31 results on '"Harmin DA"'
Search Results
2. A NPAS4-NuA4 complex couples synaptic activity to DNA repair.
- Author
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Pollina EA, Gilliam DT, Landau AT, Lin C, Pajarillo N, Davis CP, Harmin DA, Yap EL, Vogel IR, Griffith EC, Nagy MA, Ling E, Duffy EE, Sabatini BL, Weitz CJ, and Greenberg ME
- Subjects
- Basic Helix-Loop-Helix Transcription Factors, DNA Breaks, Double-Stranded, Gene Expression Regulation, Lysine Acetyltransferase 5 metabolism, Mutation, Longevity genetics, Genome, Aging genetics, Neurodegenerative Diseases, Brain metabolism, DNA Repair, Multiprotein Complexes metabolism, Neurons metabolism, Synapses metabolism
- Abstract
Neuronal activity is crucial for adaptive circuit remodelling but poses an inherent risk to the stability of the genome across the long lifespan of postmitotic neurons
1-5 . Whether neurons have acquired specialized genome protection mechanisms that enable them to withstand decades of potentially damaging stimuli during periods of heightened activity is unknown. Here we identify an activity-dependent DNA repair mechanism in which a new form of the NuA4-TIP60 chromatin modifier assembles in activated neurons around the inducible, neuronal-specific transcription factor NPAS4. We purify this complex from the brain and demonstrate its functions in eliciting activity-dependent changes to neuronal transcriptomes and circuitry. By characterizing the landscape of activity-induced DNA double-strand breaks in the brain, we show that NPAS4-NuA4 binds to recurrently damaged regulatory elements and recruits additional DNA repair machinery to stimulate their repair. Gene regulatory elements bound by NPAS4-NuA4 are partially protected against age-dependent accumulation of somatic mutations. Impaired NPAS4-NuA4 signalling leads to a cascade of cellular defects, including dysregulated activity-dependent transcriptional responses, loss of control over neuronal inhibition and genome instability, which all culminate to reduce organismal lifespan. In addition, mutations in several components of the NuA4 complex are reported to lead to neurodevelopmental and autism spectrum disorders. Together, these findings identify a neuronal-specific complex that couples neuronal activity directly to genome preservation, the disruption of which may contribute to developmental disorders, neurodegeneration and ageing., (© 2023. The Author(s).)- Published
- 2023
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3. Modeling human telencephalic development and autism-associated SHANK3 deficiency using organoids generated from single neural rosettes.
- Author
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Wang Y, Chiola S, Yang G, Russell C, Armstrong CJ, Wu Y, Spampanato J, Tarboton P, Ullah HMA, Edgar NU, Chang AN, Harmin DA, Bocchi VD, Vezzoli E, Besusso D, Cui J, Cattaneo E, Kubanek J, and Shcheglovitov A
- Subjects
- Humans, Nerve Tissue Proteins metabolism, Organoids metabolism, Protocadherins, Telencephalon, Autistic Disorder genetics
- Abstract
Human telencephalon is an evolutionarily advanced brain structure associated with many uniquely human behaviors and disorders. However, cell lineages and molecular pathways implicated in human telencephalic development remain largely unknown. We produce human telencephalic organoids from stem cell-derived single neural rosettes and investigate telencephalic development under normal and pathological conditions. We show that single neural rosette-derived organoids contain pallial and subpallial neural progenitors, excitatory and inhibitory neurons, as well as macroglial and periendothelial cells, and exhibit predictable organization and cytoarchitecture. We comprehensively characterize the properties of neurons in SNR-derived organoids and identify transcriptional programs associated with the specification of excitatory and inhibitory neural lineages from a common pool of NPs early in telencephalic development. We also demonstrate that neurons in organoids with a hemizygous deletion of an autism- and intellectual disability-associated gene SHANK3 exhibit intrinsic and excitatory synaptic deficits and impaired expression of several clustered protocadherins. Collectively, this study validates SNR-derived organoids as a reliable model for studying human telencephalic cortico-striatal development and identifies intrinsic, synaptic, and clustered protocadherin expression deficits in human telencephalic tissue with SHANK3 hemizygosity., (© 2022. The Author(s).)
- Published
- 2022
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4. Activity-dependent regulome of human GABAergic neurons reveals new patterns of gene regulation and neurological disease heritability.
- Author
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Boulting GL, Durresi E, Ataman B, Sherman MA, Mei K, Harmin DA, Carter AC, Hochbaum DR, Granger AJ, Engreitz JM, Hrvatin S, Blanchard MR, Yang MG, Griffith EC, and Greenberg ME
- Subjects
- Genome-Wide Association Study, Humans, Induced Pluripotent Stem Cells metabolism, Promoter Regions, Genetic, Brain metabolism, Epigenesis, Genetic, GABAergic Neurons metabolism, Gene Expression Regulation
- Abstract
Neuronal activity-dependent gene expression is essential for brain development. Although transcriptional and epigenetic effects of neuronal activity have been explored in mice, such an investigation is lacking in humans. Because alterations in GABAergic neuronal circuits are implicated in neurological disorders, we conducted a comprehensive activity-dependent transcriptional and epigenetic profiling of human induced pluripotent stem cell-derived GABAergic neurons similar to those of the early developing striatum. We identified genes whose expression is inducible after membrane depolarization, some of which have specifically evolved in primates and/or are associated with neurological diseases, including schizophrenia and autism spectrum disorder (ASD). We define the genome-wide profile of human neuronal activity-dependent enhancers, promoters and the transcription factors CREB and CRTC1. We found significant heritability enrichment for ASD in the inducible promoters. Our results suggest that sequence variation within activity-inducible promoters of developing human forebrain GABAergic neurons contributes to ASD risk.
- Published
- 2021
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5. Bidirectional perisomatic inhibitory plasticity of a Fos neuronal network.
- Author
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Yap EL, Pettit NL, Davis CP, Nagy MA, Harmin DA, Golden E, Dagliyan O, Lin C, Rudolph S, Sharma N, Griffith EC, Harvey CD, and Greenberg ME
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- Animals, CA1 Region, Hippocampal metabolism, Cholecystokinin metabolism, Exploratory Behavior physiology, Female, Gamma Rhythm, Interneurons metabolism, Male, Memory Consolidation, Mice, Parvalbumins metabolism, Pyramidal Cells metabolism, Secretogranin II genetics, Secretogranin II metabolism, Spatial Navigation physiology, Theta Rhythm, Nerve Net cytology, Nerve Net physiology, Neural Inhibition, Neuronal Plasticity physiology, Proto-Oncogene Proteins c-fos metabolism
- Abstract
Behavioural experiences activate the FOS transcription factor in sparse populations of neurons that are critical for encoding and recalling specific events
1-3 . However, there is limited understanding of the mechanisms by which experience drives circuit reorganization to establish a network of Fos-activated cells. It is also not known whether FOS is required in this process beyond serving as a marker of recent neural activity and, if so, which of its many gene targets underlie circuit reorganization. Here we demonstrate that when mice engage in spatial exploration of novel environments, perisomatic inhibition of Fos-activated hippocampal CA1 pyramidal neurons by parvalbumin-expressing interneurons is enhanced, whereas perisomatic inhibition by cholecystokinin-expressing interneurons is weakened. This bidirectional modulation of inhibition is abolished when the function of the FOS transcription factor complex is disrupted. Single-cell RNA-sequencing, ribosome-associated mRNA profiling and chromatin analyses, combined with electrophysiology, reveal that FOS activates the transcription of Scg2, a gene that encodes multiple distinct neuropeptides, to coordinate these changes in inhibition. As parvalbumin- and cholecystokinin-expressing interneurons mediate distinct features of pyramidal cell activity4-6 , the SCG2-dependent reorganization of inhibitory synaptic input might be predicted to affect network function in vivo. Consistent with this prediction, hippocampal gamma rhythms and pyramidal cell coupling to theta phase are significantly altered in the absence of Scg2. These findings reveal an instructive role for FOS and SCG2 in establishing a network of Fos-activated neurons via the rewiring of local inhibition to form a selectively modulated state. The opposing plasticity mechanisms acting on distinct inhibitory pathways may support the consolidation of memories over time.- Published
- 2021
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6. Mapping the cis -regulatory architecture of the human retina reveals noncoding genetic variation in disease.
- Author
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Cherry TJ, Yang MG, Harmin DA, Tao P, Timms AE, Bauwens M, Allikmets R, Jones EM, Chen R, De Baere E, and Greenberg ME
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- Adult, Animals, DNA Mutational Analysis, Epigenomics, Female, Genetic Variation, Humans, Male, Mice, Middle Aged, Mutation, RNA-Seq, Retina growth & development, Retinal Diseases pathology, Species Specificity, Evolution, Molecular, Gene Expression Regulation, Developmental, Regulatory Sequences, Nucleic Acid genetics, Retina pathology, Retinal Diseases genetics
- Abstract
The interplay of transcription factors and cis -regulatory elements (CREs) orchestrates the dynamic and diverse genetic programs that assemble the human central nervous system (CNS) during development and maintain its function throughout life. Genetic variation within CREs plays a central role in phenotypic variation in complex traits including the risk of developing disease. We took advantage of the retina, a well-characterized region of the CNS known to be affected by pathogenic variants in CREs, to establish a roadmap for characterizing regulatory variation in the human CNS. This comprehensive analysis of tissue-specific regulatory elements, transcription factor binding, and gene expression programs in three regions of the human visual system (retina, macula, and retinal pigment epithelium/choroid) reveals features of regulatory element evolution that shape tissue-specific gene expression programs and defines regulatory elements with the potential to contribute to Mendelian and complex disorders of human vision., Competing Interests: The authors declare no competing interest.
- Published
- 2020
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7. Visual Experience-Dependent Expression of Fn14 Is Required for Retinogeniculate Refinement.
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Cheadle L, Tzeng CP, Kalish BT, Harmin DA, Rivera S, Ling E, Nagy MA, Hrvatin S, Hu L, Stroud H, Burkly LC, Chen C, and Greenberg ME
- Subjects
- Animals, Female, Gene Expression, Geniculate Bodies growth & development, Male, Mice, Mice, Inbred C57BL, Mice, Knockout, Mice, Transgenic, Optic Tract growth & development, Optic Tract metabolism, Retina metabolism, TWEAK Receptor genetics, Geniculate Bodies metabolism, Retinal Ganglion Cells metabolism, TWEAK Receptor biosynthesis, Visual Perception physiology
- Abstract
Sensory experience influences the establishment of neural connectivity through molecular mechanisms that remain unclear. Here, we employ single-nucleus RNA sequencing to investigate the contribution of sensory-driven gene expression to synaptic refinement in the dorsal lateral geniculate nucleus of the thalamus, a region of the brain that processes visual information. We find that visual experience induces the expression of the cytokine receptor Fn14 in excitatory thalamocortical neurons. By combining electrophysiological and structural techniques, we show that Fn14 is dispensable for early phases of refinement mediated by spontaneous activity but that Fn14 is essential for refinement during a later, experience-dependent period of development. Refinement deficits in mice lacking Fn14 are associated with functionally weaker and structurally smaller retinogeniculate inputs, indicating that Fn14 mediates both functional and anatomical rearrangements in response to sensory experience. These findings identify Fn14 as a molecular link between sensory-driven gene expression and vision-sensitive refinement in the brain., (Copyright © 2018 Elsevier Inc. All rights reserved.)
- Published
- 2018
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8. AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection.
- Author
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Vierbuchen T, Ling E, Cowley CJ, Couch CH, Wang X, Harmin DA, Roberts CWM, and Greenberg ME
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- Animals, Chromatin genetics, Chromosomal Proteins, Non-Histone genetics, Female, Gene Expression Regulation, Neoplastic, Male, Mice, Inbred C57BL, Mice, Knockout, Nucleosomes, Promoter Regions, Genetic, Transcription Factors genetics, Chromatin metabolism, Chromosomal Proteins, Non-Histone metabolism, Enhancer Elements, Genetic, Proto-Oncogene Proteins c-fos physiology, Transcription Factors metabolism, Transcription Factors physiology
- Abstract
Enhancer elements are genomic regulatory sequences that direct the selective expression of genes so that genetically identical cells can differentiate and acquire the highly specialized forms and functions required to build a functioning animal. To differentiate, cells must select from among the ∼10
6 enhancers encoded in the genome the thousands of enhancers that drive the gene programs that impart their distinct features. We used a genetic approach to identify transcription factors (TFs) required for enhancer selection in fibroblasts. This revealed that the broadly expressed, growth-factor-inducible TFs FOS/JUN (AP-1) play a central role in enhancer selection. FOS/JUN selects enhancers together with cell-type-specific TFs by collaboratively binding to nucleosomal enhancers and recruiting the SWI/SNF (BAF) chromatin remodeling complex to establish accessible chromatin. These experiments demonstrate how environmental signals acting via FOS/JUN and BAF coordinate with cell-type-specific TFs to select enhancer repertoires that enable differentiation during development., (Copyright © 2017 Elsevier Inc. All rights reserved.)- Published
- 2017
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9. Evolution of Osteocrin as an activity-regulated factor in the primate brain.
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Ataman B, Boulting GL, Harmin DA, Yang MG, Baker-Salisbury M, Yap EL, Malik AN, Mei K, Rubin AA, Spiegel I, Durresi E, Sharma N, Hu LS, Pletikos M, Griffith EC, Partlow JN, Stevens CR, Adli M, Chahrour M, Sestan N, Walsh CA, Berezovskii VK, Livingstone MS, and Greenberg ME
- Subjects
- Animals, Base Sequence, Bone and Bones metabolism, Dendrites metabolism, Enhancer Elements, Genetic genetics, Female, Humans, MEF2 Transcription Factors metabolism, Macaca mulatta, Male, Mice, Molecular Sequence Data, Muscle Proteins genetics, Muscles metabolism, Neocortex cytology, Neurons cytology, Organ Specificity, Species Specificity, Transcription Factors genetics, Evolution, Molecular, Muscle Proteins metabolism, Neocortex metabolism, Neurons metabolism, Transcription Factors metabolism, Transcriptome
- Abstract
Sensory stimuli drive the maturation and function of the mammalian nervous system in part through the activation of gene expression networks that regulate synapse development and plasticity. These networks have primarily been studied in mice, and it is not known whether there are species- or clade-specific activity-regulated genes that control features of brain development and function. Here we use transcriptional profiling of human fetal brain cultures to identify an activity-dependent secreted factor, Osteocrin (OSTN), that is induced by membrane depolarization of human but not mouse neurons. We find that OSTN has been repurposed in primates through the evolutionary acquisition of DNA regulatory elements that bind the activity-regulated transcription factor MEF2. In addition, we demonstrate that OSTN is expressed in primate neocortex and restricts activity-dependent dendritic growth in human neurons. These findings suggest that, in response to sensory input, OSTN regulates features of neuronal structure and function that are unique to primates.
- Published
- 2016
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10. Genomic mapping and cellular expression of human CPG2 transcripts in the SYNE1 gene.
- Author
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Loebrich S, Rathje M, Hager E, Ataman B, Harmin DA, Greenberg ME, and Nedivi E
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- Animals, Brain cytology, Brain metabolism, Cells, Cultured, Chromosome Mapping methods, Cytoskeletal Proteins, Dendritic Spines metabolism, Endocytosis, HEK293 Cells, Humans, Nerve Tissue Proteins metabolism, Nuclear Proteins metabolism, Polymorphism, Single Nucleotide, Rats, Receptors, Glutamate metabolism, Synapses metabolism, Transcriptome, Genome, Human, Nerve Tissue Proteins genetics, Nuclear Proteins genetics
- Abstract
Bipolar disorder (BD) is a prevalent and severe mood disorder characterized by recurrent episodes of mania and depression. Both genetic and environmental factors have been implicated in BD etiology, but the biological underpinnings remain elusive. Recent genome-wide association studies (GWAS) for identifying genes conferring risk for schizophrenia, BD, and major depression, identified an association between single-nucleotide polymorphisms (SNPs) in the SYNE1 gene and increased risk of BD. SYNE1 has also been identified as a risk locus for multiple other neurological or neuromuscular genetic disorders. The BD associated SNPs map within the gene region homologous to part of rat Syne1 encompassing the brain specific transcripts encoding CPG2, a postsynaptic neuronal protein localized to excitatory synapses and an important regulator of glutamate receptor internalization. Here, we use RNA-seq, ChIP-seq and RACE to map the human SYNE1 transcriptome, focusing on the CPG2 locus. We validate several CPG2 transcripts, including ones not previously annotated in public databases, and identify and clone a full-length CPG2 cDNA expressed in human neocortex, hippocampus and striatum. Using lenti-viral gene knock down/replacement and surface receptor internalization assays, we demonstrate that human CPG2 protein localizes to dendritic spines in rat hippocampal neurons and is functionally equivalent to rat CPG2 in regulating glutamate receptor internalization. This study provides a valuable gene-mapping framework for relating multiple genetic disease loci in SYNE1 with their transcripts, and for evaluating the effects of missense SNPs identified by patient genome sequencing on neuronal function., (Copyright © 2015 Elsevier Inc. All rights reserved.)
- Published
- 2016
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11. Disruption of DNA-methylation-dependent long gene repression in Rett syndrome.
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Gabel HW, Kinde B, Stroud H, Gilbert CS, Harmin DA, Kastan NR, Hemberg M, Ebert DH, and Greenberg ME
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- Animals, Base Sequence, Brain metabolism, DNA (Cytosine-5-)-Methyltransferases metabolism, DNA Methyltransferase 3A, Disease Models, Animal, Female, Gene Expression Regulation, Humans, Male, Methyl-CpG-Binding Protein 2 deficiency, Mice, Molecular Sequence Data, Neurons metabolism, DNA Methylation genetics, Methyl-CpG-Binding Protein 2 genetics, Methyl-CpG-Binding Protein 2 metabolism, Mutation genetics, Rett Syndrome genetics
- Abstract
Disruption of the MECP2 gene leads to Rett syndrome (RTT), a severe neurological disorder with features of autism. MECP2 encodes a methyl-DNA-binding protein that has been proposed to function as a transcriptional repressor, but despite numerous mouse studies examining neuronal gene expression in Mecp2 mutants, no clear model has emerged for how MeCP2 protein regulates transcription. Here we identify a genome-wide length-dependent increase in gene expression in MeCP2 mutant mouse models and human RTT brains. We present evidence that MeCP2 represses gene expression by binding to methylated CA sites within long genes, and that in neurons lacking MeCP2, decreasing the expression of long genes attenuates RTT-associated cellular deficits. In addition, we find that long genes as a population are enriched for neuronal functions and selectively expressed in the brain. These findings suggest that mutations in MeCP2 may cause neurological dysfunction by specifically disrupting long gene expression in the brain.
- Published
- 2015
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12. MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers.
- Author
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Andzelm MM, Cherry TJ, Harmin DA, Boeke AC, Lee C, Hemberg M, Pawlyk B, Malik AN, Flavell SW, Sandberg MA, Raviola E, and Greenberg ME
- Subjects
- Adaptation, Ocular genetics, Age Factors, Animals, Animals, Newborn, Chromatin Immunoprecipitation, Electroretinography, Embryo, Mammalian, Eye Proteins metabolism, Genome, Green Fluorescent Proteins genetics, Green Fluorescent Proteins metabolism, MEF2 Transcription Factors genetics, MEF2 Transcription Factors metabolism, Mice, Mice, Inbred C57BL, Mice, Knockout, Mutation genetics, Retina growth & development, Gene Expression Regulation, Developmental genetics, Homeodomain Proteins metabolism, Photoreceptor Cells physiology, Retina cytology, Trans-Activators metabolism
- Abstract
Organismal development requires the precise coordination of genetic programs to regulate cell fate and function. MEF2 transcription factors (TFs) play essential roles in this process but how these broadly expressed factors contribute to the generation of specific cell types during development is poorly understood. Here we show that despite being expressed in virtually all mammalian tissues, in the retina MEF2D binds to retina-specific enhancers and controls photoreceptor cell development. MEF2D achieves specificity by cooperating with a retina-specific factor CRX, which recruits MEF2D away from canonical MEF2 binding sites and redirects it to retina-specific enhancers that lack the consensus MEF2-binding sequence. Once bound to retina-specific enhancers, MEF2D and CRX co-activate the expression of photoreceptor-specific genes that are critical for retinal function. These findings demonstrate that broadly expressed TFs acquire specific functions through competitive recruitment to enhancers by tissue-specific TFs and through selective activation of these enhancers to regulate tissue-specific genes., (Copyright © 2015 Elsevier Inc. All rights reserved.)
- Published
- 2015
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13. Genome-wide identification and characterization of functional neuronal activity-dependent enhancers.
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Malik AN, Vierbuchen T, Hemberg M, Rubin AA, Ling E, Couch CH, Stroud H, Spiegel I, Farh KK, Harmin DA, and Greenberg ME
- Subjects
- 2-Amino-5-phosphonovalerate pharmacology, Animals, CREB-Binding Protein metabolism, Embryo, Mammalian, Excitatory Amino Acid Antagonists pharmacology, Gene Expression Regulation drug effects, Genome-Wide Association Study, Humans, Jumonji Domain-Containing Histone Demethylases metabolism, MEF2 Transcription Factors genetics, MEF2 Transcription Factors metabolism, Mice, Mice, Inbred C57BL, Mutation genetics, Neurons drug effects, Oncogene Proteins v-fos metabolism, Potassium Chloride pharmacology, Sodium Channel Blockers pharmacology, Tetrodotoxin pharmacology, Time Factors, Visual Cortex cytology, Gene Expression Regulation genetics, Neurons physiology
- Abstract
Experience-dependent gene transcription is required for nervous system development and function. However, the DNA regulatory elements that control this program of gene expression are not well defined. Here we characterize the enhancers that function across the genome to mediate activity-dependent transcription in mouse cortical neurons. We find that the subset of enhancers enriched for monomethylation of histone H3 Lys4 (H3K4me1) and binding of the transcriptional coactivator CREBBP (also called CBP) that shows increased acetylation of histone H3 Lys27 (H3K27ac) after membrane depolarization of cortical neurons functions to regulate activity-dependent transcription. A subset of these enhancers appears to require binding of FOS, which was previously thought to bind primarily to promoters. These findings suggest that FOS functions at enhancers to control activity-dependent gene programs that are critical for nervous system function and provide a resource of functional cis-regulatory elements that may give insight into the genetic variants that contribute to brain development and disease.
- Published
- 2014
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14. Npas4 regulates excitatory-inhibitory balance within neural circuits through cell-type-specific gene programs.
- Author
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Spiegel I, Mardinly AR, Gabel HW, Bazinet JE, Couch CH, Tzeng CP, Harmin DA, and Greenberg ME
- Subjects
- Animals, Basic Helix-Loop-Helix Transcription Factors genetics, Cell Culture Techniques, Embryo, Mammalian cytology, Mice, Mice, Knockout, Synapses metabolism, Basic Helix-Loop-Helix Transcription Factors metabolism, Gene Expression Regulation, Neurons metabolism, Transcription, Genetic
- Abstract
The nervous system adapts to experience by inducing a transcriptional program that controls important aspects of synaptic plasticity. Although the molecular mechanisms of experience-dependent plasticity are well characterized in excitatory neurons, the mechanisms that regulate this process in inhibitory neurons are only poorly understood. Here, we describe a transcriptional program that is induced by neuronal activity in inhibitory neurons. We find that, while neuronal activity induces expression of early-response transcription factors such as Npas4 in both excitatory and inhibitory neurons, Npas4 activates distinct programs of late-response genes in inhibitory and excitatory neurons. These late-response genes differentially regulate synaptic input to these two types of neurons, promoting inhibition onto excitatory neurons while inducing excitation onto inhibitory neurons. These findings suggest that the functional outcomes of activity-induced transcriptional responses are adapted in a cell-type-specific manner to achieve a circuit-wide homeostatic response., (Copyright © 2014 Elsevier Inc. All rights reserved.)
- Published
- 2014
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15. SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample.
- Author
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Gray JM, Harmin DA, Boswell SA, Cloonan N, Mullen TE, Ling JJ, Miller N, Kuersten S, Ma YC, McCarroll SA, Grimmond SM, and Springer M
- Subjects
- Alternative Splicing, Biflavonoids pharmacology, HeLa Cells metabolism, High-Throughput Nucleotide Sequencing, Humans, Introns, Models, Theoretical, Monte Carlo Method, RNA genetics, RNA Precursors, RNA Splicing, RNA Stability, RNA, Messenger genetics, Sequence Analysis, RNA methods, Transcription, Genetic, RNA, Messenger metabolism
- Abstract
mRNA synthesis, processing, and destruction involve a complex series of molecular steps that are incompletely understood. Because the RNA intermediates in each of these steps have finite lifetimes, extensive mechanistic and dynamical information is encoded in total cellular RNA. Here we report the development of SnapShot-Seq, a set of computational methods that allow the determination of in vivo rates of pre-mRNA synthesis, splicing, intron degradation, and mRNA decay from a single RNA-Seq snapshot of total cellular RNA. SnapShot-Seq can detect in vivo changes in the rates of specific steps of splicing, and it provides genome-wide estimates of pre-mRNA synthesis rates comparable to those obtained via labeling of newly synthesized RNA. We used SnapShot-Seq to investigate the origins of the intrinsic bimodality of metazoan gene expression levels, and our results suggest that this bimodality is partly due to spillover of transcriptional activation from highly expressed genes to their poorly expressed neighbors. SnapShot-Seq dramatically expands the information obtainable from a standard RNA-Seq experiment.
- Published
- 2014
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16. Using whole-exome sequencing to identify inherited causes of autism.
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Yu TW, Chahrour MH, Coulter ME, Jiralerspong S, Okamura-Ikeda K, Ataman B, Schmitz-Abe K, Harmin DA, Adli M, Malik AN, D'Gama AM, Lim ET, Sanders SJ, Mochida GH, Partlow JN, Sunu CM, Felie JM, Rodriguez J, Nasir RH, Ware J, Joseph RM, Hill RS, Kwan BY, Al-Saffar M, Mukaddes NM, Hashmi A, Balkhy S, Gascon GG, Hisama FM, LeClair E, Poduri A, Oner O, Al-Saad S, Al-Awadi SA, Bastaki L, Ben-Omran T, Teebi AS, Al-Gazali L, Eapen V, Stevens CR, Rappaport L, Gabriel SB, Markianos K, State MW, Greenberg ME, Taniguchi H, Braverman NE, Morrow EM, and Walsh CA
- Subjects
- Adolescent, Animals, Cells, Cultured, Child, Child, Preschool, Cohort Studies, Female, Humans, Male, Pedigree, Rats, Sequence Analysis, DNA methods, Young Adult, Autistic Disorder diagnosis, Autistic Disorder genetics, Exome genetics, Genome-Wide Association Study methods
- Abstract
Despite significant heritability of autism spectrum disorders (ASDs), their extreme genetic heterogeneity has proven challenging for gene discovery. Studies of primarily simplex families have implicated de novo copy number changes and point mutations, but are not optimally designed to identify inherited risk alleles. We apply whole-exome sequencing (WES) to ASD families enriched for inherited causes due to consanguinity and find familial ASD associated with biallelic mutations in disease genes (AMT, PEX7, SYNE1, VPS13B, PAH, and POMGNT1). At least some of these genes show biallelic mutations in nonconsanguineous families as well. These mutations are often only partially disabling or present atypically, with patients lacking diagnostic features of the Mendelian disorders with which these genes are classically associated. Our study shows the utility of WES for identifying specific genetic conditions not clinically suspected and the importance of partial loss of gene function in ASDs., (Copyright © 2013 Elsevier Inc. All rights reserved.)
- Published
- 2013
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17. Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function.
- Author
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Cohen S, Gabel HW, Hemberg M, Hutchinson AN, Sadacca LA, Ebert DH, Harmin DA, Greenberg RS, Verdine VK, Zhou Z, Wetsel WC, West AE, and Greenberg ME
- Subjects
- Animals, Brain metabolism, Brain physiology, Chromatin metabolism, Chromatin Immunoprecipitation methods, Dendrites physiology, Gene Expression Regulation, Developmental genetics, Gene Knock-In Techniques methods, Methyl-CpG-Binding Protein 2 metabolism, Mice, Mice, Inbred C57BL, Neurons cytology, Neurons metabolism, Neurons physiology, Phosphorylation, Brain growth & development, Exploratory Behavior physiology, Gene Expression Regulation, Developmental physiology, Genome physiology, Methyl-CpG-Binding Protein 2 genetics, Methyl-CpG-Binding Protein 2 physiology
- Abstract
Autism spectrum disorders such as Rett syndrome (RTT) have been hypothesized to arise from defects in experience-dependent synapse maturation. RTT is caused by mutations in MECP2, a nuclear protein that becomes phosphorylated at S421 in response to neuronal activation. We show here that disruption of MeCP2 S421 phosphorylation in vivo results in defects in synapse development and behavior, implicating activity-dependent regulation of MeCP2 in brain development and RTT. We investigated the mechanism by which S421 phosphorylation regulates MeCP2 function and show by chromatin immunoprecipitation-sequencing that this modification occurs on MeCP2 bound across the genome. The phosphorylation of MeCP2 S421 appears not to regulate the expression of specific genes; rather, MeCP2 functions as a histone-like factor whose phosphorylation may facilitate a genome-wide response of chromatin to neuronal activity during nervous system development. We propose that RTT results in part from a loss of this experience-dependent chromatin remodeling., (Copyright © 2011 Elsevier Inc. All rights reserved.)
- Published
- 2011
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18. Widespread transcription at neuronal activity-regulated enhancers.
- Author
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Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, Markenscoff-Papadimitriou E, Kuhl D, Bito H, Worley PF, Kreiman G, and Greenberg ME
- Subjects
- Animals, Basic Helix-Loop-Helix Transcription Factors genetics, CREB-Binding Protein metabolism, Consensus Sequence genetics, Cytoskeletal Proteins genetics, Genes, Reporter, Genes, fos genetics, Histones metabolism, Methylation, Mice, Mice, Inbred C57BL, Nerve Tissue Proteins genetics, RNA Polymerase II metabolism, RNA, Untranslated biosynthesis, RNA, Untranslated genetics, Enhancer Elements, Genetic genetics, Gene Expression Regulation genetics, Neurons metabolism, Transcription, Genetic genetics
- Abstract
We used genome-wide sequencing methods to study stimulus-dependent enhancer function in mouse cortical neurons. We identified approximately 12,000 neuronal activity-regulated enhancers that are bound by the general transcriptional co-activator CBP in an activity-dependent manner. A function of CBP at enhancers may be to recruit RNA polymerase II (RNAPII), as we also observed activity-regulated RNAPII binding to thousands of enhancers. Notably, RNAPII at enhancers transcribes bi-directionally a novel class of enhancer RNAs (eRNAs) within enhancer domains defined by the presence of histone H3 monomethylated at lysine 4. The level of eRNA expression at neuronal enhancers positively correlates with the level of messenger RNA synthesis at nearby genes, suggesting that eRNA synthesis occurs specifically at enhancers that are actively engaged in promoting mRNA synthesis. These findings reveal that a widespread mechanism of enhancer activation involves RNAPII binding and eRNA synthesis.
- Published
- 2010
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19. Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection.
- Author
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Flavell SW, Kim TK, Gray JM, Harmin DA, Hemberg M, Hong EJ, Markenscoff-Papadimitriou E, Bear DM, and Greenberg ME
- Subjects
- Analysis of Variance, Animals, Brain Mapping, Cell Nucleus genetics, Cells, Cultured, Chromatin Immunoprecipitation, Computational Biology, DNA-Directed RNA Polymerases metabolism, Embryo, Mammalian, Exploratory Behavior, Hippocampus cytology, Humans, MEF2 Transcription Factors, Male, Myogenic Regulatory Factors metabolism, Nervous System Diseases genetics, Neurons cytology, Oligonucleotide Array Sequence Analysis methods, Photic Stimulation methods, Rats, Rats, Long-Evans, Visual Cortex physiology, Genomics, Neurons physiology, Polyadenylation genetics, Synapses genetics, Transcription, Genetic physiology
- Abstract
Although many transcription factors are known to control important aspects of neural development, the genome-wide programs that are directly regulated by these factors are not known. We have characterized the genetic program that is activated by MEF2, a key regulator of activity-dependent synapse development. These MEF2 target genes have diverse functions at synapses, revealing a broad role for MEF2 in synapse development. Several of the MEF2 targets are mutated in human neurological disorders including epilepsy and autism spectrum disorders, suggesting that these disorders may be caused by disruption of an activity-dependent gene program that controls synapse development. Our analyses also reveal that neuronal activity promotes alternative polyadenylation site usage at many of the MEF2 target genes, leading to the production of truncated mRNAs that may have different functions than their full-length counterparts. Taken together, these analyses suggest that the ubiquitously expressed transcription factor MEF2 regulates an intricate transcriptional program in neurons that controls synapse development.
- Published
- 2008
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20. START: an automated tool for serial analysis of chromatin occupancy data.
- Author
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Marinescu VD, Kohane IS, Kim TK, Harmin DA, Greenberg ME, and Riva A
- Subjects
- Artificial Intelligence, Internet, Transcription Factors genetics, Chromatin genetics, Chromosome Mapping methods, Database Management Systems, Databases, Genetic, Information Storage and Retrieval methods, Software, User-Computer Interface
- Abstract
Unlabelled: The serial analysis of chromatin occupancy technique (SACO) promises to become a widely used method for the unbiased genome-wide experimental identification of loci bound by a transcription factor of interest. We describe the first web-based automatic tool, termed sequence tag analysis and reporting tool (START), for processing SACO data generated by experiments performed for the yeast, fruit fly, mouse, rat or human genomes. The program uses as input sequences of inserts from a SACO library from which it extracts all SACO tags, maps them to genomic locations and annotates them. START returns detailed information about these tags including the genes, the genomic elements and the miRNA precursors found in their vicinity, and makes use of the MAPPER database to identify putative transcription factor binding sites located close to the tags., Availability: The program is available at http://bio.chip.org/start/., Supplementary Information: SUPPLEMENTARY INFORMATION is available at http://bio.chip.org/doc/start/START-supplementary.pdf
- Published
- 2006
- Full Text
- View/download PDF
21. Classical charge-transfer and ionization channels for ion collisions with circular Rydberg atoms.
- Author
-
Homan DM, Cavagnero MJ, and Harmin DA
- Published
- 1995
- Full Text
- View/download PDF
22. Charge transfer in ion collisions with circular Rydberg atoms.
- Author
-
Homan DM, Cavagnero MJ, and Harmin DA
- Published
- 1994
- Full Text
- View/download PDF
23. Incoherent time evolution on a grid of Landau-Zener anticrossings.
- Author
-
Harmin DA and Price PN
- Published
- 1994
- Full Text
- View/download PDF
24. Reply to "Comment on 'Differential equation for the spherical dipole matrix elements of hydrogen' "
- Author
-
Price PN and Harmin DA
- Published
- 1992
- Full Text
- View/download PDF
25. Intramanifold level mixing by time-dependent electric fields: Multilevel Landau-Zener effect.
- Author
-
Harmin DA
- Published
- 1991
- Full Text
- View/download PDF
26. Differential equation for the spherical dipole matrix elements of hydrogen.
- Author
-
Price PN and Harmin DA
- Published
- 1990
- Full Text
- View/download PDF
27. Precise theory of field enhancement of dielectronic recombination.
- Author
-
Harmin DA
- Published
- 1986
- Full Text
- View/download PDF
28. Interference narrowing at crossings of sodium Stark resonances.
- Author
-
Liu J, McNicholl P, Harmin DA, Ivri J, Bergeman T, and Metcalf HJ
- Published
- 1985
- Full Text
- View/download PDF
29. Asymmetry of field-induced shape resonances in hydrogen.
- Author
-
Harmin DA
- Published
- 1985
- Full Text
- View/download PDF
30. Erratum: Analytical study of quasidiscrete Stark levels in Rydberg atoms
- Author
-
Harmin DA
- Published
- 1985
- Full Text
- View/download PDF
31. Generalized WKB and Milne solutions to one-dimensional wave equations.
- Author
-
Robicheaux F, Fano U, Cavagnero M, and Harmin DA
- Published
- 1987
- Full Text
- View/download PDF
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