Epigenome analysis of brain between human and chimpanzee
Ontology highlight
ABSTRACT:
ORGANISM(S): Pan troglodytes
SUBMITTER: Junko Ueda
PROVIDER: E-GEOD-38804 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Genome wide DNA methylation profiling of brain and liver from human and chimpanzee. The Illumina HumanMethylation27 DNA Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs for each sample. Samples included liver and NeuN-positive/NeuN-negative/unsorted brain in three individuals from each of two species (human and chimpanzee).
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Project description:We performed deep strand-specific sequencing of poly-adenylated RNA (polyA+ RNAseq) from human, chimpanzee, macaque and mouse tissues, with the goal of detecting numerous non-annotated poorly expressed and antisense genes. We identified thousands of annotated and novel genes, especially in testis. We discovered that ~2% of the human and chimpanzee multiexonic genes were specific from such species. We generated RNA-Seq data (∼2.10 billion paired-end reads, 25-100 bp length) for the polyadenylated RNA fraction of brain (cerebral cortex), heart, liver and testis. In human and chimpanzee, we generated 2 samples per tissue corresponding to different individuals. In macaque, only 1 sample per tissue was generated. In mouse, considered as the evolutionary outgroup, we generated three pools of brain samples, and one pool of heart, liver and testis samples. We generated an additional sample in Testis without including reverse transcriptase as a control of DNA contamination.
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Project description:We compared the genome-wide patterns of DNA methylation in the brains of humans to those of our closest evolutionary relative, chimpanzees, using base-pair resolution whole-genome methylation maps of the prefrontal cortex. Our data reveal that the prefrontal cortex is the most heavily methylated among the human tissues examined so far. Nevertheless, hundreds of genes exhibit dramatically reduced levels of promoter DNA methylation in the human brain relative to the chimpanzee brain. Many of these genes are associated with neurological disorders, psychological disorders, and cancers, and are enriched for functions related to cellular metabolic processes and protein binding. Moreover, the majority of these genes exhibit higher expression in the human brain compared to the chimpanzee brain. Profiling DNA methylation map in prefrontal cortex regions of postmortem brains of three humans and three chimpanzees
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Project description:We compared the genome-wide patterns of DNA methylation in the brains of humans to those of our closest evolutionary relative, chimpanzees, using base-pair resolution whole-genome methylation maps of the prefrontal cortex. Our data reveal that the prefrontal cortex is the most heavily methylated among the human tissues examined so far. Nevertheless, hundreds of genes exhibit dramatically reduced levels of promoter DNA methylation in the human brain relative to the chimpanzee brain. Many of these genes are associated with neurological disorders, psychological disorders, and cancers, and are enriched for functions related to cellular metabolic processes and protein binding. Moreover, the majority of these genes exhibit higher expression in the human brain compared to the chimpanzee brain.
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Project description:Accelerated brain development is a unique feature of the human species. Not only the size but also morphology, in particular the connections between frontal cortex and basal ganglia distinguish the human brain from great apes and other primates. Recent findings suggest that structural features which may be important for language acquisition are influenced by FOXP2, key regulator of CNTNAP2. CNTNAP2 is one of the largest genes in the chimpanzee genome, encompassing 2.5 Mb. It encodes a neurexin with essential roles in the vertebrate nervous system. The aim of our study was to compare the methylation patterns of CNTNAP2 in human and chimpanzee brains, assuming that epigenetic regulation is essential for brain development and human language abilities. To this end, we designed a NimbleGen tiling array covering the entire chimpanzee CNTNAP2 gene plus 0.1 Mb up- and downstream flanking sequence with an average resolution of 13 bp. Methylated DNA ImmunoPreciptation (MeDIP) was used to enrich cytosine-methylated DNA fragments for downstream analysis with high-resolution tiling arrays.
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Project description:The origin of humans was accompanied by the emergence of new behavioral and cognitive functions, including language and specialized forms of abstract representation. However, the molecular foundations of these human capabilities are poorly understood. Because of the extensive similarity between human and chimpanzee DNA sequences, it has been suggested that many of the key phenotypic differences between species result primarily from alterations in the regulation of genes rather than in their sequences. To characterize gene expression patterns accross the brain and investigate the genetic basis of human specializations in brain organization and cognition, we used microarrays to quantify the transcript levels of thousands of genes in tissue samples from different brain regions of several human and chimpanzee individuals. Our results indicated that the human brain displays a distinctive pattern of gene expression relative to non-human primates, with higher expression levels for many genes belonging to a wide variety of functional classes. The increased expression of these genes could provide the basis for extensive modifications of cerebral physiology and function in humans, and suggests that the human brain is characterized by elevated levels of neuronal activity. Keywords: Species comparative study
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