scholarly journals Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation

2019 ◽  
Author(s):  
Amanda J. Price ◽  
Taeyoung Hwang ◽  
Ran Tao ◽  
Emily E. Burke ◽  
Anandita Rajpurohi ◽  
...  
Keyword(s):  
Brain Development ◽  
Rna Binding ◽  
Regulation Of Gene Expression ◽  
Adult Brain ◽  
Developmental Expression ◽  
Psychiatric Disease ◽  
Nuclear Pore ◽  
Nuclear Retention ◽  
Gene Sets ◽  
The Brain

AbstractTranscriptome compartmentalization by the nuclear membrane provides both stochastic and functional buffering of transcript activity in the cytoplasm and has recently been implicated in neurodegenerative disease processes. Although many mechanisms regulating transcript compartmentalization are also prevalent in brain development, the extent to which subcellular localization differs as the brain matures has yet to be addressed. To characterize the nuclear and cytoplasmic transcriptomes during brain development, we sequenced both RNA fractions from homogenate prenatal and adult human postmortem cortex using PolyA+ and RiboZero library preparation methods. We find that while many genes are differentially expressed by fraction and developmental expression changes are similarly detectable in nuclear and cytoplasmic RNA, the compartmented transcriptomes become more distinct as the brain matures, perhaps reflecting increased utilization of nuclear retention as a regulatory strategy in adult brain. We examined potential mechanisms of this developmental divergence including alternative splicing, RNA editing, nuclear pore composition, RNA binding protein motif enrichment, and RNA secondary structure. Intron retention is associated with greater nuclear abundance in a subset of transcripts, as is enrichment for several splicing factor binding motifs. Finally, we examined disease association with fraction-regulated gene sets and found nuclear-enriched genes were also preferentially enriched in gene sets associated with neurodevelopmental psychiatric diseases. These results suggest that although gene-level expression is globally comparable between fractions, nuclear retention of transcripts may play an underappreciated role in developmental regulation of gene expression in brain, particularly in genes whose dysregulation is related to neuropsychiatric disorders.

scholarly journals Broad Influence of Mutant Ataxin-3 on the Proteome of the Adult Brain, Young Neurons, and Axons Reveals Central Molecular Processes and Biomarkers in SCA3/MJD Using Knock-In Mouse Model

2021 ◽  
Vol 14 ◽  
Author(s):  
Kalina Wiatr ◽  
Łukasz Marczak ◽  
Jean-Baptiste Pérot ◽  
Emmanuel Brouillet ◽  
Julien Flament ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Disease Progression ◽  
Rna Binding ◽  
Brain Magnetic Resonance Imaging ◽  
Adult Brain ◽  
Spinocerebellar Ataxia Type ◽  
Cellular Transport ◽  
Cerebellar Neurons ◽  
Protein Synthesis Machinery ◽  
The Brain

Spinocerebellar ataxia type 3 (SCA3/MJD) is caused by CAG expansion mutation resulting in a long polyQ domain in mutant ataxin-3. The mutant protein is a special type of protease, deubiquitinase, which may indicate its prominent impact on the regulation of cellular proteins levels and activity. Yet, the global model picture of SCA3 disease progression on the protein level, molecular pathways in the brain, and neurons, is largely unknown. Here, we investigated the molecular SCA3 mechanism using an interdisciplinary research paradigm combining behavioral and molecular aspects of SCA3 in the knock-in ki91 model. We used the behavior, brain magnetic resonance imaging (MRI) and brain tissue examination to correlate the disease stages with brain proteomics, precise axonal proteomics, neuronal energy recordings, and labeling of vesicles. We have demonstrated that altered metabolic and mitochondrial proteins in the brain and the lack of weight gain in Ki91 SCA3/MJD mice is reflected by the failure of energy metabolism recorded in neonatal SCA3 cerebellar neurons. We have determined that further, during disease progression, proteins responsible for metabolism, cytoskeletal architecture, vesicular, and axonal transport are disturbed, revealing axons as one of the essential cell compartments in SCA3 pathogenesis. Therefore we focus on SCA3 pathogenesis in axonal and somatodendritic compartments revealing highly increased axonal localization of protein synthesis machinery, including ribosomes, translation factors, and RNA binding proteins, while the level of proteins responsible for cellular transport and mitochondria was decreased. We demonstrate the accumulation of axonal vesicles in neonatal SCA3 cerebellar neurons and increased phosphorylation of SMI-312 positive adult cerebellar axons, which indicate axonal dysfunction in SCA3. In summary, the SCA3 disease mechanism is based on the broad influence of mutant ataxin-3 on the neuronal proteome. Processes central in our SCA3 model include disturbed localization of proteins between axonal and somatodendritic compartment, early neuronal energy deficit, altered neuronal cytoskeletal structure, an overabundance of various components of protein synthesis machinery in axons.

scholarly journals Activation of endogenous retroviruses during brain development causes neuroinflammation

2020 ◽  
Author(s):  
Marie E Jönsson ◽  
Raquel Garza ◽  
Yogita Sharma ◽  
Rebecca Petri ◽  
Erik Södersten ◽  
...  
Keyword(s):  
Brain Development ◽  
Transcriptional Activation ◽  
Neural Progenitor Cells ◽  
Large Fraction ◽  
Endogenous Retroviruses ◽  
Adult Brain ◽  
Potential Trigger ◽  
Mammalian Genomes ◽  
The Brain

AbstractEndogenous retroviruses (ERVs) make up a large fraction of mammalian genomes and are thought to contribute to human disease, including brain disorders. In the brain, aberrant activation of ERVs is a potential trigger for neuroinflammation, but mechanistic insight into this phenomenon remains lacking. Using CRISPR/Cas9-based gene disruption of the epigenetic co-repressor protein Trim28, we found a dynamic H3K9me3-dependent regulation of ERVs in proliferating neural progenitor cells (NPCs), but not in adult neurons. In vivo deletion of Trim28 in cortical NPCs during mouse brain development resulted in viable offspring expressing high levels of ERV expression in excitatory neurons in the adult brain. Neuronal ERV expression was linked to inflammation, including activated microglia, and aggregates of ERV-derived proteins. This study demonstrates that brain development is a critical period for the silencing of ERVs and provides causal in vivo evidence demonstrating that transcriptional activation of ERV in neurons results in neuroinflammation.

scholarly journals Functional analysis of enhancer elements regulating the expression of the Drosophila homeodomain transcription factor DRx by gene targeting

Hereditas ◽  
2021 ◽  
Vol 158 (1) ◽  
Author(s):  
Christine Klöppel ◽  
Kirsten Hildebrandt ◽  
Dieter Kolb ◽  
Nora Fürst ◽  
Isabelle Bley ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Brain Development ◽  
Gene Targeting ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Adult Brain ◽  
Central Complex ◽  
Larval Brain ◽  
Endogenous Expression ◽  
The Brain

Abstract Background The Drosophila brain is an ideal model system to study stem cells, here called neuroblasts, and the generation of neural lineages. Many transcriptional activators are involved in formation of the brain during the development of Drosophila melanogaster. The transcription factor Drosophila Retinal homeobox (DRx), a member of the 57B homeobox gene cluster, is also one of these factors for brain development. Results In this study a detailed expression analysis of DRx in different developmental stages was conducted. We show that DRx is expressed in the embryonic brain in the protocerebrum, in the larval brain in the DM and DL lineages, the medulla and the lobula complex and in the central complex of the adult brain. We generated a DRx enhancer trap strain by gene targeting and reintegration of Gal4, which mimics the endogenous expression of DRx. With the help of eight existing enhancer-Gal4 strains and one made by our group, we mapped various enhancers necessary for the expression of DRx during all stages of brain development from the embryo to the adult. We made an analysis of some larger enhancer regions by gene targeting. Deletion of three of these enhancers showing the most prominent expression patterns in the brain resulted in specific temporal and spatial loss of DRx expression in defined brain structures. Conclusion Our data show that DRx is expressed in specific neuroblasts and defined neural lineages and suggest that DRx is another important factor for Drosophila brain development.

scholarly journals Channel nuclear pore protein 54 directs sexual differentiation and neuronal wiring of female reproductive behaviors in Drosophila

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Mohanakarthik P. Nallasivan ◽  
Irmgard U. Haussmann ◽  
Alberto Civetta ◽  
Matthias Soller
Keyword(s):  
Sexual Differentiation ◽  
Egg Laying ◽  
Adult Brain ◽  
Nuclear Pore ◽  
Reproductive Behaviors ◽  
Mating Response ◽  
Nuclear Pore Protein ◽  
Sex Peptide ◽  
The Brain ◽  
Pore Protein

Abstract Background Female reproductive behaviors and physiology change profoundly after mating. The control of pregnancy-associated changes in physiology and behaviors are largely hard-wired into the brain to guarantee reproductive success, yet the gene expression programs that direct neuronal differentiation and circuit wiring at the end of the sex determination pathway in response to mating are largely unknown. In Drosophila, the post-mating response induced by male-derived sex-peptide in females is a well-established model to elucidate how complex innate behaviors are hard-wired into the brain. Here, we use a genetic approach to further characterize the molecular and cellular architecture of the sex-peptide response in Drosophila females. Results Screening for mutations that affect the sensitivity to sex-peptide, we identified the channel nuclear pore protein Nup54 gene as an essential component for mediating the sex-peptide response, with viable mutant alleles leading to the inability of laying eggs and reducing receptivity upon sex-peptide exposure. Nup54 directs correct wiring of eight adult brain neurons that express pickpocket and are required for egg-laying, while additional channel Nups also mediate sexual differentiation. Consistent with links of Nups to speciation, the Nup54 promoter is a hot spot for rapid evolution and promoter variants alter nucleo-cytoplasmic shuttling. Conclusions These results implicate nuclear pore functionality to neuronal wiring underlying the sex-peptide response and sexual differentiation as a response to sexual conflict arising from male-derived sex-peptide to direct the female post-mating response.

scholarly journals Broad influence of mutant ataxin-3 on the proteome of the adult brain, young neurons, and axons reveals central molecular processes and biomarkers in SCA3/MJD using knock-in mouse model

2021 ◽  
Author(s):  
Kalina Wiatr ◽  
Łukasz Marczak ◽  
Jean-Baptiste Perot ◽  
Emmanuel Brouillet ◽  
Julien Flament ◽  
...  
Keyword(s):  
Disease Progression ◽  
Rna Binding ◽  
Adult Brain ◽  
Energy Deficit ◽  
Spinocerebellar Ataxia Type ◽  
Cellular Transport ◽  
Molecular Processes ◽  
Disease Mechanism ◽  
Cerebellar Neurons ◽  
The Brain

AbstractSpinocerebellar ataxia type 3 (SCA3/MJD) has a polyQ etiology but, the current knowledge on molecular processes and proteins involved in pathogenesis is not sufficient to fully determine the disease mechanism and find drug targets. Proteases and deubiquitinases, such as Ataxin-3, often have a profound impact on other proteins, yet the global model picture of SCA3 disease progression on the protein level, showing the most crucial proteins and pathways in the brain, and neurons, was not investigated previously. Here, we investigated molecular SCA3 mechanism using interdisciplinary research paradigm combining SCA3 knock-in model, behavior, MRI, brain proteomics, precise axonal proteomics, neuronal energy recordings, labeling of vesicles, and inclusions and focusing in axonal compartment. We have demonstrated that altered metabolic and mitochondrial proteins in the brain and the lack of weight gain in Ki91 SCA3/MJD mice is reflected by the failure of energy metabolism recorded in neonatal SCA3 cerebellar neurons. We have determined that further, during disease progression, proteins responsible for metabolism, cytoskeletal architecture, vesicular and axonal transport proteins are disturbed, revealing axons as one of the essential cell compartments in SCA3 pathogenesis. Therefore we focus on SCA3 pathogenesis in axonal and somatodendritic compartments revealing highly increased axonal localization of protein synthesis machinery, including ribosomes, translation factors, and RNA binding proteins, while the level of proteins responsible for cellular transport, and mitochondria was decreased. We demonstrate the accumulation of axonal vesicles in neonatal SCA3 cerebellar neurons and increased phosphorylation of SMI-312 positive adult cerebellar axons, which indicate axonal dysfunction in SCA3. In summary, the SCA3 disease mechanism is based on the broad influence of mutant ataxin-3 on the neuronal proteome. Processes central in our SCA3 model include disturbed localization of proteins between axonal and somatodendritic compartment, early neuronal energy deficit, altered neuronal cytoskeletal structure, an overabundance of protein synthetic machinery in axons.

scholarly journals Expression of Brain-Specific Angiogenesis Inhibitor 2 (BAI2) in Normal and Ischemic Brain: Involvement of BAI2 in the Ischemia-Induced Brain Angiogenesis

2002 ◽  
Vol 22 (9) ◽  
pp. 1054-1067 ◽  
Author(s):  
Hae Jin Kee ◽  
Jeong Tae Koh ◽  
Mi-Young Kim ◽  
Kyu Youn Ahn ◽  
Jong Keun Kim ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Angiogenesis Inhibitor ◽  
Adult Brain ◽  
Developmental Expression ◽  
Hypoxic Cell ◽  
Type I ◽  
Rt Pcr ◽  
The Brain ◽  
Developmental Expression Pattern ◽  
Brain Angiogenesis

Previously, the authors cloned and characterized murine brain-specific angiogenesis inhibitor 1 (mBAI1). In this study, the authors cloned mBAI2 and analyzed its functional characteristics. Northern and Western blot analyses demonstrated a unique developmental expression pattern of mBAI2 in the brain. The expression level of mBAI2 appeared to increase as the development of the brain progressed. Reverse transcription-polymerase chain reaction (RT-PCR) analyses demonstrated the existence of alternative splice variants of mBAI2, which were defective in parts of type I repeat of thrombospondin or the third cytoplasmic loop of the seven-span transmembrane domain that were considered essential to the functions of mBAI2. The expressions of spliced variants in the brain were differently regulated compared with wild-type mBAI2 during development and ischemic conditions. In situ hybridization analyses of the brain showed the same localization of BAI2 as BAI1, such as in most neurons of cerebral cortex. In the in vivo focal cerebral ischemia model and the in vitro hypoxic cell culture model with cobalt, BAI2 expression decreased after hypoxia and preceded the increased expression of vascular endothelial growth factor (VEGF). RT-PCR analysis of antisense BAI2 cDNA-transfected SHSY5Y cells showed an increased VEGF expression as well as a decreased BAI2 expression. Immunohistochemical study of focal ischemic cortex showed that the regional localization of decreased BAI2 was related to the formation of new vessels. These results suggest that the brain-specific developmental expression pattern of angiostatic BAI2 is correlated with the decreased neovascularization in the adult brain, and that angiostatic BAI2 participates in the ischemia-induced brain angiogenesis in concert with angiogenic VEGF.

Brain Fuel Utilization in the Developing Brain

2019 ◽  
Vol 75 (1) ◽  
pp. 8-18 ◽  
Author(s):  
Pascal Steiner
Keyword(s):  
Brain Development ◽  
Ketone Bodies ◽  
Brain Connectivity ◽  
Signal Transmission ◽  
Neuronal Cell ◽  
Building Blocks ◽  
The Body ◽  
Adult Brain ◽  
Acid Oxidation ◽  
The Brain

During pregnancy and infancy, the human brain is growing extremely fast; the brain volume increases significantly, reaching 36, 72, and 83% of the volume of adults at 2–4 weeks, 1 year, and 2 years of age, respectively, which is essential to establish the neuronal networks and capacity for the development of cognitive, motor, social, and emotional skills that will be continually refined throughout childhood and adulthood. Such dramatic changes in brain structure and function are associated with very large energetic demands exceeding by far those of other organs of the body. It has been estimated that during childhood the brain may account for up to 60% of the body basal energetic requirements. While the main source of energy for the adult brain is glucose, it appears that it is not sufficient to sustain the dramatic metabolic demands of the brain during its development. Recently, it has been proposed that this energetic challenge is solved by the ability of the brain to use ketone bodies (KBs), produced from fatty acid oxidation, as a complement source of energy. Here, we first describe the main cellular and physiological processes that drive brain development along time and how different brain metabolic pathways are engaged to support them. It has been assumed that the majority of energetic substrates are used to support neuronal activity and signal transmission. We discuss how glucose and KBs are metabolized to provide the carbon backbones used to synthesize lipids, nucleic acid, and cholesterol, which are indispensable building blocks of neuronal cell proliferation and are also used to establish and refine brain connectivity through synapse formation/elimination and myelination. We conclude that glucose and KBs are not only important to support the energy needs of the brain under development, but they are also essential substrates for the biosynthesis of macromolecules underlying structural brain growth and reorganization. We emphasize that glucose and fatty acids supporting the production of KBs are provided in complex food matrices, such as breast milk, and understanding how their availability impacts the brain will be key to promote adequate nutrition to support brain metabolism and, therefore, optimal brain development.

scholarly journals Nuclear RNA binding regulates TDP-43 nuclear localization and passive nuclear export

2021 ◽  
Author(s):  
Lauren Duan ◽  
Benjamin L. Zaepfel ◽  
Vasilisa Aksenova ◽  
Mary Dasso ◽  
Jeffrey D. Rothstein ◽  
...  
Keyword(s):  
Nuclear Localization ◽  
Nuclear Export ◽  
Rna Binding ◽  
Nuclear Accumulation ◽  
Nuclear Pore ◽  
Nuclear Retention ◽  
Rna Recognition Motifs ◽  
Nuclear Abundance ◽  
Recognition Motifs

AbstractNuclear clearance of the DNA/RNA-binding protein TDP-43 is a pathologic hallmark of amyotrophic lateral sclerosis and frontotemporal dementia that remains unexplained. Moreover, our current understanding of TDP-43 nucleocytoplasmic shuttling does not fully explain the predominantly nuclear localization of TDP-43 in healthy cells. Here, we used permeabilized and live-cell models to investigate TDP-43 nuclear export and the role of RNA in TDP-43 localization. We show that TDP-43 nuclear efflux occurs in low-ATP conditions and independent of active mRNA export, consistent with export by passive diffusion through nuclear pore channels. TDP-43 nuclear residence requires binding to GU-rich nuclear intronic pre-mRNAs, based on the induction of TDP-43 nuclear efflux by RNase and GU-rich oligomers and TDP-43 nuclear retention conferred by pre-mRNA splicing inhibitors. Mutation of TDP-43 RNA recognition motifs disrupts TDP-43 nuclear accumulation and abolishes transcriptional blockade-induced TDP-43 nuclear efflux, demonstrating strict dependence of TDP-43 nuclear localization on RNA binding. Thus, the nuclear abundance of GU-rich intronic pre-mRNAs, as dictated by the balance of transcription and pre-mRNA processing, regulates TDP-43 nuclear sequestration and availability for passive nuclear export.

scholarly journals Regulatory modules mediating the complex neural expression patterns of the homeobrain gene during Drosophila brain development

Hereditas ◽  
2022 ◽  
Vol 159 (1) ◽  
Author(s):  
Kirsten Hildebrandt ◽  
Dieter Kolb ◽  
Christine Klöppel ◽  
Petra Kaspar ◽  
Fabienne Wittling ◽  
...  
Keyword(s):  
Brain Development ◽  
Gene Targeting ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Adult Brain ◽  
Specific Cell ◽  
Larval Brain ◽  
Developmental Defects ◽  
The Brain

Abstract Background The homeobox gene homeobrain (hbn) is located in the 57B region together with two other homeobox genes, Drosophila Retinal homeobox (DRx) and orthopedia (otp). All three genes encode transcription factors with important functions in brain development. Hbn mutants are embryonic lethal and characterized by a reduction in the anterior protocerebrum, including the mushroom bodies, and a loss of the supraoesophageal brain commissure. Results In this study we conducted a detailed expression analysis of Hbn in later developmental stages. In the larval brain, Hbn is expressed in all type II lineages and the optic lobes, including the medulla and lobula plug. The gene is expressed in the cortex of the medulla and the lobula rim in the adult brain. We generated a new hbnKOGal4 enhancer trap strain by reintegrating Gal4 in the hbn locus through gene targeting, which reflects the complete hbn expression during development. Eight different enhancer-Gal4 strains covering 12 kb upstream of hbn, the two large introns and 5 kb downstream of the gene, were established and hbn expression was investigated. We characterized several enhancers that drive expression in specific areas of the brain throughout development, from embryo to the adulthood. Finally, we generated deletions of four of these enhancer regions through gene targeting and analysed their effects on the expression and function of hbn. Conclusion The complex expression of Hbn in the developing brain is regulated by several specific enhancers within the hbn locus. Each enhancer fragment drives hbn expression in several specific cell lineages, and with largely overlapping patterns, suggesting the presence of shadow enhancers and enhancer redundancy. Specific enhancer deletion strains generated by gene targeting display developmental defects in the brain. This analysis opens an avenue for a deeper analysis of hbn regulatory elements in the future.

Elementary, my dear Watson, the clue is in the genes…or is it?

2003 ◽  
Author(s):  
ANNETTE KARMILOFF-SMITH
Keyword(s):  
Regulation Of Gene Expression ◽  
Gene Interaction ◽  
Developmental Time ◽  
Vital Role ◽  
Adult Brain ◽  
Environment Interaction ◽  
Gene Environment Interaction ◽  
Gene Environment ◽  
Infant Brain ◽  
The Brain

This chapter argues that there is no one-to-one, direct mapping between specific sets of genes and cognitive-level outcomes. Rather, there are very indirect mappings, with the regulation of gene expression more likely to contribute to very broad differences in developmental timing, neuronal type, neuronal density, firing thresholds, neurotransmitter types, etc. It presents the neuroconstructivist framework where gene/gene interaction, gene/environment interaction and, crucially, the process of ontogeny itself (pre- and postnatal development) are all considered to play a vital role in how genes are expressed and how the brain progressively sculpts itself, slowly becoming specialised over developmental time. The infant brain is not simply a miniature version of the adult brain.

Sign in / Sign up

Export Citation Format

Share Document