Characterization of the transcriptional landscape of human developing hippocampus by ATAC-seq
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE131256 | GEO | 2019/11/13
REPOSITORIES: GEO
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Project description:Human hippocampus enabled further processing of higher brain functions. However, very little is known about human hippocampus development, which is largely accomplished during fetal stage. Our current study elucidates the transcriptomic profiling of the developing human fetal hippocampus using single-cell RNA-seq (scRNA-seq), allowing us to reconstruct the order of neurogenesis and their lineage relationships.
2019-11-13 | GSE119212 | GEO
Project description:<p>Non-coding regions comprise most of the human genome and harbor a significant fraction of risk alleles for neuropsychiatric diseases, yet their functions remain poorly defined. We created a high-resolution map of non-coding elements involved in human cortical neurogenesis by contrasting chromatin accessibility and gene expression in the germinal zone and cortical plate of the developing cerebral cortex. To obtain a high resolution depiction of chromatin structure and gene expression in developing human fetal cortex, we dissected the post-conception week (PCW) 15-17 human neocortex into two major anatomical divisions to distinguish between proliferating neural progenitors and post mitotic neurons: (1) GZ: the neural progenitor-enriched region encompassing the ventricular zone (VZ), subventricular zone (SVZ), and intermediate zone (IZ) and (2) CP: the neuron-enriched region containing the subplate (SP), cortical plate (CP), and marginal zone (MZ). Tissues were obtained from three independent donors and three to four technical replicates from each tissue were processed for ATAC-seq to define the landscape of accessible chromatin and RNA-seq for genome-wide gene expression profiling.</p>
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Project description:Immature neurons arising from adult neurogenesis contribute to plasticity and unique functionsinthe adult mammalian brain. Whether immature dentate granule cells (imGCs) exist in the adult human hippocampusis under debate. Herewe performedsingle-nucleus transcriptomicanalysis aided by a validated machinelearning approach to quantify the abundance of imGCs in the 5postnatal human hippocampus and to investigate their molecular properties. We show the sustained presence of human imGCs through prenatal, infant, child, adolescent, adult,andaging stages andreveal their shared and differentmolecular characteristicsacross agesandspecies. Furthermore, we directly demonstrate the capacity for neurogenesis in the postnatal human hippocampus using surgical specimensin culture. Together, these resultsprovide novel insights10into molecular propertiesof imGCs in humans across the lifespan.
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Project description:Human frontal cortex and hippocampus play key roles in learning and cognition, and are representative structures of the six-layer neocortex and the more ancient allocortex, respectively. Here we investigated the epigenomic and 3D-chromatin conformational dynamics of human frontal cortex and hippocampus development using more than 53,000 joint single-nucleus profiles of chromatin conformation and DNA methylation (sn-m3C-seq) generated from mid-gestational, late-gestational, infant and adult human brains. We found that the remodeling of DNA methylation predominantly happens during late-gestational to early-post-natal development, and is temporally uncoupled from the dynamics of chromatin conformation. We reconstructed regulatory hierarchies of cortical and hippocampal cell differentiation and maturation and identified brain regional-specific regulatory signatures. The single-cell 3D-regulatome approach further enabled the cell-type-specific dissection of neuropsychiatric risk loci during key neurodevelopmental stages and in adult human brains.
2022-10-07 | GSE213950 | GEO
Project description:The functional output of the hippocampus, a brain region subserving memory processes, depends on highly orchestrated cellular and molecular processes that regulate synaptic plasticity throughout life. The structural requirements of such plasticity and molecular processes involved in this regulation are poorly understood. Specific molecules, including tissue inhibitor of metalloproteinases-2 (TIMP2) have been implicated in serving a pro-plasticity role in the hippocampus, a role that decreases with brain aging. Here, we report that TIMP2 is highly expressed by neurons within the hippocampus and its loss drives changes in cellular programs related to adult neurogenesis and dendritic spine turnover with corresponding impairments in hippocampus-dependent memory. We find that TIMP2 regulates accumulation of extracellular matrix (ECM) around synapses in the hippocampus with concomitant hindrance in migration of newborn neurons through a denser ECM network. A conditional TIMP2 KO mouse reveals that neuronal TIMP2 regulates adult neurogenesis, accumulation of ECM, and ultimately hippocampus-dependent memory. Our results define a mechanism whereby hippocampus-dependent function is regulated by TIMP2 and its interactions with the ECM to regulate diverse processes associated with synaptic plasticity.
2023-11-02 | GSE223188 | GEO
Project description:Characterization of the transcriptional landscape of human developing hippocampus by scRNA-seq
| PRJNA488472 | ENA
Project description:Characterization of the transcriptional landscape of human developing hippocampus by ATAC-seq
| PRJNA543066 | ENA
Project description:The role of the hippocampus in learning and memory has been widely studied. However, studies of differences along the longitudinal axis indicate that the hippocampus is perhaps not a singular structure, but instead it is thought that the dorsal and ventral poles of the hippocampus have functional differences. An anatomical gradient of hippocampal inputs along the dorsal-ventral axis supports this notion. It has been recently shown that there is transcriptional differentiation along the longitudinal axis of the adult hippocampus, coinciding with functional and anatomical gradients. Understanding the development of the dorsal-ventral hippocampal axis will further our understanding of the different hippocmapal functional contributions along the longitudinal axis. However, analysis of transcriptional gradients along the dorsal ventral axis have not been studied in the neonatal rat during development. We performed an extensive bead-chip based geneome-wide analysis of transcriptional differences in dorsal, intermediate, and ventral hippocampal tissue of rats aged postnatal day 0 (P0), P9, P18 and P60.
2015-05-01 | E-MTAB-2617 | biostudies-arrayexpress
Project description:Curcumin has been demonstrated to have many neuroprotective properties, including improvement of cognition in humans and neurogenesis in animals, yet the mechanism of such effects remains unclear. Here, we assessed behavioural performance and hippocampal cell proliferation in aged rats after 6- and 12-week curcumin-fortified diets. Curcumin enhanced non-spatial and spatial memory, as well as dentate gyrate cell proliferation as compared to control diet rats. We also investigated underlying mechanistic pathways that might link curcumin treatment to increased cognition and neurogenesis via microarray analysis of cortical and hippocampal mRNA transcription. We used microarrays to investigate the effects of short-term (6-week) and long-term (12-week) curcumin-supplemented diet on gene expression of hippocampus and cortex in aged rats. The hippocampus and cortex of every three rats from one group were pooled together, respectively and used for RNA extraction and hybridization on Affymetrix microarrays. To ensure the reliability of the data, we conducted hybridization experiments in duplicate microarrays from each RNA sample. The tissues examined by microarray are as follows: the hippocampus and cortex of 6-week curcumin-treated 15-month-old rats, the hippocampus and cortex of 6-week no curcumin-treated 15-month-old rats (control rats), the hippocampus and cortex of 12-week curcumin-treated 15-month-old rats, the hippocampus and cortex of 12-week no curcumin-treated 15-month-old rats (control rats).
2011-10-21 | E-GEOD-33137 | biostudies-arrayexpress
Project description:The transcriptional repressor REST (RE1 Silencing Transcription Factor) is a master regulator of thousands of neuronal genes that together impart the terminally differentiated neuronal phenotype. Because of this unique feature, REST has been, and continues to be, a widely used model for understanding neurogenesis and neuronal cell function. These studies have focused primarily on murine embryonic development, but recent studies have pointed to distinct postnatal roles for REST in stroke, epilepsy, aging and cognitive decline. The function of REST in healthy human brain tissue, however, still remains poorly characterized. Here, we present deep sequencing chromatin immunoprecipitation evidence for divergent REST function in normal mouse and human postmortem adult hippocampus. In mouse, REST occupies only 221 peaks that are divided between prototypical REST target genes shared with non-neuronal cells, as well as peaks unique to the hippocampus. Surprisingly, the mouse hippocampal-unique sites are not conserved in human, which contains 1886 REST peaks unique to the hippocampus. Further, the REST peaks unique to the hippocampus represent a potentially new category of target genes encoding proteins important in the immune response. Our results suggest the possibility that REST protects against aberrant immunological responses during normal human aging and that mouse may not model this aging function.
2020-07-24 | GSE144226 | GEO