scholarly journals Human-specific genomic features of pluripotency regulatory networks link NANOG with fetal and adult brain development

2015 ◽  
Author(s):  
Gennadi V. Glinsky
Keyword(s):  
Human Brain ◽  
Brain Development ◽  
Binding Sites ◽  
Regulatory Networks ◽  
Embryonic Stem ◽  
Adult Brain ◽  
Genomic Features ◽  
Non Coding Rna ◽  
Regulatory Loci ◽  
Human Specific

AbstractGenome-wide proximity placement analysis of diverse families of human-specific genomic regulatory loci (HSGRL) identified topologically-associating domains (TADs) that are significantly enriched for HSGRL and termed rapidly-evolving in humans TADs (revTADs; Genome Biol Evol. 2016 8; 2774-88). Here, human-specific genomic features of pluripotency regulatory networks in hESC have been analyzed. The primary focus was on identification of human-specific elements of the interphase chromatin architecture of TADs responsible for transcriptional regulatory control of the NANOG, POU5F1, and POU3F2 genes. Comparative analyses of the four adjacent TADs spanning ~3.3 Mb NANOG locus-associated genomic region were carried-out to highlight primate-specific genomic features. Lastly, the putative mechanisms of the genome-wide regulatory effects of human-specific NANOG-binding sites (HSNBS) on expression of genes implicated in the fetal and adult brain development have been examined. Acquisition of primate-specific regulatory loci appears to rewire TADs exerting transcriptional control on pluripotency regulators, revealing a genomic placement pattern consistent with the enhanced regulatory impact of NANOG in primates. Proximity placement analysis of HSNBS identified a large expression signature in the human fetal neocortex temporal lobe comprising 4,957 genes, which appear to retain acquired in the embryo expression changes for many years of human brain development and maintain highly concordant expression profiles in the neocortex and prefrontal cortex regions of adult human brain. Collectively, reported herein observations indicate that genomic elements of pluripotency regulatory circuitry associated with HSNBS, specifically proteins of the classical NurD chromatin remodeling complex, contribute to transcriptional regulation of a large set of genes implicated in development and function of human brain.List of abbreviations5hmC, 5-HydromethylcytosineCTCF, CCCTC-binding factorDHS, DNase hypersensitivity sitesFHSRR, fixed human-specific regulatory regionsGRNs, genomic regulatory networksHAR, human accelerated regionshCONDEL, human-specific conserved deletionshESC, human embryonic stem cellsHSGRL, human-specific genomic regulatory lociHSNBS, human-specific NANOG-binding sitesHSTFBS, human-specific transcription factor-binding sitesLAD, lamina-associated domainLINE, long interspersed nuclear elementlncRNA, long non-coding RNALTR, long terminal repeatMADE, methylation-associated DNA editingmC, methylcytosinemESC, mouse embryonic stem cellsNANOG, Nanog homeoboxnt, nucleotidePOU5F1, POU class 5 homeobox 1PSDS, partial strand displacement stateTAD, topologically associating domainsTE, transposable elementsTF, transcription factorTSC, triple-stranded complexTSS, transcription start sitesSE, super-enhancersSED, super-enhancer domainssncRNA, small non coding RNA

scholarly journals Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development

2022 ◽  
Author(s):  
Christopher J Playfoot ◽  
Shaoline Sheppard ◽  
Evarist Planet ◽  
Didier Trono
Keyword(s):  
Transposable Elements ◽  
Human Brain ◽  
Brain Development ◽  
Mirna Expression ◽  
Web Application ◽  
Regulatory Networks ◽  
Adult Brain ◽  
Control Of Gene Expression ◽  
Human Brain Development ◽  
Gene Regulatory

Transposable elements (TEs) contribute to the evolution of gene regulatory networks and are dynamically expressed throughout human brain development and disease. One gene regulatory mechanism influenced by TEs is the miRNA system of post-transcriptional control. miRNA sequences frequently overlap TE loci and this miRNA expression landscape is crucial for control of gene expression in adult brain and different cellular contexts. Despite this, a thorough investigation of the spatiotemporal expression of TE-embedded miRNAs in human brain development is lacking. Here, we identify a spatiotemporally dynamic TE-embedded miRNA expression landscape between childhood and adolescent stages of human brain development. These miRNAs sometimes arise from two apposed TEs of the same subfamily, such as for L2 or MIR elements, but in the majority of cases stem from solo TEs. They give rise to in silico predicted high-confidence pre-miRNA hairpin structures, likely represent functional miRNAs and have predicted genic targets associated with neurogenesis. TE-embedded miRNA expression is distinct in the cerebellum when compared to other brain regions, as has previously been described for gene and TE expression. Furthermore, we detect expression of previously non-annotated TE-embedded miRNAs throughout human brain development, suggestive of a previously undetected miRNA control network. Together, as with non-TE-embedded miRNAs, TE-embedded sequences give rise to spatiotemporally dynamic miRNA expression networks, the implications of which for human brain development constitute extensive avenues of future experimental research. To facilitate interactive exploration of these spatiotemporal miRNA expression dynamics, we provide the 'Brain miRTExplorer' web application freely accessible for the community.

scholarly journals Unraveling Human Brain Development and Evolution Using Organoid Models

2021 ◽  
Vol 9 ◽  
Author(s):  
Sarah Fernandes ◽  
Davis Klein ◽  
Maria C. Marchetto
Keyword(s):  
Human Brain ◽  
Brain Development ◽  
Brain Region ◽  
Model Systems ◽  
Transcriptional Signature ◽  
Human Brain Development ◽  
Advanced Stages ◽  
Brain Organoid ◽  
Development And Evolution ◽  
Human Specific

Brain organoids are proving to be physiologically relevant models for studying human brain development in terms of temporal transcriptional signature recapitulation, dynamic cytoarchitectural development, and functional electrophysiological maturation. Several studies have employed brain organoid technologies to elucidate human-specific processes of brain development, gene expression, and cellular maturation by comparing human-derived brain organoids to those of non-human primates (NHPs). Brain organoids have been established from a variety of NHP pluripotent stem cell (PSC) lines and many protocols are now available for generating brain organoids capable of reproducibly representing specific brain region identities. Innumerous combinations of brain region specific organoids derived from different human and NHP PSCs, with CRISPR-Cas9 gene editing techniques and strategies to promote advanced stages of maturation, will successfully establish complex brain model systems for the accurate representation and elucidation of human brain development. Identified human-specific processes of brain development are likely vulnerable to dysregulation and could result in the identification of therapeutic targets or disease prevention strategies. Here, we discuss the potential of brain organoids to successfully model human-specific processes of brain development and explore current strategies for pinpointing these differences.

scholarly journals Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo

2017 ◽  
Author(s):  
Luca Tosti ◽  
James Ashmore ◽  
Boon Siang Nicholas Tan ◽  
Benedetta Carbone ◽  
Tapan K Mistri ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Binding Sites ◽  
Mammalian Cells ◽  
Regulatory Networks ◽  
Embryonic Stem ◽  
Specific Cell ◽  
Dna Interactions

AbstractThe identification of transcription factor (TF) binding sites in the genome is critical to understanding gene regulatory networks (GRNs). While ChIP-seq is commonly used to identify TF targets, it requires specific ChIP-grade antibodies and high cell numbers, often limiting its applicability. DNA adenine methyltransferase identification (DamID), developed and widely used in Drosophila, is a distinct technology to investigate protein-DNA interactions. Unlike ChIP-seq, it does not require antibodies, precipitation steps or chemical protein-DNA crosslinking, but to date it has been seldom used in mammalian cells due to technical impediments. Here we describe an optimised DamID method coupled with next generation sequencing (DamID-seq) in mouse cells, and demonstrate the identification of the binding sites of two TFs, OCT4 and SOX2, in as few as 1,000 embryonic stem cells (ESCs) and neural stem cells (NSCs), respectively. Furthermore, we have applied this technique in vivo for the first time in mammals. Oct4 DamID-seq in the gastrulating mouse embryo at 7.5 days post coitum (dpc) successfully identified multiple Oct4 binding sites proximal to genes involved in embryo development, neural tube formation, mesoderm-cardiac tissue development, consistent with the pivotal role of this TF in post-implantation embryo. This technology paves the way to unprecedented investigations of TF-DNA interactions and GRNs in specific cell types with limited availability in mammals including in vivo samples.

scholarly journals Organoids: the third dimension of human brain development and disease

2021 ◽  
Author(s):  
Georgia Kouroupi ◽  
Kanella Prodromidou ◽  
Florentia Papastefanaki ◽  
Era Taoufik ◽  
Rebecca Matsas
Keyword(s):  
Stem Cells ◽  
Human Brain ◽  
Brain Development ◽  
Cell Biology ◽  
Embryonic Stem ◽  
Two Dimensional ◽  
The Third ◽  
Human Brain Development ◽  
Third Dimension

Stem cell technologies have opened up new avenues in the study of human biology and disease. Especially, the advent of human embryonic stem cells followed by reprograming technologies for generation of induced pluripotent stem cells have instigated studies for modeling human brain development and disease by providing a means to simulate a human tissue with otherwise limited or no accessibility to researchers. Brain development is a complex process achieved in a remarkably controlled spatial and temporal manner through coordinated cellular and molecular events. In vitro models aim to mimic these processes and recapitulate brain organogenesis. Initially, two-dimensional neural cultures presented an innovative landmark for investigating human neuronal and, more recently, glial biology as well as for modeling brain neurodevelopmental and neurodegenerative diseases. The establishment of three-dimensional cultures in the form of brain organoids was an equally important milestone in the field. Brain organoids mimic more closely the in vivo tissue composition and architecture and are more physiologically relevant than monolayer cultures. They therefore represent a more realistic cellular environment for modeling the cell biology and pathology of the nervous system. Here we highlight the journey to recapitulate human brain development and disease in-a-dish, starting from two-dimensional in vitro systems up to the third dimension provided by brain organoids. We discuss the potential of these approaches for modeling human brain development and evolution and their promise for understanding and treating brain disease.

scholarly journals The Transcription Regulator Patz1 Is Essential for Neural Stem Cell Maintenance and Proliferation

2021 ◽  
Vol 9 ◽  
Author(s):  
Sara Mancinelli ◽  
Michela Vitiello ◽  
Maria Donnini ◽  
Francesca Mantile ◽  
Giuseppe Palma ◽  
...  
Keyword(s):  
Stem Cell ◽  
Brain Development ◽  
Ex Vivo ◽  
Embryonic Stem ◽  
Adult Brain ◽  
Transcription Regulator ◽  
Stem Cell Maintenance ◽  
Stem And Progenitor Cells ◽  
Cell Maintenance

Proper regulation of neurogenesis, the process by which new neurons are generated from neural stem and progenitor cells (NS/PCs), is essential for embryonic brain development and adult brain function. The transcription regulator Patz1 is ubiquitously expressed in early mouse embryos and has a key role in embryonic stem cell maintenance. At later stages, the detection of Patz1 expression mainly in the developing brain suggests a specific involvement of Patz1 in neurogenesis. To address this point, we first got insights in Patz1 expression profile in different brain territories at both embryonic and postnatal stages, evidencing a general decreasing trend with respect to time. Then, we performed in vivo and ex vivo analysis of Patz1-knockout mice, focusing on the ventricular and subventricular zone, where we confirmed Patz1 enrichment through the analysis of public RNA-seq datasets. Both embryos and adults showed a significant reduction in the number of Patz1-null NS/PCs, as well as of their self-renewal capability, compared to controls. Consistently, molecular analysis revealed the downregulation of stemness markers in NS/PCs derived from Patz1-null mice. Overall, these data demonstrate the requirement of Patz1 for NS/PC maintenance and proliferation, suggesting new roles for this key transcription factor specifically in brain development and plasticity, with possible implications for neurodegenerative disorders and glial brain tumors.

scholarly journals Neuroserpin expression during human brain development and in adult brain revealed by immunohistochemistry and single cell RNA sequencing

2019 ◽  
Vol 235 (3) ◽  
pp. 543-554 ◽  
Author(s):  
Istvan Adorjan ◽  
Teadora Tyler ◽  
Aparna Bhaduri ◽  
Samuel Demharter ◽  
Cintia Klaudia Finszter ◽  
...  
Keyword(s):  
Human Brain ◽  
Brain Development ◽  
Single Cell ◽  
Rna Sequencing ◽  
Adult Brain ◽  
Human Brain Development ◽  
Single Cell Rna Sequencing

scholarly journals Analysis of genomic loci harboring 59,732 human-specific regulatory sequences reveals unique to human regulatory patterns associated with brain development

2018 ◽  
Author(s):  
Gennadi V. Glinsky
Keyword(s):  
Gene Expression ◽  
Brain Development ◽  
Regulatory Networks ◽  
Radial Glia ◽  
De Novo ◽  
Incomplete Lineage Sorting ◽  
Preimplantation Embryos ◽  
Regulatory Sequences ◽  
Genes Encoding ◽  
Human Specific

AbstractExtensive searches for genomic regions harboring various types of candidate human-specific regulatory sequences (HSRS) identified thousands’ HSRS using high-resolution next-generation sequencing technologies and methodologically diverse comparative analyses of human and non-human primates’ reference genomes. Here, a comprehensive catalogue of 59,732 genomic loci harboring candidate HSRS has been assembled to facilitate the systematic analyses of genomic sequences that were either inherited from extinct common ancestors (ECAs) or created de novo in human genomes. Present analyses identified thousands of HSRS that appear inherited from ECAs yet absent in genomes of our closest evolutionary relatives, Chimpanzee and Bonobo, presumably due to the incomplete lineage sorting and/or species-specific loss or regulatory DNA. This pattern is particularly prominent for HSRS that have been putatively associated with human-specific (HS) gene expression changes in cerebral organoid models. Significant fractions of retrotransposon-derived loci transcriptionally-active in human dorsolateral prefrontal cortex (DLPFC) are highly conserved in genomes of Gorilla, Orangutan, Gibbon, and Rhesus (1,688; 1,371; 1,148; and 1,045 loci, respectively), yet they are absent in genomes of both Chimpanzee and Bonobo. A prominent majority of regions harboring HS mutations associated with HS expression changes during brain development is highly conserved in Chimpanzee, Bonobo, and Gorilla genomes. Among non-human primates (NHP), dominant fractions of HSRS associated with HS gene expression in both excitatory neurons (347 loci; 67%) and radial glia (683 loci; 72%) are highly conserved in the Gorilla genome. Analysis of 4,433 genes encoding virus-interacting proteins (VIPs) revealed that 95.9% of human VIPs are components of HS regulatory networks that appear to operate in distinct types of human cells from preimplantation embryos to adult DLPFC. Present analyses demonstrate that Modern Humans captured unique combinations of regulatory sequences, divergent subsets of which are highly conserved in distinct species of six NHP separated by 30 million years of evolution. Concurrently, this unique-to-human mosaic of genomic regulatory patterns inherited from ECAs was supplemented with 12,486 created de novo HSRS. Present analyses of HSRS support the model of complex continuous speciation process during evolution of the human lineage that is not likely to occur as an instantaneous event. Genes encoding VIPs may represent a principal genomic target of HS regulatory networks, thus affecting a functionally diverse spectrum of biological processes controlled by VIP-containing liquid-liquid phase separated condensates.

scholarly journals Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

2018 ◽  
Author(s):  
Alex A Pollen ◽  
Aparna Bhaduri ◽  
Madeline G Andrews ◽  
Tomasz J Nowakowski ◽  
Olivia S Meyerson ◽  
...  
Keyword(s):  
Human Brain ◽  
Regulatory Networks ◽  
Radial Glia ◽  
Brain Size ◽  
Metabolic Stress ◽  
Brain Evolution ◽  
Cell Types ◽  
Segmental Duplications ◽  
Systematic Analysis ◽  
Human Specific

Direct comparisons of human and non-human primate brain tissue have the potential to reveal molecular pathways underlying remarkable specializations of the human brain. However, chimpanzee tissue is largely inaccessible during neocortical neurogenesis when differences in brain size first appear. To identify human-specific features of cortical development, we leveraged recent innovations that permit generating pluripotent stem cell-derived cerebral organoids from chimpanzee. First, we systematically evaluated the fidelity of organoid models to primary human and macaque cortex, finding organoid models preserve gene regulatory networks related to cell types and developmental processes but exhibit increased metabolic stress. Second, we identified 261 genes differentially expressed in human compared to chimpanzee organoids and macaque cortex. Many of these genes overlap with human-specific segmental duplications and a subset suggest increased PI3K/AKT/mTOR activation in human outer radial glia. Together, our findings establish a platform for systematic analysis of molecular changes contributing to human brain development and evolution.

scholarly journals One-stop Microfluidic Assembly of Human Brain Organoids to Model Prenatal Cannabis Exposure

2020 ◽  
Author(s):  
Zheng Ao ◽  
Hongwei Cai ◽  
Daniel J Havert ◽  
Zhuhao Wu ◽  
Zhiyi Gong ◽  
...  
Keyword(s):  
Human Brain ◽  
Brain Development ◽  
Developmental Disorders ◽  
Embryonic Stem ◽  
Microfluidic Platform ◽  
Cell Culture Techniques ◽  
Human Brain Development ◽  
One Stop ◽  
On Chip ◽  
Early Human

AbstractPrenatal cannabis exposure (PCE) influences human brain development, but it is challenging to model PCE using animals and current cell culture techniques. Here, we developed a one-stop microfluidic platform to assemble and culture human cerebral organoids from human embryonic stem cells (hESC) to investigate the effect of PCE on early human brain development. By incorporating perfusable culture chambers, air-liquid interface, and one-stop protocol, this microfluidic platform can simplify the fabrication procedure, and produce a large number of organoids (169 organoids per 3.5 cm x 3.5 cm device area) without fusion, as compared with conventional fabrication methods. These one-stop microfluidic assembled cerebral organoids not only recapitulate early human brain structure, biology, and electrophysiology but also have minimal size variation and hypoxia. Under on-chip exposure to the psychoactive cannabinoid, delta-9-tetrahydrocannabinol (THC), cerebral organoids exhibited reduced neuronal maturation, downregulation of cannabinoid receptor type 1 (CB1) receptors, and impaired neurite outgrowth. Moreover, transient on-chip THC treatment also decreased spontaneous firing in microfluidic assembled brain organoids. This one-stop microfluidic technique enables a simple, scalable, and repeatable organoid culture method that can be used not only for human brain organoids, but also for many other human organoids including liver, kidney, retina, and tumor organoids. This technology could be widely used in modeling brain and other organ development, developmental disorders, developmental pharmacology and toxicology, and drug screening.

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