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1.
Science ; 385(6707): 370-371, 2024 Jul 26.
Artigo em Inglês | MEDLINE | ID: mdl-39052818

RESUMO

The genomic landscape of a cell surface protein reveals how neuron identity is displayed.


Assuntos
Caderinas , Coesinas , Regulação da Expressão Gênica , Neurônios , Animais , Humanos , Camundongos , Neurônios/citologia , Neurônios/fisiologia , Coesinas/genética , Caderinas/genética , Caderinas/metabolismo
2.
J Nucl Med ; 65(8): 1293-1300, 2024 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-38960711

RESUMO

Despite the recent advances in understanding the mechanisms of olfaction, no tools are currently available to noninvasively identify loss of smell. Because of the substantial increase in patients presenting with coronavirus disease 2019-related loss of smell, the pandemic has highlighted the urgent need to develop quantitative methods. Methods: Our group investigated the use of a novel fluorescent probe named Tsp1a-IR800P as a tool to diagnose loss of smell. Tsp1a-IR800P targets sodium channel 1.7, which plays a critical role in olfaction by aiding the signal propagation to the olfactory bulb. Results: Intuitively, we have identified that conditions leading to loss of smell, including chronic inflammation and coronavirus disease 2019, correlate with the downregulation of sodium channel 1.7 expression in the olfactory epithelium, both at the transcript and at the protein levels. We demonstrated that lower Tsp1a-IR800P fluorescence emissions significantly correlate with loss of smell in live animals-thus representing a potential tool for its semiquantitative assessment. Currently available methods rely on delayed subjective behavioral studies. Conclusion: This method could aid in significantly improving preclinical and clinical studies by providing a way to objectively diagnose loss of smell and therefore aid the development of therapeutic interventions.


Assuntos
Transtornos do Olfato , Transtornos do Olfato/diagnóstico por imagem , Animais , Humanos , Imagem Óptica/métodos , Olfato , Corantes Fluorescentes/química , Camundongos , COVID-19/diagnóstico por imagem , Masculino
3.
Nat Methods ; 21(6): 934-935, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38622458
4.
Nature ; 625(7993): 181-188, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38123679

RESUMO

Olfactory receptor (OR) choice provides an extreme example of allelic competition for transcriptional dominance, where every olfactory neuron stably transcribes one of approximately 2,000 or more OR alleles1,2. OR gene choice is mediated by a multichromosomal enhancer hub that activates transcription at a single OR3,4, followed by OR-translation-dependent feedback that stabilizes this choice5,6. Here, using single-cell genomics, we show formation of many competing hubs with variable enhancer composition, only one of which retains euchromatic features and transcriptional competence. Furthermore, we provide evidence that OR transcription recruits enhancers and reinforces enhancer hub activity locally, whereas OR RNA inhibits transcription of competing ORs over distance, promoting transition to transcriptional singularity. Whereas OR transcription is sufficient to break the symmetry between equipotent enhancer hubs, OR translation stabilizes transcription at the prevailing hub, indicating that there may be sequential non-coding and coding mechanisms that are implemented by OR alleles for transcriptional prevalence. We propose that coding OR mRNAs possess non-coding functions that influence nuclear architecture, enhance their own transcription and inhibit transcription from their competitors, with generalizable implications for probabilistic cell fate decisions.


Assuntos
Neurônios Receptores Olfatórios , RNA , Receptores Odorantes , Alelos , Linhagem da Célula , Elementos Facilitadores Genéticos/genética , Regulação da Expressão Gênica , Neurônios Receptores Olfatórios/metabolismo , Receptores Odorantes/genética , Receptores Odorantes/metabolismo , Sequências Reguladoras de Ácido Nucleico/genética , RNA/genética , Transcrição Gênica , Genômica , Análise de Célula Única
5.
Elife ; 122023 Dec 18.
Artigo em Inglês | MEDLINE | ID: mdl-38108811

RESUMO

Olfactory receptor (OR) choice represents an example of genetically hardwired stochasticity, where every olfactory neuron expresses one out of ~2000 OR alleles in the mouse genome in a probabilistic, yet stereotypic fashion. Here, we propose that topographic restrictions in OR expression are established in neuronal progenitors by two opposing forces: polygenic transcription and genomic silencing, both of which are influenced by dorsoventral gradients of transcription factors NFIA, B, and X. Polygenic transcription of OR genes may define spatially constrained OR repertoires, among which one OR allele is selected for singular expression later in development. Heterochromatin assembly and genomic compartmentalization of OR alleles also vary across the axes of the olfactory epithelium and may preferentially eliminate ectopically expressed ORs with more dorsal expression destinations from this 'privileged' repertoire. Our experiments identify early transcription as a potential 'epigenetic' contributor to future developmental patterning and reveal how two spatially responsive probabilistic processes may act in concert to establish deterministic, precise, and reproducible territories of stochastic gene expression.


Assuntos
Neurônios Receptores Olfatórios , Receptores Odorantes , Animais , Camundongos , Receptores Odorantes/genética , Epigenômica , Alelos , Epigênese Genética
6.
bioRxiv ; 2023 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-36993168

RESUMO

Olfactory receptor (OR) choice represents an example of genetically hardwired stochasticity, where every olfactory neuron expresses one out of ~2000 OR alleles in a probabilistic, yet stereotypic fashion. Here, we propose that topographic restrictions in OR expression are established in neuronal progenitors by two opposing forces: polygenic transcription and genomic silencing, both of which are influenced by dorsoventral gradients of transcription factors NFIA, B, and X. Polygenic transcription of OR genes may define spatially constrained OR repertoires, among which one OR allele is selected for singular expression later in development. Heterochromatin assembly and genomic compartmentalization of OR alleles also vary across the axes of the olfactory epithelium and may preferentially eliminate ectopically expressed ORs with more dorsal expression destinations from this "privileged" repertoire. Our experiments identify early transcription as a potential "epigenetic" contributor to future developmental patterning and reveal how two spatially responsive probabilistic processes may act in concert to establish deterministic, precise, and reproducible territories of stochastic gene expression.

7.
Cell ; 185(21): 3896-3912.e22, 2022 10 13.
Artigo em Inglês | MEDLINE | ID: mdl-36167070

RESUMO

Olfactory sensory neurons (OSNs) convert the stochastic choice of one of >1,000 olfactory receptor (OR) genes into precise and stereotyped axon targeting of OR-specific glomeruli in the olfactory bulb. Here, we show that the PERK arm of the unfolded protein response (UPR) regulates both the glomerular coalescence of like axons and the specificity of their projections. Subtle differences in OR protein sequences lead to distinct patterns of endoplasmic reticulum (ER) stress during OSN development, converting OR identity into distinct gene expression signatures. We identify the transcription factor Ddit3 as a key effector of PERK signaling that maps OR-dependent ER stress patterns to the transcriptional regulation of axon guidance and cell-adhesion genes, instructing targeting precision. Our results extend the known functions of the UPR from a quality-control pathway that protects cells from misfolded proteins to a sensor of cellular identity that interprets physiological states to direct axon wiring.


Assuntos
Axônios/metabolismo , Estresse do Retículo Endoplasmático , Receptores Odorantes , Animais , Camundongos , Bulbo Olfatório , Neurônios Receptores Olfatórios/metabolismo , Receptores Odorantes/genética , Receptores Odorantes/metabolismo , Fatores de Transcrição/metabolismo
8.
Sci Transl Med ; 14(664): eabq3059, 2022 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-35857629

RESUMO

The host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can result in prolonged pathologies collectively referred to as post-acute sequalae of COVID-19 (PASC) or long COVID. To better understand the mechanism underlying long COVID biology, we compared the short- and long-term systemic responses in the golden hamster after either SARS-CoV-2 or influenza A virus (IAV) infection. Results demonstrated that SARS-CoV-2 exceeded IAV in its capacity to cause permanent injury to the lung and kidney and uniquely affected the olfactory bulb (OB) and olfactory epithelium (OE). Despite a lack of detectable infectious virus, the OB and OE demonstrated myeloid and T cell activation, proinflammatory cytokine production, and an interferon response that correlated with behavioral changes extending a month after viral clearance. These sustained transcriptional changes could also be corroborated from tissue isolated from individuals who recovered from COVID-19. These data highlight a molecular mechanism for persistent COVID-19 symptomology and provide a small animal model to explore future therapeutics.


Assuntos
COVID-19 , Animais , COVID-19/complicações , Cricetinae , Humanos , Interferons , Mesocricetus , SARS-CoV-2 , Síndrome de COVID-19 Pós-Aguda
9.
Cell ; 185(6): 1052-1064.e12, 2022 03 17.
Artigo em Inglês | MEDLINE | ID: mdl-35180380

RESUMO

SARS-CoV-2 infects less than 1% of cells in the human body, yet it can cause severe damage in a variety of organs. Thus, deciphering the non-cell-autonomous effects of SARS-CoV-2 infection is imperative for understanding the cellular and molecular disruption it elicits. Neurological and cognitive defects are among the least understood symptoms of COVID-19 patients, with olfactory dysfunction being their most common sensory deficit. Here, we show that both in humans and hamsters, SARS-CoV-2 infection causes widespread downregulation of olfactory receptors (ORs) and of their signaling components. This non-cell-autonomous effect is preceded by a dramatic reorganization of the neuronal nuclear architecture, which results in dissipation of genomic compartments harboring OR genes. Our data provide a potential mechanism by which SARS-CoV-2 infection alters the cellular morphology and the transcriptome of cells it cannot infect, offering insight to its systemic effects in olfaction and beyond.


Assuntos
Anosmia , COVID-19 , Animais , Cricetinae , Regulação para Baixo , Humanos , Receptores Odorantes , SARS-CoV-2 , Olfato
10.
Curr Opin Genet Dev ; 72: 101-109, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34896807

RESUMO

The mammalian genome possesses >2000 olfactory receptor (OR) alleles regulated by 63 known OR-Enhancer elements, yet each olfactory sensory neuron (OSN) expresses only a single OR allele. Choreographed changes to OSN nuclear architecture are evidently necessary for OR expression. Additionally, the insulated organization of OR-enhancers around an OR allele is a hallmark of the chosen OR. However, the biology guiding OR choice itself is unclear. Innovations in single-cell and biophysics-based analysis of nuclear architecture are revising previous models of the nucleus to include its dynamic and probabilistic nature. In this review, we ground current knowledge of OR gene regulation in these emerging theories to speculate on mechanisms that may give rise to diverse and singular OR expression.


Assuntos
Neurônios Receptores Olfatórios , Receptores Odorantes , Animais , Núcleo Celular/metabolismo , Regulação da Expressão Gênica/genética , Mamíferos/genética , Neurônios Receptores Olfatórios/metabolismo , Receptores Odorantes/genética , Receptores Odorantes/metabolismo , Sequências Reguladoras de Ácido Nucleico
11.
bioRxiv ; 2021 Feb 09.
Artigo em Inglês | MEDLINE | ID: mdl-33594368

RESUMO

Olfaction relies on a coordinated partnership between odorant flow and neuronal communication. Disruption in our ability to detect odors, or anosmia, has emerged as a hallmark symptom of infection with SARS-CoV-2, yet the mechanism behind this abrupt sensory deficit remains elusive. Here, using molecular evaluation of human olfactory epithelium (OE) from subjects succumbing to COVID-19 and a hamster model of SARS-CoV-2 infection, we discovered widespread downregulation of olfactory receptors (ORs) as well as key components of their signaling pathway. OR downregulation likely represents a non-cell autonomous effect, since SARS-CoV-2 detection in OSNs is extremely rare both in human and hamster OEs. A likely explanation for the reduction of OR transcription is the striking reorganization of nuclear architecture observed in the OSN lineage, which disrupts multi-chromosomal compartments regulating OR expression in humans and hamsters. Our experiments uncover a novel molecular mechanism by which a virus with a very selective tropism can elicit persistent transcriptional changes in cells that evade it, contributing to the severity of COVID-19.

12.
Curr Opin Neurobiol ; 59: iii-v, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31787169
13.
Neuron ; 104(3): 471-487.e12, 2019 11 06.
Artigo em Inglês | MEDLINE | ID: mdl-31606247

RESUMO

SETD1A, a lysine-methyltransferase, is a key schizophrenia susceptibility gene. Mice carrying a heterozygous loss-of-function mutation of the orthologous gene exhibit alterations in axonal branching and cortical synaptic dynamics accompanied by working memory deficits. We show that Setd1a binds both promoters and enhancers with a striking overlap between Setd1a and Mef2 on enhancers. Setd1a targets are highly expressed in pyramidal neurons and display a complex pattern of transcriptional up- and downregulations shaped by presumed opposing functions of Setd1a on promoters and Mef2-bound enhancers. Notably, evolutionarily conserved Setd1a targets are associated with neuropsychiatric genetic risk burden. Reinstating Setd1a expression in adulthood rescues cognitive deficits. Finally, we identify LSD1 as a major counteracting demethylase for Setd1a and show that its pharmacological antagonism results in a full rescue of the behavioral and morphological deficits in Setd1a-deficient mice. Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions.


Assuntos
Córtex Cerebral/metabolismo , Disfunção Cognitiva/genética , Histona Desmetilases/metabolismo , Histona-Lisina N-Metiltransferase/genética , Memória de Curto Prazo , Esquizofrenia/genética , Psicologia do Esquizofrênico , Animais , Axônios/patologia , Encéfalo/metabolismo , Córtex Cerebral/patologia , Elementos Facilitadores Genéticos , Predisposição Genética para Doença , Histona Desmetilases/antagonistas & inibidores , Mutação com Perda de Função , Fatores de Transcrição MEF2/genética , Camundongos , Neocórtex/metabolismo , Neurônios/metabolismo , Fenótipo , Córtex Pré-Frontal/metabolismo , Regiões Promotoras Genéticas , Células Piramidais/metabolismo , Sinapses/patologia
14.
Curr Opin Genet Dev ; 55: 106-113, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-31491591

RESUMO

The partitioning of the interphase nucleus into chromosome territories generally precludes DNA from making specific and reproducible inter-chromosomal contacts. However, with the development of powerful genomic and imaging tools for the analysis of the 3D genome, and with their application on an increasing number of cell types, it becomes apparent that regulated, specific, and functionally important inter-chromosomal contacts exist. Widespread and stereotypic inter-chromosomal interactions are at the center of chemosensation, where they regulate the singular and stochastic expression of olfactory receptor genes. In olfactory sensory neurons (OSNs) coalescence of multiple intergenic enhancers to a multi-chromosomal hub orchestrates the expression of a single OR allele, whereas convergence of the remaining OR genes from 18 chromosomes into a few heterochromatic compartments mediates their effective transcriptional silencing. In this review we describe the role of interchromosomal interactions in OR gene choice, and we describe other biological systems where such genomic interactions may contribute to regulatory robustness and transcriptional diversification.


Assuntos
Núcleo Celular/metabolismo , Cromossomos/metabolismo , Neurônios Receptores Olfatórios/metabolismo , Receptores Odorantes/metabolismo , Animais , Núcleo Celular/genética , Cromossomos/genética , Regulação da Expressão Gênica , Humanos , Receptores Odorantes/genética , Sequências Reguladoras de Ácido Nucleico
15.
Elife ; 82019 05 24.
Artigo em Inglês | MEDLINE | ID: mdl-31124784

RESUMO

Enhancers are important regulatory elements that can control gene activity across vast genetic distances. However, the underlying nature of this regulation remains obscured because it has been difficult to observe in living cells. Here, we visualize the spatial organization and transcriptional output of the key pluripotency regulator Sox2 and its essential enhancer Sox2 Control Region (SCR) in living embryonic stem cells (ESCs). We find that Sox2 and SCR show no evidence of enhanced spatial proximity and that spatial dynamics of this pair is limited over tens of minutes. Sox2 transcription occurs in short, intermittent bursts in ESCs and, intriguingly, we find this activity demonstrates no association with enhancer proximity, suggesting that direct enhancer-promoter contacts do not drive contemporaneous Sox2 transcription. Our study establishes a framework for interrogation of enhancer function in living cells and supports an unexpected mechanism for enhancer control of Sox2 expression that uncouples transcription from enhancer proximity.


Assuntos
Células-Tronco Embrionárias/fisiologia , Elementos Facilitadores Genéticos , Regulação da Expressão Gênica , Fatores de Transcrição SOXB1/biossíntese , Transcrição Gênica , Animais , Camundongos , Fatores de Transcrição SOXB1/genética
16.
Cell ; 177(3): 639-653.e15, 2019 04 18.
Artigo em Inglês | MEDLINE | ID: mdl-30955885

RESUMO

Stochastic activation of clustered Protocadherin (Pcdh) α, ß, and γ genes generates a cell-surface identity code in individual neurons that functions in neural circuit assembly. Here, we show that Pcdhα gene choice involves the activation of an antisense promoter located in the first exon of each Pcdhα alternate gene. Transcription of an antisense long noncoding RNA (lncRNA) from this antisense promoter extends through the sense promoter, leading to DNA demethylation of the CTCF binding sites proximal to each promoter. Demethylation-dependent CTCF binding to both promoters facilitates cohesin-mediated DNA looping with a distal enhancer (HS5-1), locking in the transcriptional state of the chosen Pcdhα gene. Uncoupling DNA demethylation from antisense transcription by Tet3 overexpression in mouse olfactory neurons promotes CTCF binding to all Pcdhα promoters, resulting in proximity-biased DNA looping of the HS5-1 enhancer. Thus, antisense transcription-mediated promoter demethylation functions as a mechanism for distance-independent enhancer/promoter DNA looping to ensure stochastic Pcdhα promoter choice.


Assuntos
Caderinas/genética , Desmetilação do DNA , RNA Antissenso/metabolismo , RNA Longo não Codificante/genética , Animais , Sítios de Ligação , Fator de Ligação a CCCTC/química , Fator de Ligação a CCCTC/metabolismo , Caderinas/metabolismo , Linhagem Celular , Elementos Facilitadores Genéticos , Éxons , Feminino , Humanos , Camundongos , Camundongos Transgênicos , Família Multigênica , Neurônios/citologia , Neurônios/metabolismo , Regiões Promotoras Genéticas , RNA Polimerase II/metabolismo , RNA Antissenso/genética , Transcrição Gênica
17.
Nature ; 565(7740): 448-453, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30626972

RESUMO

The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. This architecture is constrained by the DNA polymer, which precludes interactions between genes on different chromosomes. Here we report a marked divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons. Chromatin conformation capture using in situ Hi-C on fluorescence-activated cell-sorted olfactory sensory neurons and their progenitors shows that olfactory receptor gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation of the cells. These contacts are orchestrated by intergenic olfactory receptor enhancers, the 'Greek islands', which first contribute to the formation of olfactory receptor compartments and then form a multi-chromosomal super-enhancer that associates with the single active olfactory receptor gene. The Greek-island-bound transcription factor LHX2 and adaptor protein LDB1 regulate the assembly and maintenance of olfactory receptor compartments, Greek island hubs and olfactory receptor transcription, providing mechanistic insights into and functional support for the role of trans interactions in gene expression.


Assuntos
Cromossomos de Mamíferos/genética , Proteínas de Ligação a DNA/metabolismo , Elementos Facilitadores Genéticos/genética , Regulação da Expressão Gênica , Proteínas com Domínio LIM/metabolismo , Proteínas com Homeodomínio LIM/metabolismo , Receptores Odorantes/genética , Fatores de Transcrição/metabolismo , Transcrição Gênica , Animais , Diferenciação Celular/genética , Cromatina/genética , Cromatina/metabolismo , Posicionamento Cromossômico/genética , Cromossomos de Mamíferos/metabolismo , Feminino , Masculino , Camundongos , Família Multigênica/genética , Neurônios Receptores Olfatórios/metabolismo , Receptores Odorantes/metabolismo
18.
Nat Commun ; 9(1): 2189, 2018 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-29875359

RESUMO

Alternative splicing (AS) is one crucial step of gene expression that must be tightly regulated during neurodevelopment. However, the precise timing of developmental splicing switches and the underlying regulatory mechanisms are poorly understood. Here we systematically analyze the temporal regulation of AS in a large number of transcriptome profiles of developing mouse cortices, in vivo purified neuronal subtypes, and neurons differentiated in vitro. Our analysis reveals early-switch and late-switch exons in genes with distinct functions, and these switches accurately define neuronal maturation stages. Integrative modeling suggests that these switches are under direct and combinatorial regulation by distinct sets of neuronal RNA-binding proteins including Nova, Rbfox, Mbnl, and Ptbp. Surprisingly, various neuronal subtypes in the sensory systems lack Nova and/or Rbfox expression. These neurons retain the "immature" splicing program in early-switch exons, affecting numerous synaptic genes. These results provide new insights into the organization and regulation of the neurodevelopmental transcriptome.


Assuntos
Processamento Alternativo , Sistema Nervoso Central/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Neurogênese/genética , Animais , Diferenciação Celular/genética , Sistema Nervoso Central/embriologia , Sistema Nervoso Central/crescimento & desenvolvimento , Camundongos Knockout , Camundongos Transgênicos , Modelos Genéticos , Modelos Neurológicos , Neurônios/citologia , Neurônios/metabolismo , Proteínas de Ligação a RNA/genética , Fatores de Tempo
19.
Nature ; 552(7684): 278, 2017 12 14.
Artigo em Inglês | MEDLINE | ID: mdl-29168505

RESUMO

This corrects the article DOI: 10.1038/nature23884.

20.
Elife ; 62017 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-28933695

RESUMO

The monogenic and monoallelic expression of only one out of >1000 mouse olfactory receptor (ORs) genes requires the formation of large heterochromatic chromatin domains that sequester the OR gene clusters. Within these domains, intergenic transcriptional enhancers evade heterochromatic silencing and converge into interchromosomal hubs that assemble over the transcriptionally active OR. The significance of this nuclear organization in OR choice remains elusive. Here, we show that transcription factors Lhx2 and Ebf specify OR enhancers by binding in a functionally cooperative fashion to stereotypically spaced motifs that defy heterochromatin. Specific displacement of Lhx2 and Ebf from OR enhancers resulted in pervasive, long-range, and trans downregulation of OR transcription, whereas pre-assembly of a multi-enhancer hub increased the frequency of OR choice in cis. Our data provide genetic support for the requirement and sufficiency of interchromosomal interactions in singular OR choice and generate general regulatory principles for stochastic, mutually exclusive gene expression programs.


Assuntos
Regulação da Expressão Gênica , Proteínas com Homeodomínio LIM/metabolismo , Neurônios/fisiologia , Receptores Odorantes/biossíntese , Receptores Odorantes/genética , Transativadores/metabolismo , Fatores de Transcrição/metabolismo , Animais , Camundongos , Ligação Proteica , Sequências Reguladoras de Ácido Nucleico
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