Stress-associated H3K4 methylation accumulates during postnatal development and aging of Rhesus macaque brain
Ontology highlight
ABSTRACT:
ORGANISM(S): Macaca mulatta
SUBMITTER: Dali Han
PROVIDER: E-GEOD-41128 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:We addressed the lack of experimentally supported transcript annotations in the Rhesus macaque genome by ab initio identification of the transcription start sites (TSSs). We took advantage of histone H3 lysine 4 trimethylation (H3K4me3)'s ability to mark TSSs and the recently developed ChIP-Seq and RNA-Seq technology to survey the transcript structures in the macaque brain. We then integrated the two types of our newly generated data with genomic sequence features and extended a TSS prediction algorithm to ab initio predict and verify 16,833 of previously electronically annotated transcription start sites at 500 bp resolution and predicted ~10,000 new TSSs. We took advantage of histone H3 lysine 4 trimethylation (H3K4me3)M-bM-^@M-^Ys ability to mark transcription start sites (TSSs) and the recently developed ChIP-Seq and RNA-Seq technology to survey the transcript structures. By integrating the ChIP-seq, RNA-seq and small RNA-seq data (previously uploaded to GEO as GSM450615 by our collaborator) with genomic sequence features and extending and improving a state-of-the-art TSS prediction algorithm, we ab initio predicted and verified previously electronically annotated TSSs at a high resolution, and predicted some novel TSSs.
2010-10-18 | E-GEOD-24538 | biostudies-arrayexpress
Project description:Gene expression changes determine functional differentiation during development and are associated with functional decline during aging. While developmental changes are tightly regulated, regulation of aging changes is not well established. To assess the regulatory basis of age-related changes and investigate the mechanism of regulatory transition between development and aging, we measured mRNA and microRNA expression patterns in brains of humans and rhesus macaques over the entire species’ lifespan. We find that in both species, developmental and aging changes overlap in the course of lifetime with many changes found at the late age initiating in early childhood. Keywords: miRNA Age Series Keywords: Non-coding RNA profiling by high throughput sequencing rhesus macaque post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. The age ranges of the indibiual in rhesus macaque covered the whole life span fom newborn to death.
2010-06-09 | E-GEOD-18013 | biostudies-arrayexpress
Project description:We search for developmental changes specific to humans by examining gene expression profiles in the human, chimpanzee and rhesus macaque prefrontal and cerebellar cortex. In both brain regions, developmental patterns were more evolved in humans than in chimpanzees. To distinguish whether the human specific developmental pattern represent novel human-specific developmental patterns or a shift in the timing of the existing patterns, we measured mRNA expression patterns in macaque brains from prenatal to neonatal. Our results show that the major human-specific developmental patterns identified in the PFC reflects an extreme shift in timing of synaptic development. Rhesus macaque post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. Six fetal and six newborn samples were used. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays.
2012-02-02 | E-GEOD-29138 | biostudies-arrayexpress
Project description:Gene expression changes determine functional differentiation during development and are associated with functional decline during aging. While developmental changes are tightly regulated, regulation of aging changes is not well established. To assess the regulatory basis of age-related changes and investigate the mechanism of regulatory transition between development and aging, we measured mRNA and microRNA expression patterns in brains (superior frontal gyrus) of humans and rhesus macaques over the entire speciesâ lifespan. We find that in both species, developmental and aging changes overlap in the course of lifetime with many changes found at the late age initiating in early childhood. Human post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. The age ranges of the indibiual in human covered its whole life span fom newborn to death. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays. Rhesus macaque post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. The age ranges of the indibiual in rhesus macaque covered the whole life span fom newborn to death. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays.
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Project description:This SuperSeries is composed of the following subset Series: GSE17757: Gene expression data from primate postnatal brain in prefrontal cortex: time course GSE18012: miRNA expression data from human postnatal brain in prefrontal cortex: time course GSE18013: miRNA expression data from rhesus macaque postnatal brain in prefrontal cortex: time course Refer to individual Series
2010-06-09 | E-GEOD-18069 | biostudies-arrayexpress
Project description:Piwi-interacting RNA (piRNA) are small RNA abundant in the germline across animal species. In fruit flies and mice, piRNA were implicated in maintenance of genomic integrity by transposable elements silencing. Outside of the germline, piRNA have only been found in Drosophila ovarian follicle cells. Previous studies further reported the presence of multiple piRNA-like small RNA (pilRNA) in fly heads and a small number of pilRNA in mouse tissues and human NK cells. Here, by analyzing high-throughput small RNA sequencing data in more than 130 fruit fly, mouse and rhesus macaque samples, we show widespread presence of pilRNA displaying all known characteristics of piRNA in multiple somatic tissues of these three species. In mouse pancreas and macaque epididymis, pilRNA abundance was compatible with piRNA abundance in the germline. Using in situ hybridizations, we further demonstrate pilRNA co-localization with mRNA expression of Piwi-family genes in all macaque tissues. These findings indicate that piRNA-like molecules might play important roles outside of the germline. Small RNA expression profiles were examined in five rhesus macaque tissues (testis, epididymis, prostate, seminal vesicles, cortex) and one mouse tissue (epididymis).
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Project description:In development, timing is of the utmost importance, and the timing of various developmental processes are often changed during evolution. During human evolution sexual maturation has been delayed relative to other primates and this may have played a critical role for both the increase of human brain size and the rise of human-specific cognitive traits . We measured the timing of gene expression changes in the superior frontal gyrus region of the brains of humans, chimpanzees, and rhesus macaques throughout postnatal development. Keywords: Age series Human, chimpanzee and rhesus macaque post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. The age ranges of the individuals in all three species covered the respective species' postnatal maturation period from infancy to adulthood. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays.
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Project description:We investigated molecular changes during human, chimpanzee, and rhesus macaque postnatal brain development at the transcriptome, proteome, and metabolome levels in two brain regions: the prefrontal cortex (PFC) that is involved in several human-specific cognitive processes, and the cerebellar cortex (CBC) that may be functionally more conserved. We find a nearly three-fold excess of human-specific gene expression changes in PFC compared to CBC. The most prominent human-specific mRNA expression pattern in the PFC is a developmental delay of approximately 5 years in the expression of genes associated with learning and memory, such as synaptic transmission and long-term potentiation. This pattern is supported by correlated changes in concentrations of proteins and the respective neurotransmitters and its magnitude is beyond the shift expected from the life-histories of the species. Mechanistically, it might be driven by change in timing of expression of four or more transcription factors. We speculate that delayed synaptic maturation in PFC may play a role in the emergence of human-specific cognitive abilities. Keywords: Age series Human, chimpanzee and rhesus macaque post-mortem brain samples from the cerebellar cortex were collected. The age ranges of the individuals in all three species covered the respective species' postnatal maturation period from infancy to old adulthood. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays. CBC samples.
2011-12-09 | E-GEOD-22569 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE22521: Gene expression in primate postnatal brain through lifespan - prefrontal cortex GSE22569: Gene expression in primate postnatal brain through lifespan - cerebellar cortex Refer to individual Series
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