Ontology highlight
ABSTRACT:
PROVIDER: PRJNA790674 | ENA |
REPOSITORIES: ENA
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Project description:While genome sequencing has identified numerous non-coding alterations between primate species, which of these are regulatory and potentially relevant to the evolution of the human brain is unclear. Here, we annotate cis-regulatory elements (CREs) in the human, rhesus macaque and chimpanzee genome using ChIP-sequencing in different anatomical parts of the adult brain. We find high similarity in the genomic positioning of CREs between rhesus macaque and humans, suggesting that the majority of these elements were already present in a common ancestor 25 million years ago. Most of the observed regulatory changes between humans and rhesus macaque occurred prior to the ancestral separation of humans and chimpanzee, leaving a modest set of regulatory elements with predicted human-specificity. Our data refine previous predictions and hypotheses on the consequences of genomic changes between primate species, and allow the identification of regulatory alterations relevant to the evolution of the brain. ChIP-Sequencing for H3K27ac on 8 distinct brain regions from human (three biological replicates per brain region), chimpanzee (two biological replicates per brain region) and rhesus macaque (three biological replicates per brain region).
2016-01-13 | E-GEOD-67978 | biostudies-arrayexpress
Project description:Copy number variants (CNVs) are heritable gains and losses of genomic DNA in normal individuals. While copy number variation is widely studied in humans, our knowledge of CNVs in other mammalian species is more limited. We have designed a custom array-based comparative genomic hybridization (aCGH) platform with 385,000 oligonucleotide probes based on the reference genome sequence of the rhesus macaque (Macaca mulatta), the most widely studied non-human primate in biomedical research. We used this platform to identify 123 CNVs among 10 unrelated macaque individuals, with 24% of the CNVs observed in multiple individuals. We found that segmental duplications were significantly enriched at macaque CNV loci. We also observed significant overlap between rhesus macaque and human CNVs, suggesting that certain genomic regions are prone to recurrent CNV formation and instability, even across a total of ~50 million years of primate evolution (~25 million years in each lineage). Furthermore, for 8 of the CNVs that were observed in both humans and macaques, previous human studies have reported a relationship between copy number and gene expression or disease susceptibility. Therefore, the rhesus macaque offers an intriguing, non-human primate model organism for which hypotheses concerning the specific functions of phenotypically-relevant human CNVs can be tested. Keywords: array-based comparative genomic hybridization, oligonucleotide probes
2008-01-15 | GSE9220 | GEO
Project description:While genome sequencing has identified numerous non-coding alterations between primate species, which of these are regulatory and potentially relevant to the evolution of the human brain is unclear. Here, we annotate cis-regulatory elements (CREs) in the human, rhesus macaque and chimpanzee genome using ChIP-sequencing in different anatomical parts of the adult brain. We find high similarity in the genomic positioning of CREs between rhesus macaque and humans, suggesting that the majority of these elements were already present in a common ancestor 25 million years ago. Most of the observed regulatory changes between humans and rhesus macaque occurred prior to the ancestral separation of humans and chimpanzee, leaving a modest set of regulatory elements with predicted human-specificity. Our data refine previous predictions and hypotheses on the consequences of genomic changes between primate species, and allow the identification of regulatory alterations relevant to the evolution of the brain.
2016-01-13 | GSE67978 | GEO
Project description:Induced pluripotent stem cells (iPSCs) are regarded as a central tool to understand human biology in health and disease. Similarly, iPSCs from closely related species should be a central tool to understand human evolution and to identify conserved and variable patterns of iPSC disease models. Here, we have generated human, gorilla, bonobo and cynomolgus monkey iPSCs. We show that these cells are well comparable in their differentiation potential and generally similar to human, cynomolgus and rhesus monkey embryonic stem cells (ESCs). RNA sequencing reveals that expression differences among clones, individuals and stem cell type are all of very similar magnitude within a species. In contrast, expression differences between closely related primate species are three times larger and most genes show significant expression differences among the analysed species. However, pseudogenes differ more than twice as much, suggesting that evolution of expression levels in primate stem cells is rapid, but constrained. These patterns in pluripotent stem cells are comparable to those found in other tissues except testis. Hence, primate iPSCs reveal insights into general primate gene expression evolution and should provide a rich source to identify conserved and species-specific gene expression patterns for cellular phenotypes. Contributors: Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany We used expression profiling to characterize five gorilla, two bonobo and three macaque iPS clones as well as three iPS clones from two human individuals, three human embryonic stem (ES) cell lines and three macaque ES cell lines. We generated tagged RNA-Seq libraries from these 19 samples including four technical replicates (23 samples). Over 100 million single end reads were generated on the Illumina platform.
2014-02-19 | E-GEOD-50781 | biostudies-arrayexpress
Project description:How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. Moreover, within as little as six million years, the splicing profiles of physiologically-equivalent organs have diverged to the extent that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are governed by the highly variable use of a largely conserved cis-regulatory code. However, a smaller number of pronounced species-dependent splicing changes are predicted to remodel interactions involving factors acting at multiple steps in gene regulation. These events are expected to further contribute to the dramatic diversification of alternative splicing as well as to other gene regulatory changes that contribute to phenotypic differences among vertebrate species. mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq
2012-12-22 | E-GEOD-41338 | biostudies-arrayexpress
Project description:The dosage compensation complex (DCC) of Drosophila identifies its X chromosomal binding sites with exquisite selectivity. The principles that assure this vital targeting are known from the D. melanogaster model: DCC-intrinsic specificity of DNA binding, cooperativity with the CLAMP protein, and non-coding roX2 RNA transcribed from the X chromosome. We found that in D. virilis, a species separated from melanogaster by 40 million years of evolution, all principles are active, but contribute differently to X-specificity. In melanogaster, the DCC subunit MSL2 evolved intrinsic DNA-binding selectivity for rare PionX sites, which mark the X chromosome. In virilis, PionX sites are abundant and not X-enriched. Accordingly, MSL2 lacks specific recognition. Here, roX2 RNA plays a more instructive role, counteracting a non-productive interaction of CLAMP and modulating DCC binding selectivity. Remarkably, roX2 triggers a low-diffusion chromatin binding mode characteristic of DCC. Evidently, X-specific regulation is achieved by divergent evolution of similar components.
2021-06-23 | PXD023747 | Pride
Project description:The dosage compensation complex (DCC) of Drosophila identifies its X chromosomal binding sites with exquisite selectivity. The principles that assure this vital targeting are known from the D. melanogaster model: DCC-intrinsic specificity of DNA binding, cooperativity with the CLAMP protein, and non-coding roX2 RNA transcribed from the X chromosome. We found that in D. virilis, a species separated from melanogaster by 40 million years of evolution, all principles are active, but contribute differently to X-specificity. In melanogaster, the DCC subunit MSL2 evolved intrinsic DNA-binding selectivity for rare PionX sites, which mark the X chromosome. In virilis, PionX sites are abundant and not X-enriched. Accordingly, MSL2 lacks specific recognition. Here, roX2 RNA plays a more instructive role, counteracting a non-productive interaction of CLAMP and modulating DCC binding selectivity. Remarkably, roX2 triggers a low-diffusion chromatin binding mode characteristic of DCC. Evidently, X-specific regulation is achieved by divergent evolution of similar components.
2021-07-07 | GSE165833 | GEO
Project description:How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. Moreover, within as little as six million years, the splicing profiles of physiologically-equivalent organs have diverged to the extent that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are governed by the highly variable use of a largely conserved cis-regulatory code. However, a smaller number of pronounced species-dependent splicing changes are predicted to remodel interactions involving factors acting at multiple steps in gene regulation. These events are expected to further contribute to the dramatic diversification of alternative splicing as well as to other gene regulatory changes that contribute to phenotypic differences among vertebrate species.
2012-12-22 | GSE41338 | GEO
Project description:Alternative splicing (AS) influences the expression of human genes in diverse ways. We previously used subcellular fraction-sequencing (Frac-Seq) to reveal an unexpected connection between alternative splicing and isoform-specific mRNA translation. Here we apply comparative transcriptomics to explore alternative splicing coupled translational control (AS-TC) across 13 million years of primate evolution. We used Frac-seq to identify polyribosome associated mRNA isoforms from human, chimpanzee and orangutan induced pluripotent stem cell lines. We discovered orthologous AS-TC events with either conserved or species-specific translation patterns. Exons sequences associated with similar sedimentation profiles between species show strong sequence conservation compared to orthologous exons with divergent sedimentation profiles, suggesting exonic cis-regulatory elements influence to translational control. To test this hypothesis we created luciferase reporters from orthologous exons with divergent sedimentation profiles differing by a single nucleotide. Remarkably, single nucleotide substitutions were sufficient to drive species-specific expression of luciferase reporters. Together these data establish that cis-acting elements regulate AS-TC across primate species.
2024-04-30 | GSE230441 | GEO
Project description:Regulation and functionality of species-specific alternative splicing has remained enigmatic for many years. Calcium/calmodulin-dependent protein kinase IIβ (CaMKIIβ) is expressed in several splice variants and plays a key role in learning and memory. Here, we identify and characterize several primate-specific CAMK2B splice isoforms, which show altered kinetic properties and changes in substrate specificity. Furthermore, we demonstrate that primate-specific Camk2β alternative splicing is achieved through branch point weakening during evolution. We show that reducing branch point and splice site strength during evolution globally renders constitutive exons alternative, thus providing a paradigm for cis-directed species-specific alternative splicing regulation. Using CRISPR/Cas9 we introduced the weaker human branch point into the mouse genome, resulting in human-like CAMK2B splicing in the brain of mutant mice. We observe a strong impairment of long-term potentiation in CA3-CA1 synapses of mutant mice, thus connecting branch point-controlled, species-specific alternative splicing with a fundamental function in learning and memory.
2022-12-19 | PXD035346 | Pride