Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 55
Filtrar
Más filtros

Banco de datos
Tipo del documento
Intervalo de año de publicación
1.
Cell ; 180(6): 1262-1271.e15, 2020 03 19.
Artículo en Inglés | MEDLINE | ID: mdl-32169219

RESUMEN

Establishing causal links between non-coding variants and human phenotypes is an increasing challenge. Here, we introduce a high-throughput mouse reporter assay for assessing the pathogenic potential of human enhancer variants in vivo and examine nearly a thousand variants in an enhancer repeatedly linked to polydactyly. We show that 71% of all rare non-coding variants previously proposed as causal lead to reporter gene expression in a pattern consistent with their pathogenic role. Variants observed to alter enhancer activity were further confirmed to cause polydactyly in knockin mice. We also used combinatorial and single-nucleotide mutagenesis to evaluate the in vivo impact of mutations affecting all positions of the enhancer and identified additional functional substitutions, including potentially pathogenic variants hitherto not observed in humans. Our results uncover the functional consequences of hundreds of mutations in a phenotype-associated enhancer and establish a widely applicable strategy for systematic in vivo evaluation of human enhancer variants.


Asunto(s)
Elementos de Facilitación Genéticos/genética , Ensayos Analíticos de Alto Rendimiento/métodos , Polidactilia/genética , Animales , Elementos de Facilitación Genéticos/fisiología , Regulación del Desarrollo de la Expresión Génica/genética , Técnicas de Sustitución del Gen/métodos , Proteínas Hedgehog/genética , Proteínas Hedgehog/metabolismo , Humanos , Ratones , Mutación , Fenotipo , Polidactilia/metabolismo , ARN no Traducido/genética
2.
Cell ; 172(3): 491-499.e15, 2018 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-29358049

RESUMEN

Non-coding "ultraconserved" regions containing hundreds of consecutive bases of perfect sequence conservation across mammalian genomes can function as distant-acting enhancers. However, initial deletion studies in mice revealed that loss of such extraordinarily constrained sequences had no immediate impact on viability. Here, we show that ultraconserved enhancers are required for normal development. Focusing on some of the longest ultraconserved sites genome wide, located near the essential neuronal transcription factor Arx, we used genome editing to create an expanded series of knockout mice lacking individual or combinations of ultraconserved enhancers. Mice with single or pairwise deletions of ultraconserved enhancers were viable and fertile but in nearly all cases showed neurological or growth abnormalities, including substantial alterations of neuron populations and structural brain defects. Our results demonstrate the functional importance of ultraconserved enhancers and indicate that remarkably strong sequence conservation likely results from fitness deficits that appear subtle in a laboratory setting.


Asunto(s)
Secuencia Conservada , Desarrollo Embrionario/genética , Elementos de Facilitación Genéticos , Animales , Encéfalo/anomalías , Encéfalo/embriología , Encéfalo/metabolismo , Femenino , Eliminación de Gen , Proteínas de Homeodominio/genética , Proteínas de Homeodominio/metabolismo , Masculino , Ratones , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
3.
Cell ; 171(3): 710-722.e12, 2017 Oct 19.
Artículo en Inglés | MEDLINE | ID: mdl-28965761

RESUMEN

To further our understanding of the genetic etiology of autism, we generated and analyzed genome sequence data from 516 idiopathic autism families (2,064 individuals). This resource includes >59 million single-nucleotide variants (SNVs) and 9,212 private copy number variants (CNVs), of which 133,992 and 88 are de novo mutations (DNMs), respectively. We estimate a mutation rate of ∼1.5 × 10-8 SNVs per site per generation with a significantly higher mutation rate in repetitive DNA. Comparing probands and unaffected siblings, we observe several DNM trends. Probands carry more gene-disruptive CNVs and SNVs, resulting in severe missense mutations and mapping to predicted fetal brain promoters and embryonic stem cell enhancers. These differences become more pronounced for autism genes (p = 1.8 × 10-3, OR = 2.2). Patients are more likely to carry multiple coding and noncoding DNMs in different genes, which are enriched for expression in striatal neurons (p = 3 × 10-3), suggesting a path forward for genetically characterizing more complex cases of autism.


Asunto(s)
Trastorno Autístico/genética , Variaciones en el Número de Copia de ADN , Polimorfismo de Nucleótido Simple , Animales , Análisis Mutacional de ADN , Femenino , Estudio de Asociación del Genoma Completo , Humanos , Mutación INDEL , Masculino , Ratones
4.
Cell ; 167(5): 1163-1166, 2016 11 17.
Artículo en Inglés | MEDLINE | ID: mdl-27863237

RESUMEN

Coupling chromosome conformation capture to molecular enrichment for promoter-containing DNA fragments enables the systematic mapping of interactions between individual distal regulatory sequences and their target genes. In this Minireview, we describe recent progress in the application of this technique and related complementary approaches to gain insight into the lineage- and cell-type-specific dynamics of interactions between regulators and gene promoters.


Asunto(s)
Elementos de Facilitación Genéticos , Regiones Promotoras Genéticas , Enfermedad/genética , Epigenómica , Regulación de la Expresión Génica , Humanos , Especificidad de Órganos
5.
Cell ; 167(3): 633-642.e11, 2016 Oct 20.
Artículo en Inglés | MEDLINE | ID: mdl-27768887

RESUMEN

The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. PAPERCLIP.


Asunto(s)
Evolución Biológica , Elementos de Facilitación Genéticos , Extremidades/crecimiento & desarrollo , Proteínas Hedgehog/genética , Serpientes/genética , Animales , Secuencia de Bases , Evolución Molecular , Técnicas de Sustitución del Gen , Ratones , Ratones Transgénicos , Mutación , Filogenia , Serpientes/clasificación
6.
Nature ; 623(7988): 772-781, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37968388

RESUMEN

Mouse models are a critical tool for studying human diseases, particularly developmental disorders1. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse2. Here we set out to establish single-cell RNA sequencing of the whole embryo as a scalable platform for the systematic phenotyping of mouse genetic models. We applied combinatorial indexing-based single-cell RNA sequencing3 to profile 101 embryos of 22 mutant and 4 wild-type genotypes at embryonic day 13.5, altogether profiling more than 1.6 million nuclei. The 22 mutants represent a range of anticipated phenotypic severities, from established multisystem disorders to deletions of individual regulatory regions4,5. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibit changes in dozens of trajectories whereas others exhibit changes in only a few cell types. We also identify differences between widely used wild-type strains, compare phenotyping of gain- versus loss-of-function mutants and characterize deletions of topological associating domain boundaries. Notably, some changes are shared among mutants, suggesting that developmental pleiotropy might be 'decomposable' through further scaling of this approach. Overall, our findings show how single-cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution.


Asunto(s)
Discapacidades del Desarrollo , Embrión de Mamíferos , Mutación , Fenotipo , Análisis de Expresión Génica de una Sola Célula , Animales , Ratones , Núcleo Celular/genética , Discapacidades del Desarrollo/genética , Discapacidades del Desarrollo/patología , Embrión de Mamíferos/metabolismo , Embrión de Mamíferos/patología , Mutación con Ganancia de Función , Genotipo , Mutación con Pérdida de Función , Modelos Genéticos , Modelos Animales de Enfermedad
7.
Nat Rev Genet ; 23(3): 182-194, 2022 03.
Artículo en Inglés | MEDLINE | ID: mdl-34764456

RESUMEN

Across the human genome, there are nearly 500 'ultraconserved' elements: regions of at least 200 contiguous nucleotides that are perfectly conserved in both the mouse and rat genomes. Remarkably, the majority of these sequences are non-coding, and many can function as enhancers that activate tissue-specific gene expression during embryonic development. From their first description more than 15 years ago, their extreme conservation has both fascinated and perplexed researchers in genomics and evolutionary biology. The intrigue around ultraconserved elements only grew with the observation that they are dispensable for viability. Here, we review recent progress towards understanding the general importance and the specific functions of ultraconserved sequences in mammalian development and human disease and discuss possible explanations for their extreme conservation.


Asunto(s)
Secuencia Conservada/fisiología , Genoma/genética , Animales , Desarrollo Embrionario/genética , Elementos de Facilitación Genéticos , Femenino , Genómica/métodos , Genómica/tendencias , Historia del Siglo XXI , Humanos , Mamíferos/genética , Ratones , Embarazo , Ratas
8.
Nature ; 583(7818): 752-759, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32728242

RESUMEN

Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited1,2. Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood. We identified 1,808,810 genomic regions that showed variations in CG methylation by comparing the methylomes of different tissues or organs from different developmental stages. These DNA elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. During late stages of fetal development, non-CG methylation accumulated within the bodies of key developmental transcription factor genes, coinciding with their transcriptional repression. Integration of genome-wide DNA methylation, histone modification and chromatin accessibility data enabled us to predict 461,141 putative developmental tissue-specific enhancers, the human orthologues of which were enriched for disease-associated genetic variants. These spatiotemporal epigenome maps provide a resource for studies of gene regulation during tissue or organ progression, and a starting point for investigating regulatory elements that are involved in human developmental disorders.


Asunto(s)
Metilación de ADN , Epigenoma , Feto/embriología , Feto/metabolismo , Animales , Animales Recién Nacidos , Cromatina/genética , Cromatina/metabolismo , Enfermedad/genética , Regulación hacia Abajo , Elementos de Facilitación Genéticos/genética , Represión Epigenética , Femenino , Silenciador del Gen , Humanos , Ratones , Ratones Endogámicos C57BL , Modelos Animales , Anotación de Secuencia Molecular , Polimorfismo de Nucleótido Simple , Análisis Espacio-Temporal
9.
Nature ; 583(7818): 760-767, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32728245

RESUMEN

During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system1. Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17 tissues and organs. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif codes of their promoters. We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for one-third of differential gene expression and more than 40% of identified cell types. By integrating promoter sequence motifs with companion ENCODE epigenomic profiles, we identified a prominent promoter de-repression mechanism in neuronal expression clusters that was attributable to known and novel repressors. Focusing on the developing limb, single-cell RNA data identified 25 candidate cell types that included progenitor and differentiating states with computationally inferred lineage relationships. We extracted cell-type transcription factor networks and complementary sets of candidate enhancer elements by using single-cell RNA-seq to decompose integrative cis-element (IDEAS) models that were derived from whole-tissue epigenome chromatin data. These ENCODE reference data, computed network components and IDEAS chromatin segmentations are companion resources to the matching epigenomic developmental matrix, and are available for researchers to further mine and integrate.


Asunto(s)
Embrión de Mamíferos/citología , Embrión de Mamíferos/embriología , Desarrollo Embrionario/genética , Regulación del Desarrollo de la Expresión Génica , Análisis de la Célula Individual , Transcriptoma , Animales , Diferenciación Celular/genética , Linaje de la Célula/genética , Cromatina/genética , Embrión de Mamíferos/metabolismo , Elementos de Facilitación Genéticos , Epigenómica , Extremidades/embriología , Femenino , Masculino , Ratones , Poli A/genética , Poli A/metabolismo , Regiones Promotoras Genéticas , RNA-Seq , Factores de Transcripción/metabolismo
10.
Nature ; 583(7818): 744-751, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32728240

RESUMEN

The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP-seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC-seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.


Asunto(s)
Cromatina/genética , Cromatina/metabolismo , Conjuntos de Datos como Asunto , Desarrollo Fetal/genética , Histonas/metabolismo , Anotación de Secuencia Molecular , Secuencias Reguladoras de Ácidos Nucleicos/genética , Animales , Cromatina/química , Secuenciación de Inmunoprecipitación de Cromatina , Enfermedad/genética , Elementos de Facilitación Genéticos/genética , Femenino , Regulación del Desarrollo de la Expresión Génica/genética , Variación Genética , Histonas/química , Humanos , Masculino , Ratones , Ratones Endogámicos C57BL , Especificidad de Órganos/genética , Reproducibilidad de los Resultados , Transposasas/metabolismo
12.
Nature ; 583(7818): 699-710, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32728249

RESUMEN

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.


Asunto(s)
ADN/genética , Bases de Datos Genéticas , Genoma/genética , Genómica , Anotación de Secuencia Molecular , Sistema de Registros , Secuencias Reguladoras de Ácidos Nucleicos/genética , Animales , Cromatina/genética , Cromatina/metabolismo , ADN/química , Huella de ADN , Metilación de ADN/genética , Momento de Replicación del ADN , Desoxirribonucleasa I/metabolismo , Genoma Humano , Histonas/metabolismo , Humanos , Ratones , Ratones Transgénicos , Proteínas de Unión al ARN/genética , Transcripción Genética/genética , Transposasas/metabolismo
13.
Nature ; 571(7763): 107-111, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-31217582

RESUMEN

Large-scale genome sequencing is poised to provide a substantial increase in the rate of discovery of disease-associated mutations, but the functional interpretation of such mutations remains challenging. Here we show that deletions of a sequence on human chromosome 16 that we term the intestine-critical region (ICR) cause intractable congenital diarrhoea in infants1,2. Reporter assays in transgenic mice show that the ICR contains a regulatory sequence that activates transcription during the development of the gastrointestinal system. Targeted deletion of the ICR in mice caused symptoms that recapitulated the human condition. Transcriptome analysis revealed that an unannotated open reading frame (Percc1) flanks the regulatory sequence, and the expression of this gene was lost in the developing gut of mice that lacked the ICR. Percc1-knockout mice displayed phenotypes similar to those observed upon ICR deletion in mice and patients, whereas an ICR-driven Percc1 transgene was sufficient to rescue the phenotypes found in mice that lacked the ICR. Together, our results identify a gene that is critical for intestinal function and underscore the need for targeted in vivo studies to interpret the growing number of clinical genetic findings that do not affect known protein-coding genes.


Asunto(s)
Diarrea/congénito , Diarrea/genética , Elementos de Facilitación Genéticos/genética , Regulación del Desarrollo de la Expresión Génica , Genes , Intestinos/fisiología , Eliminación de Secuencia/genética , Animales , Cromosomas Humanos Par 16/genética , Modelos Animales de Enfermedad , Femenino , Genes Reporteros , Sitios Genéticos/genética , Humanos , Masculino , Ratones , Ratones Noqueados , Ratones Transgénicos , Linaje , Fenotipo , Activación Transcripcional , Transcriptoma/genética , Transgenes/genética
14.
Nature ; 554(7691): 239-243, 2018 02 08.
Artículo en Inglés | MEDLINE | ID: mdl-29420474

RESUMEN

Distant-acting tissue-specific enhancers, which regulate gene expression, vastly outnumber protein-coding genes in mammalian genomes, but the functional importance of this regulatory complexity remains unclear. Here we show that the pervasive presence of multiple enhancers with similar activities near the same gene confers phenotypic robustness to loss-of-function mutations in individual enhancers. We used genome editing to create 23 mouse deletion lines and inter-crosses, including both single and combinatorial enhancer deletions at seven distinct loci required for limb development. Unexpectedly, none of the ten deletions of individual enhancers caused noticeable changes in limb morphology. By contrast, the removal of pairs of limb enhancers near the same gene resulted in discernible phenotypes, indicating that enhancers function redundantly in establishing normal morphology. In a genetic background sensitized by reduced baseline expression of the target gene, even single enhancer deletions caused limb abnormalities, suggesting that functional redundancy is conferred by additive effects of enhancers on gene expression levels. A genome-wide analysis integrating epigenomic and transcriptomic data from 29 developmental mouse tissues revealed that mammalian genes are very commonly associated with multiple enhancers that have similar spatiotemporal activity. Systematic exploration of three representative developmental structures (limb, brain and heart) uncovered more than one thousand cases in which five or more enhancers with redundant activity patterns were found near the same gene. Together, our data indicate that enhancer redundancy is a remarkably widespread feature of mammalian genomes that provides an effective regulatory buffer to prevent deleterious phenotypic consequences upon the loss of individual enhancers.


Asunto(s)
Elementos de Facilitación Genéticos/genética , Extremidades/embriología , Regulación del Desarrollo de la Expresión Génica/genética , Fenotipo , Animales , Encéfalo/embriología , Femenino , Genoma , Corazón/embriología , Deformidades Congénitas de las Extremidades/embriología , Deformidades Congénitas de las Extremidades/genética , Masculino , Ratones , Eliminación de Secuencia , Análisis Espacio-Temporal
15.
Proc Natl Acad Sci U S A ; 118(51)2021 12 21.
Artículo en Inglés | MEDLINE | ID: mdl-34921112

RESUMEN

We uncovered a transcription factor (TF) network that regulates cortical regional patterning in radial glial stem cells. Screening the expression of hundreds of TFs in the developing mouse cortex identified 38 TFs that are expressed in gradients in the ventricular zone (VZ). We tested whether their cortical expression was altered in mutant mice with known patterning defects (Emx2, Nr2f1, and Pax6), which enabled us to define a cortical regionalization TF network (CRTFN). To identify genomic programming underlying this network, we performed TF ChIP-seq and chromatin-looping conformation to identify enhancer-gene interactions. To map enhancers involved in regional patterning of cortical progenitors, we performed assays for epigenomic marks and DNA accessibility in VZ cells purified from wild-type and patterning mutant mice. This integrated approach has identified a CRTFN and VZ enhancers involved in cortical regional patterning in the mouse.


Asunto(s)
Corteza Cerebral/embriología , Redes Reguladoras de Genes , Elementos Reguladores de la Transcripción , Factores de Transcripción/metabolismo , Animales , Factor de Transcripción COUP I/metabolismo , Corteza Cerebral/metabolismo , Epigenoma , Proteínas de Homeodominio/metabolismo , Proteínas con Homeodominio LIM/metabolismo , Ratones , Factor de Transcripción PAX6/metabolismo , Factor de Transcripción 1 de la Leucemia de Células Pre-B/metabolismo , Factores de Transcripción/genética
16.
Nat Methods ; 17(8): 807-814, 2020 08.
Artículo en Inglés | MEDLINE | ID: mdl-32737473

RESUMEN

Enhancers are important non-coding elements, but they have traditionally been hard to characterize experimentally. The development of massively parallel assays allows the characterization of large numbers of enhancers for the first time. Here, we developed a framework using Drosophila STARR-seq to create shape-matching filters based on meta-profiles of epigenetic features. We integrated these features with supervised machine-learning algorithms to predict enhancers. We further demonstrated that our model could be transferred to predict enhancers in mammals. We comprehensively validated the predictions using a combination of in vivo and in vitro approaches, involving transgenic assays in mice and transduction-based reporter assays in human cell lines (153 enhancers in total). The results confirmed that our model can accurately predict enhancers in different species without re-parameterization. Finally, we examined the transcription factor binding patterns at predicted enhancers versus promoters. We demonstrated that these patterns enable the construction of a secondary model that effectively distinguishes enhancers and promoters.


Asunto(s)
Epigénesis Genética/fisiología , Reconocimiento de Normas Patrones Automatizadas/métodos , Animales , Línea Celular , Drosophila , Histonas/genética , Histonas/metabolismo , Humanos , Ratones , Ratones Transgénicos , Reproducibilidad de los Resultados
18.
Hum Genomics ; 15(1): 44, 2021 07 13.
Artículo en Inglés | MEDLINE | ID: mdl-34256850

RESUMEN

BACKGROUND: Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. RESULTS: We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10-3), and combined dataset (p = 1.1 × 10-4). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10-35, loss-of-function p = 2.26 × 10-13) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10-6, OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. CONCLUSIONS: In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.


Asunto(s)
Trastorno Autístico/genética , Predisposición Genética a la Enfermedad , Hipotonía Muscular/genética , Trastornos del Neurodesarrollo/genética , Factores de Transcripción/genética , Trastorno Autístico/epidemiología , Trastorno Autístico/patología , Elementos de Facilitación Genéticos/genética , Exoma/genética , Femenino , Redes Reguladoras de Genes/genética , Humanos , Masculino , Hipotonía Muscular/epidemiología , Hipotonía Muscular/patología , Mutación/genética , Trastornos del Neurodesarrollo/epidemiología , Trastornos del Neurodesarrollo/patología , Neuronas/metabolismo , Neuronas/patología
20.
Am J Hum Genet ; 103(6): 874-892, 2018 12 06.
Artículo en Inglés | MEDLINE | ID: mdl-30503521

RESUMEN

The progressive loss of midbrain (MB) dopaminergic (DA) neurons defines the motor features of Parkinson disease (PD), and modulation of risk by common variants in PD has been well established through genome-wide association studies (GWASs). We acquired open chromatin signatures of purified embryonic mouse MB DA neurons because we anticipated that a fraction of PD-associated genetic variation might mediate the variants' effects within this neuronal population. Correlation with >2,300 putative enhancers assayed in mice revealed enrichment for MB cis-regulatory elements (CREs), and these data were reinforced by transgenic analyses of six additional sequences in zebrafish and mice. One CRE, within intron 4 of the familial PD gene SNCA, directed reporter expression in catecholaminergic neurons from transgenic mice and zebrafish. Sequencing of this CRE in 986 individuals with PD and 992 controls revealed two common variants associated with elevated PD risk. To assess potential mechanisms of action, we screened >16,000 proteins for DNA binding capacity and identified a subset whose binding is impacted by these enhancer variants. Additional genotyping across the SNCA locus identified a single PD-associated haplotype, containing the minor alleles of both of the aforementioned PD-risk variants. Our work posits a model for how common variation at SNCA might modulate PD risk and highlights the value of cell-context-dependent guided searches for functional non-coding variation.


Asunto(s)
Cromatina/genética , Neuronas Dopaminérgicas/patología , Elementos de Facilitación Genéticos/genética , Predisposición Genética a la Enfermedad/genética , Enfermedad de Parkinson/genética , alfa-Sinucleína/genética , Adulto , Anciano , Anciano de 80 o más Años , Alelos , Animales , Modelos Animales de Enfermedad , Femenino , Genotipo , Humanos , Intrones/genética , Masculino , Ratones , Ratones Transgénicos , Persona de Mediana Edad , Embarazo , Pez Cebra
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA