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1.
Mol Cell ; 78(3): 506-521.e6, 2020 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-32386543

RESUMO

Higher-order chromatin structure and DNA methylation are implicated in multiple developmental processes, but their relationship to cell state is unknown. Here, we find that large (>7.3 kb) DNA methylation nadirs (termed "grand canyons") can form long loops connecting anchor loci that may be dozens of megabases (Mb) apart, as well as inter-chromosomal links. The interacting loci cover a total of ∼3.5 Mb of the human genome. The strongest interactions are associated with repressive marks made by the Polycomb complex and are diminished upon EZH2 inhibitor treatment. The data are suggestive of the formation of these loops by interactions between repressive elements in the loci, forming a genomic subcompartment, rather than by cohesion/CTCF-mediated extrusion. Interestingly, unlike previously characterized subcompartments, these interactions are present only in particular cell types, such as stem and progenitor cells. Our work reveals that H3K27me3-marked large DNA methylation grand canyons represent a set of very-long-range loops associated with cellular identity.


Assuntos
Cromatina/química , Cromatina/genética , Metilação de DNA , Células-Tronco Hematopoéticas/citologia , Células-Tronco Hematopoéticas/fisiologia , Fator de Ligação a CCCTC/genética , Fator de Ligação a CCCTC/metabolismo , Diferenciação Celular , Cromatina/metabolismo , Proteína Potenciadora do Homólogo 2 de Zeste/genética , Proteína Potenciadora do Homólogo 2 de Zeste/metabolismo , Epigênese Genética , Regulação da Expressão Gênica , Histonas/genética , Histonas/metabolismo , Proteínas de Homeodomínio/genética , Humanos , Hibridização in Situ Fluorescente , Lisina/genética , Lisina/metabolismo , Proteínas Nucleares/genética , Fatores de Transcrição SOXB1/genética , Proteína de Homoeobox de Baixa Estatura/genética , Fatores de Transcrição/genética
2.
Nature ; 563(7732): 501-507, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30429615

RESUMO

Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector.


Assuntos
Aedes/genética , Infecções por Arbovirus/virologia , Arbovírus , Genoma de Inseto/genética , Genômica/normas , Controle de Insetos , Mosquitos Vetores/genética , Mosquitos Vetores/virologia , Aedes/virologia , Animais , Infecções por Arbovirus/transmissão , Arbovírus/isolamento & purificação , Variações do Número de Cópias de DNA/genética , Vírus da Dengue/isolamento & purificação , Feminino , Variação Genética/genética , Genética Populacional , Glutationa Transferase/genética , Resistência a Inseticidas/efeitos dos fármacos , Masculino , Anotação de Sequência Molecular , Família Multigênica/genética , Piretrinas/farmacologia , Padrões de Referência , Processos de Determinação Sexual/genética
3.
PLoS One ; 18(11): e0294283, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-38032990

RESUMO

Early detection of SARS-CoV-2 infection is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying SARS-CoV-2 infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this method amplifies the entirety of the SARS-CoV-2 genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only a few loci. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing and de novo genome assembly. Using this method, we can reliably (>95% accuracy) detect SARS-CoV-2 at a concentration of 84 genome equivalents per milliliter (GE/mL). The vast majority of diagnostic methods meeting our analytical criteria that are currently authorized for use by the United States Food and Drug Administration with the Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require higher concentrations of the virus to achieve this degree of sensitivity and specificity. In addition, we can reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy given sufficient viral load. The genotypic data in these genome assemblies enable the more effective analysis of disease spread than is possible with an ordinary binary diagnostic. These data can also help identify vaccine and drug targets. Finally, we show that the diagnoses obtained using POLAR of positive and negative clinical nasal mid-turbinate swab samples 100% match those obtained in a clinical diagnostic lab using the Center for Disease Control's 2019-Novel Coronavirus test. Using POLAR, a single person can manually process 192 samples over an 8-hour experiment at the cost of ~$36 per patient (as of December 7th, 2022), enabling a 24-hour turnaround with sequencing and data analysis time. We anticipate that further testing and refinement will allow greater sensitivity using this approach.


Assuntos
COVID-19 , SARS-CoV-2 , Estados Unidos , Humanos , SARS-CoV-2/genética , COVID-19/diagnóstico , Teste para COVID-19 , Sensibilidade e Especificidade , Análise de Sequência de DNA
4.
Nat Commun ; 14(1): 3303, 2023 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-37280210

RESUMO

Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF's RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted.


Assuntos
Cromatina , Elementos Facilitadores Genéticos , Cromatina/genética , Fator de Ligação a CCCTC/genética , Fator de Ligação a CCCTC/metabolismo , Elementos Facilitadores Genéticos/genética , Núcleo Celular/genética , Núcleo Celular/metabolismo , Regiões Promotoras Genéticas
5.
Cell Rep ; 26(3): 788-801.e6, 2019 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-30650367

RESUMO

EndoC-ßH1 is emerging as a critical human ß cell model to study the genetic and environmental etiologies of ß cell (dys)function and diabetes. Comprehensive knowledge of its molecular landscape is lacking, yet required, for effective use of this model. Here, we report chromosomal (spectral karyotyping), genetic (genotyping), epigenomic (ChIP-seq and ATAC-seq), chromatin interaction (Hi-C and Pol2 ChIA-PET), and transcriptomic (RNA-seq and miRNA-seq) maps of EndoC-ßH1. Analyses of these maps define known (e.g., PDX1 and ISL1) and putative (e.g., PCSK1 and mir-375) ß cell-specific transcriptional cis-regulatory networks and identify allelic effects on cis-regulatory element use. Importantly, comparison with maps generated in primary human islets and/or ß cells indicates preservation of chromatin looping but also highlights chromosomal aberrations and fetal genomic signatures in EndoC-ßH1. Together, these maps, and a web application we created for their exploration, provide important tools for the design of experiments to probe and manipulate the genetic programs governing ß cell identity and (dys)function in diabetes.


Assuntos
Redes Reguladoras de Genes/genética , Células Secretoras de Insulina/metabolismo , Linhagem Celular , Humanos
6.
Science ; 356(6333): 92-95, 2017 04 07.
Artigo em Inglês | MEDLINE | ID: mdl-28336562

RESUMO

The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective way. Here we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67× coverage). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Aeaegypti and Culex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that almost all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, and accurate, and can be applied to many species.


Assuntos
Aedes/genética , Mapeamento de Sequências Contíguas/métodos , Genoma de Inseto , Animais , Sequência Conservada , Culex/genética , Rearranjo Gênico , Humanos , Conformação de Ácido Nucleico
7.
Science ; 331(6014): 176-82, 2011 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-21163965

RESUMO

We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of 'culturomics,' focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. Culturomics extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities.


Assuntos
Livros , Cultura , Ciências Humanas , Linguística , Literatura , Ciências Sociais , Vocabulário , Algoritmos , Evolução Cultural , Coleta de Dados , Dicionários como Assunto , Enciclopédias como Assunto , Pessoas Famosas , Tecnologia
8.
Cell Stem Cell ; 6(6): 591-602, 2010 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-20569696

RESUMO

Wilms tumor is the most common pediatric kidney cancer. To identify transcriptional and epigenetic mechanisms that drive this disease, we compared genome-wide chromatin profiles of Wilms tumors, embryonic stem cells (ESCs), and normal kidney. Wilms tumors prominently exhibit large active chromatin domains previously observed in ESCs. In the cancer, these domains frequently correspond to genes that are critical for kidney development and expressed in the renal stem cell compartment. Wilms cells also express "embryonic" chromatin regulators and maintain stem cell-like p16 silencing. Finally, Wilms and ESCs both exhibit "bivalent" chromatin modifications at silent promoters that may be poised for activation. In Wilms tumor, bivalent promoters correlate to genes expressed in specific kidney compartments and point to a kidney-specific differentiation program arrested at an early-progenitor stage. We suggest that Wilms cells share a transcriptional and epigenetic landscape with a normal renal stem cell, which is inherently susceptible to transformation and may represent a cell of origin for this disease.


Assuntos
Cromatina/metabolismo , Neoplasias Renais/genética , Rim/metabolismo , Proteínas de Neoplasias/metabolismo , Tumor de Wilms/genética , Proteínas Adaptadoras de Transdução de Sinal , Diferenciação Celular/genética , Transformação Celular Neoplásica/genética , Cromatina/genética , Imunoprecipitação da Cromatina , Inibidor p16 de Quinase Dependente de Ciclina , Metilação de DNA , Células-Tronco Embrionárias/metabolismo , Células-Tronco Embrionárias/patologia , Regulação da Expressão Gênica no Desenvolvimento , Redes Reguladoras de Genes , Estudo de Associação Genômica Ampla , Humanos , Rim/patologia , Neoplasias Renais/patologia , Neoplasias Renais/fisiopatologia , Mutação/genética , Proteínas de Neoplasias/genética , Especificidade de Órgãos , Transcrição Gênica , Proteínas Supressoras de Tumor/biossíntese , Proteínas Supressoras de Tumor/genética , Tumor de Wilms/patologia , Tumor de Wilms/fisiopatologia
9.
Nat Rev Microbiol ; 7(6): 460-6, 2009 06.
Artigo em Inglês | MEDLINE | ID: mdl-19444248

RESUMO

Large-scale, systems biology approaches now allow us to systematically map synergistic and antagonistic interactions between drugs. Consequently, drug antagonism is emerging as a powerful tool to study biological function and relatedness between cellular components as well as to uncover mechanisms of drug action. Furthermore, theoretical models and new experiments suggest that antagonistic interactions between antibiotics can counteract the evolution of drug resistance.


Assuntos
Interações Medicamentosas , Resistência Microbiana a Medicamentos , Antagonismo de Drogas , Sinergismo Farmacológico , Modelos Teóricos , Transdução de Sinais/efeitos dos fármacos , Transdução de Sinais/fisiologia
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