 | ENA
Project description:MHC class II alleles in Great Apes
| PRJEB27405 | ENA
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.
2013-06-01 | GSE41782 | GEO
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.
2013-06-01 | E-GEOD-41782 | biostudies-arrayexpress
Project description:We generated induced excitatory sensory neurons (iNeurons, iNs) from pluripotent stem cells of great apes (Human, Chimpanzee and Bonobo) by expressing the transcription factor neurogenin 2 (Ngn2). Single cell-RNA sequencing was performed to identify gene expressions differing in dendrite and synapse development during iNs maturation. Briefly, cultured cells were first dissociated and yield a concentration of 500 to 1000 cells/ml to obtain approximately 3000 cells per lane of a 10X microfluidic chip device. Single cell gene expression libraries were generated using the 10X Chromium Single Cell 3’ v2 Kit following the manufacturer’s instructions. Quantification and quality control of libraries was performed using a High Sensitivity DNA chip for Agilent’s Bioanalyzer and sequenced on a HiSeq2500 in Rapid sequencing mode. Our single-cell RNA-Seq data can be explored using our ShinyApp-based browser called iNeuronExplorer: https://bioinf.eva.mpg.de/shiny/iNeuron_Explorer/ (for details, please see this paper: DOI: 10.7554/eLife.59323). Sequencing raw data for all iNeurons from 409B2 line, one culture of day 35 iNeurons from H9 line and one culture of day 35 iNeurons from SC102A1 line are deposited under Mendeley Data with doi: 10.17632/y3s4hnyvg6, their corresponding gene counts (UMIs) are deposited in this ArrayExpress experiment with accession number MTAB-9233.
2020-12-15 | E-MTAB-9233 | biostudies-arrayexpress
Project description:A genome-wide comparative study of DNA methylation in great apes
| PRJNA178170 | ENA
Project description:Identifying cellular and molecular differences between human and non-human primates (NHPs) is essential to the basic understanding of the evolution and diversity of our own species. Until now, preserved tissues have been the main source for most comparative studies between humans, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). However, these tissue samples do not fairly represent the distinctive traits of live cell behaviour and are not amenable to genetic manipulation. We propose that induced pluripotent stem (iPS) cells could be a unique biological resource to determine relevant phenotypical differences between human and NHPs, and that those differences could have potential adaptation and speciation value. Here we describe the generation and initial characterization of iPS cells from chimpanzees and bonobos as new tools to explore factors that may have contributed to great ape evolution. Comparative gene expression analysis of human and NHP iPS cells revealed differences in the regulation of long interspersed element-1 (L1, also known as LINE-1) transposons. A force of change in mammalian evolution, L1 elements are retrotransposons that have remained active during primate evolution. Decreased levels of L1-restricting factors APOBEC3B (also known as A3B) and PIWIL2 (ref. 7) in NHP iPS cells correlated with increased L1 mobility and endogenous L1 messenger RNA levels. Moreover, results from the manipulation of A3B and PIWIL2 levels in iPS cells supported a causal inverse relationship between levels of these proteins and L1 retrotransposition. Finally, we found increased copy numbers of species-specific L1 elements in the genome of chimpanzees compared to humans, supporting the idea that increased L1 mobility in NHPs is not limited to iPS cells in culture and may have also occurred in the germ line or embryonic cells developmentally upstream to germline specification during primate evolution. We propose that differences in L1 mobility may have differentially shaped the genomes of humans and NHPs and could have continuing adaptive significance.
| S-EPMC4064720 | biostudies-literature