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1.
Cell ; 162(5): 1051-65, 2015 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-26300125

RESUMO

Deciphering the impact of genetic variants on gene regulation is fundamental to understanding human disease. Although gene regulation often involves long-range interactions, it is unknown to what extent non-coding genetic variants influence distal molecular phenotypes. Here, we integrate chromatin profiling for three histone marks in lymphoblastoid cell lines (LCLs) from 75 sequenced individuals with LCL-specific Hi-C and ChIA-PET-based chromatin contact maps to uncover one of the largest collections of local and distal histone quantitative trait loci (hQTLs). Distal QTLs are enriched within topologically associated domains and exhibit largely concordant variation of chromatin state coordinated by proximal and distal non-coding genetic variants. Histone QTLs are enriched for common variants associated with autoimmune diseases and enable identification of putative target genes of disease-associated variants from genome-wide association studies. These analyses provide insights into how genetic variation can affect human disease phenotypes by coordinated changes in chromatin at interacting regulatory elements.


Assuntos
Cromatina/metabolismo , Cromossomos Humanos/metabolismo , Projeto Genoma Humano , Linhagem Celular , Cromossomos Humanos/química , Estudos de Coortes , Feminino , Redes Reguladoras de Genes , Estudo de Associação Genômica Ampla , Histonas/metabolismo , Humanos , Linfócitos/metabolismo , Masculino , Locos de Características Quantitativas , Elementos Reguladores de Transcrição
2.
Cell ; 148(6): 1293-307, 2012 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-22424236

RESUMO

Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here, we present an integrative personal omics profile (iPOP), an analysis that combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. Our iPOP analysis revealed various medical risks, including type 2 diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. Extremely high-coverage genomic and transcriptomic data, which provide the basis of our iPOP, revealed extensive heteroallelic changes during healthy and diseased states and an unexpected RNA editing mechanism. This study demonstrates that longitudinal iPOP can be used to interpret healthy and diseased states by connecting genomic information with additional dynamic omics activity.


Assuntos
Genoma Humano , Genômica , Medicina de Precisão , Diabetes Mellitus Tipo 2/genética , Feminino , Perfilação da Expressão Gênica , Humanos , Masculino , Metabolômica , Pessoa de Meia-Idade , Mutação , Proteômica , Vírus Sinciciais Respiratórios/isolamento & purificação , Rhinovirus/isolamento & purificação
3.
Nature ; 583(7818): 737-743, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32728247

RESUMO

Physical interactions between distal regulatory elements have a key role in regulating gene expression, but the extent to which these interactions vary between cell types and contribute to cell-type-specific gene expression remains unclear. Here, to address these questions as part of phase III of the Encyclopedia of DNA Elements (ENCODE), we mapped cohesin-mediated chromatin loops, using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), and analysed gene expression in 24 diverse human cell types, including core ENCODE cell lines. Twenty-eight per cent of all chromatin loops vary across cell types; these variations modestly correlate with changes in gene expression and are effective at grouping cell types according to their tissue of origin. The connectivity of genes corresponds to different functional classes, with housekeeping genes having few contacts, and dosage-sensitive genes being more connected to enhancer elements. This atlas of chromatin loops complements the diverse maps of regulatory architecture that comprise the ENCODE Encyclopedia, and will help to support emerging analyses of genome structure and function.


Assuntos
Proteínas de Ciclo Celular/metabolismo , Cromatina/química , Cromatina/genética , Proteínas Cromossômicas não Histona/metabolismo , Genoma Humano/genética , Anotação de Sequência Molecular , Processamento Alternativo/genética , Diferenciação Celular/genética , Linhagem Celular , Células/metabolismo , Cromatina/metabolismo , Sequenciamento de Cromatina por Imunoprecipitação , Elementos Facilitadores Genéticos/genética , Regulação da Expressão Gênica , Humanos , Conformação Molecular , Regiões Promotoras Genéticas/genética , Coesinas
4.
Genome Res ; 25(11): 1610-21, 2015 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-26297486

RESUMO

Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy--many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation.


Assuntos
Polimorfismo de Nucleotídeo Único , Biossíntese de Proteínas , RNA/metabolismo , Cromatina/genética , Cromatina/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Humanos , Proteômica , Locos de Características Quantitativas , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Ribossomos/genética , Ribossomos/metabolismo , Alinhamento de Sequência , Análise de Sequência de RNA
5.
Nature ; 489(7414): 91-100, 2012 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-22955619

RESUMO

Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes; the ensemble of these binding events forms a regulatory network, constituting the wiring diagram for a cell. To examine the principles of the human transcriptional regulatory network, we determined the genomic binding information of 119 transcription-related factors in over 450 distinct experiments. We found the combinatorial, co-association of transcription factors to be highly context specific: distinct combinations of factors bind at specific genomic locations. In particular, there are significant differences in the binding proximal and distal to genes. We organized all the transcription factor binding into a hierarchy and integrated it with other genomic information (for example, microRNA regulation), forming a dense meta-network. Factors at different levels have different properties; for instance, top-level transcription factors more strongly influence expression and middle-level ones co-regulate targets to mitigate information-flow bottlenecks. Moreover, these co-regulations give rise to many enriched network motifs (for example, noise-buffering feed-forward loops). Finally, more connected network components are under stronger selection and exhibit a greater degree of allele-specific activity (that is, differential binding to the two parental alleles). The regulatory information obtained in this study will be crucial for interpreting personal genome sequences and understanding basic principles of human biology and disease.


Assuntos
DNA/genética , Enciclopédias como Assunto , Redes Reguladoras de Genes/genética , Genoma Humano/genética , Anotação de Sequência Molecular , Sequências Reguladoras de Ácido Nucleico/genética , Fatores de Transcrição/metabolismo , Alelos , Linhagem Celular , Fator de Transcrição GATA1/metabolismo , Perfilação da Expressão Gênica , Genômica , Humanos , Células K562 , Especificidade de Órgãos , Fosforilação/genética , Polimorfismo de Nucleotídeo Único/genética , Mapas de Interação de Proteínas , RNA não Traduzido/genética , RNA não Traduzido/metabolismo , Seleção Genética/genética , Sítio de Iniciação de Transcrição
6.
Am J Respir Crit Care Med ; 195(7): 930-941, 2017 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-27779452

RESUMO

RATIONALE: Idiopathic or heritable pulmonary arterial hypertension is characterized by loss and obliteration of lung vasculature. Endothelial cell dysfunction is pivotal to the pathophysiology, but different causal mechanisms may reflect a need for patient-tailored therapies. OBJECTIVES: Endothelial cells differentiated from induced pluripotent stem cells were compared with pulmonary arterial endothelial cells from the same patients with idiopathic or heritable pulmonary arterial hypertension, to determine whether they shared functional abnormalities and altered gene expression patterns that differed from those in unused donor cells. We then investigated whether endothelial cells differentiated from pluripotent cells could serve as surrogates to test emerging therapies. METHODS: Functional changes assessed included adhesion, migration, tube formation, and propensity to apoptosis. Expression of bone morphogenetic protein receptor type 2 (BMPR2) and its target, collagen IV, signaling of the phosphorylated form of the mothers against decapentaplegic proteins (pSMAD1/5), and transcriptomic profiles were also analyzed. MEASUREMENTS AND MAIN RESULTS: Native pulmonary arterial and induced pluripotent stem cell-derived endothelial cells from patients with idiopathic and heritable pulmonary arterial hypertension compared with control subjects showed a similar reduction in adhesion, migration, survival, and tube formation, and decreased BMPR2 and downstream signaling and collagen IV expression. Transcriptomic profiling revealed high kisspeptin 1 (KISS1) related to reduced migration and low carboxylesterase 1 (CES1), to impaired survival in patient cells. A beneficial angiogenic response to potential therapies, FK506 and Elafin, was related to reduced slit guidance ligand 3 (SLIT3), an antimigratory factor. CONCLUSIONS: Despite the site of disease in the lung, our study indicates that induced pluripotent stem cell-derived endothelial cells are useful surrogates to uncover novel features related to disease mechanisms and to better match patients to therapies.


Assuntos
Receptores de Proteínas Morfogenéticas Ósseas Tipo II/genética , Expressão Gênica/genética , Hipertensão Pulmonar/genética , Hipertensão Pulmonar/fisiopatologia , Células-Tronco Pluripotentes Induzidas , Adolescente , Adulto , Diferenciação Celular/genética , Células Cultivadas , Células Endoteliais/fisiologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Sensibilidade e Especificidade , Transdução de Sinais/genética
7.
Genome Res ; 24(12): 1905-17, 2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-25228660

RESUMO

Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer-promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus.


Assuntos
Mapeamento Cromossômico , Epistasia Genética , Genoma Humano , Estudo de Associação Genômica Ampla , Sequências Reguladoras de Ácido Nucleico , Fator de Ligação a CCCTC , Proteínas de Ciclo Celular/genética , Linhagem Celular , Cromatina/genética , Cromatina/metabolismo , Imunoprecipitação da Cromatina , Proteínas Cromossômicas não Histona/genética , Análise por Conglomerados , Biologia Computacional , Conjuntos de Dados como Assunto , Elementos Facilitadores Genéticos , Regulação da Expressão Gênica , Redes Reguladoras de Genes , Loci Gênicos , Genômica/métodos , Humanos , Especificidade de Órgãos/genética , Regiões Promotoras Genéticas , Proteínas Repressoras/genética , Transativadores/genética , Fatores de Transcrição/metabolismo , Coesinas
8.
Nature ; 470(7332): 59-65, 2011 Feb 03.
Artigo em Inglês | MEDLINE | ID: mdl-21293372

RESUMO

Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.


Assuntos
Variações do Número de Cópias de DNA/genética , Genética Populacional , Genoma Humano/genética , Genômica , Duplicação Gênica/genética , Predisposição Genética para Doença/genética , Genótipo , Humanos , Mutagênese Insercional/genética , Reprodutibilidade dos Testes , Análise de Sequência de DNA , Deleção de Sequência/genética
9.
Proc Natl Acad Sci U S A ; 111(27): 9869-74, 2014 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-24961374

RESUMO

Personal transcriptomes in which all of an individual's genetic variants (e.g., single nucleotide variants) and transcript isoforms (transcription start sites, splice sites, and polyA sites) are defined and quantified for full-length transcripts are expected to be important for understanding individual biology and disease, but have not been described previously. To obtain such transcriptomes, we sequenced the lymphoblastoid transcriptomes of three family members (GM12878 and the parents GM12891 and GM12892) by using a Pacific Biosciences long-read approach complemented with Illumina 101-bp sequencing and made the following observations. First, we found that reads representing all splice sites of a transcript are evident for most sufficiently expressed genes ≤3 kb and often for genes longer than that. Second, we added and quantified previously unidentified splicing isoforms to an existing annotation, thus creating the first personalized annotation to our knowledge. Third, we determined SNVs in a de novo manner and connected them to RNA haplotypes, including HLA haplotypes, thereby assigning single full-length RNA molecules to their transcribed allele, and demonstrated Mendelian inheritance of RNA molecules. Fourth, we show how RNA molecules can be linked to personal variants on a one-by-one basis, which allows us to assess differential allelic expression (DAE) and differential allelic isoforms (DAI) from the phased full-length isoform reads. The DAI method is largely independent of the distance between exon and SNV--in contrast to fragmentation-based methods. Overall, in addition to improving eukaryotic transcriptome annotation, these results describe, to our knowledge, the first large-scale and full-length personal transcriptome.


Assuntos
Alelos , Transcriptoma , Expressão Gênica , Haplótipos , Humanos , Polimorfismo de Nucleotídeo Único , RNA/genética
10.
PLoS Genet ; 10(8): e1004549, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-25121757

RESUMO

Large-scale sequencing efforts have documented extensive genetic variation within the human genome. However, our understanding of the origins, global distribution, and functional consequences of this variation is far from complete. While regulatory variation influencing gene expression has been studied within a handful of populations, the breadth of transcriptome differences across diverse human populations has not been systematically analyzed. To better understand the spectrum of gene expression variation, alternative splicing, and the population genetics of regulatory variation in humans, we have sequenced the genomes, exomes, and transcriptomes of EBV transformed lymphoblastoid cell lines derived from 45 individuals in the Human Genome Diversity Panel (HGDP). The populations sampled span the geographic breadth of human migration history and include Namibian San, Mbuti Pygmies of the Democratic Republic of Congo, Algerian Mozabites, Pathan of Pakistan, Cambodians of East Asia, Yakut of Siberia, and Mayans of Mexico. We discover that approximately 25.0% of the variation in gene expression found amongst individuals can be attributed to population differences. However, we find few genes that are systematically differentially expressed among populations. Of this population-specific variation, 75.5% is due to expression rather than splicing variability, and we find few genes with strong evidence for differential splicing across populations. Allelic expression analyses indicate that previously mapped common regulatory variants identified in eight populations from the International Haplotype Map Phase 3 project have similar effects in our seven sampled HGDP populations, suggesting that the cellular effects of common variants are shared across diverse populations. Together, these results provide a resource for studies analyzing functional differences across populations by estimating the degree of shared gene expression, alternative splicing, and regulatory genetics across populations from the broadest points of human migration history yet sampled.


Assuntos
Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Genética Populacional , Haplótipos/genética , Genoma Humano , Projeto HapMap , Projeto Genoma Humano , Migração Humana , Humanos , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas/genética
11.
Hum Mol Genet ; 21(10): 2205-10, 2012 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-22328086

RESUMO

Autosomal dominant cerebellar ataxia, deafness and narcolepsy (ADCA-DN) is characterized by late onset (30-40 years old) cerebellar ataxia, sensory neuronal deafness, narcolepsy-cataplexy and dementia. We performed exome sequencing in five individuals from three ADCA-DN kindreds and identified DNMT1 as the only gene with mutations found in all five affected individuals. Sanger sequencing confirmed the de novo mutation p.Ala570Val in one family, and showed co-segregation of p.Val606Phe and p.Ala570Val, with the ADCA-DN phenotype, in two other kindreds. An additional ADCA-DN kindred with a p.GLY605Ala mutation was subsequently identified. Narcolepsy and deafness were the first symptoms to appear in all pedigrees, followed by ataxia. DNMT1 is a widely expressed DNA methyltransferase maintaining methylation patterns in development, and mediating transcriptional repression by direct binding to HDAC2. It is also highly expressed in immune cells and required for the differentiation of CD4+ into T regulatory cells. Mutations in exon 20 of this gene were recently reported to cause hereditary sensory neuropathy with dementia and hearing loss (HSAN1). Our mutations are all located in exon 21 and in very close spatial proximity, suggesting distinct phenotypes depending on mutation location within this gene.


Assuntos
Ataxia Cerebelar/genética , DNA (Citosina-5-)-Metiltransferases/genética , Surdez/genética , Genes Dominantes , Mutação , Narcolepsia/genética , Sequência de Aminoácidos , DNA (Citosina-5-)-Metiltransferase 1 , Exoma , Éxons , Humanos , Dados de Sequência Molecular , Linhagem , Fenótipo
12.
PLoS Genet ; 7(8): e1002236, 2011 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-21876680

RESUMO

As a consequence of the accumulation of insertion events over evolutionary time, mobile elements now comprise nearly half of the human genome. The Alu, L1, and SVA mobile element families are still duplicating, generating variation between individual genomes. Mobile element insertions (MEI) have been identified as causes for genetic diseases, including hemophilia, neurofibromatosis, and various cancers. Here we present a comprehensive map of 7,380 MEI polymorphisms from the 1000 Genomes Project whole-genome sequencing data of 185 samples in three major populations detected with two detection methods. This catalog enables us to systematically study mutation rates, population segregation, genomic distribution, and functional properties of MEI polymorphisms and to compare MEI to SNP variation from the same individuals. Population allele frequencies of MEI and SNPs are described, broadly, by the same neutral ancestral processes despite vastly different mutation mechanisms and rates, except in coding regions where MEI are virtually absent, presumably due to strong negative selection. A direct comparison of MEI and SNP diversity levels suggests a differential mobile element insertion rate among populations.


Assuntos
Elementos de DNA Transponíveis , Genoma Humano , Polimorfismo de Nucleotídeo Único , Frequência do Gene , Genótipo , Heterozigoto , Humanos , Mutagênese Insercional , Taxa de Mutação
13.
Child Dev ; 84(1): 34-48, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23311762

RESUMO

Structural variation of the human genome sequence is the insertion, deletion, or rearrangement of stretches of DNA sequence sized from around 1,000 to millions of base pairs. Over the past few years, structural variation has been shown to be far more common in human genomes than previously thought. Very little is currently known about the effects of structural variation on normal child development, but such effects could be of considerable significance. This review provides an overview of the phenomenon of structural variation in the human genome sequence, describing the novel genomics technologies that are revolutionizing the way structural variation is studied and giving examples of genomic structural variations that affect child development.


Assuntos
Deficiências do Desenvolvimento/genética , Variação Estrutural do Genoma/genética , Criança , Variações do Número de Cópias de DNA , Replicação do DNA/genética , Duplicação Gênica/genética , Rearranjo Gênico/genética , Genoma Humano/genética , Humanos , Recombinação Genética/genética , Análise de Sequência de DNA , Deleção de Sequência/genética , Inversão de Sequência/genética
14.
BMC Bioinformatics ; 13: 305, 2012 Nov 17.
Artigo em Inglês | MEDLINE | ID: mdl-23157288

RESUMO

BACKGROUND: DNA capture technologies combined with high-throughput sequencing now enable cost-effective, deep-coverage, targeted sequencing of complete exomes. This is well suited for SNP discovery and genotyping. However there has been little attention devoted to Copy Number Variation (CNV) detection from exome capture datasets despite the potentially high impact of CNVs in exonic regions on protein function. RESULTS: As members of the 1000 Genomes Project analysis effort, we investigated 697 samples in which 931 genes were targeted and sampled with 454 or Illumina paired-end sequencing. We developed a rigorous Bayesian method to detect CNVs in the genes, based on read depth within target regions. Despite substantial variability in read coverage across samples and targeted exons, we were able to identify 107 heterozygous deletions in the dataset. The experimentally determined false discovery rate (FDR) of the cleanest dataset from the Wellcome Trust Sanger Institute is 12.5%. We were able to substantially improve the FDR in a subset of gene deletion candidates that were adjacent to another gene deletion call (17 calls). The estimated sensitivity of our call-set was 45%. CONCLUSIONS: This study demonstrates that exonic sequencing datasets, collected both in population based and medical sequencing projects, will be a useful substrate for detecting genic CNV events, particularly deletions. Based on the number of events we found and the sensitivity of the methods in the present dataset, we estimate on average 16 genic heterozygous deletions per individual genome. Our power analysis informs ongoing and future projects about sequencing depth and uniformity of read coverage required for efficient detection.


Assuntos
Variações do Número de Cópias de DNA , Genoma/genética , Sequenciamento de Nucleotídeos em Larga Escala/estatística & dados numéricos , Teorema de Bayes , Exoma , Éxons , Genótipo , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA
15.
Proc Natl Acad Sci U S A ; 106(29): 12031-6, 2009 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-19597142

RESUMO

Down syndrome (DS), or trisomy 21, is a common disorder associated with several complex clinical phenotypes. Although several hypotheses have been put forward, it is unclear as to whether particular gene loci on chromosome 21 (HSA21) are sufficient to cause DS and its associated features. Here we present a high-resolution genetic map of DS phenotypes based on an analysis of 30 subjects carrying rare segmental trisomies of various regions of HSA21. By using state-of-the-art genomics technologies we mapped segmental trisomies at exon-level resolution and identified discrete regions of 1.8-16.3 Mb likely to be involved in the development of 8 DS phenotypes, 4 of which are congenital malformations, including acute megakaryocytic leukemia, transient myeloproliferative disorder, Hirschsprung disease, duodenal stenosis, imperforate anus, severe mental retardation, DS-Alzheimer Disease, and DS-specific congenital heart disease (DSCHD). Our DS-phenotypic maps located DSCHD to a <2-Mb interval. Furthermore, the map enabled us to present evidence against the necessary involvement of other loci as well as specific hypotheses that have been put forward in relation to the etiology of DS-i.e., the presence of a single DS consensus region and the sufficiency of DSCR1 and DYRK1A, or APP, in causing several severe DS phenotypes. Our study demonstrates the value of combining advanced genomics with cohorts of rare patients for studying DS, a prototype for the role of copy-number variation in complex disease.


Assuntos
Mapeamento Cromossômico , Cromossomos Humanos Par 21/genética , Síndrome de Down/genética , Trissomia/genética , Humanos , Lactente , Metanálise como Assunto , Fenótipo
16.
Proc Natl Acad Sci U S A ; 105(40): 15499-504, 2008 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-18832167

RESUMO

Highly specific amplification of complex DNA pools without bias or template-independent products (TIPs) remains a challenge. We have developed a method using phi29 DNA polymerase and trehalose and optimized control of amplification to create micrograms of specific amplicons without TIPs from down to subfemtograms of DNA. With an input of as little as 0.5-2.5 ng of human gDNA or a few cells, the product could be close to native DNA in locus representation. The amplicons from 5 and 0.5 ng of DNA faithfully demonstrated all previously known heterozygous segmental duplications and deletions (3 Mb to 18 kb) located on chromosome 22 and even a homozygous deletion smaller than 1 kb with high-resolution chromosome-wide comparative genomic hybridization. With 550k Infinium BeadChip SNP typing, the >99.7% accuracy was compared favorably with results on unamplified DNA. Importantly, underrepresentation of chromosome termini that occurred with GenomiPhi v2 was greatly rescued with the present procedure, and the call rate and accuracy of SNP typing were also improved for the amplicons with a 0.5-ng, partially degraded DNA input. In addition, the amplification proceeded logarithmically in terms of total yield before saturation; the intact cells was amplified >50 times more efficiently than an equivalent amount of extracted DNA; and the locus imbalance for amplicons with 0.1 ng or lower input of DNA was variable, whereas for higher input it was largely reproducible. This procedure facilitates genomic analysis with single cells or other traces of DNA, and generates products suitable for analysis by massively parallel sequencing as well as microarray hybridization.


Assuntos
DNA/análise , Genoma , Técnicas de Amplificação de Ácido Nucleico/métodos , Genômica , Hibridização de Ácido Nucleico/métodos , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Polimorfismo de Nucleotídeo Único , Sensibilidade e Especificidade
17.
Nat Commun ; 11(1): 1673, 2020 04 03.
Artigo em Inglês | MEDLINE | ID: mdl-32245974

RESUMO

Environmental and epigenetic factors often play an important role in polygenic disorders. However, how such factors affect disease-specific tissues at the molecular level remains to be understood. Here, we address this in pulmonary arterial hypertension (PAH). We obtain pulmonary arterial endothelial cells (PAECs) from lungs of patients and controls (n = 19), and perform chromatin, transcriptomic and interaction profiling. Overall, we observe extensive remodeling at active enhancers in PAH PAECs and identify hundreds of differentially active TFs, yet find very little transcriptomic changes in steady-state. We devise a disease-specific enhancer-gene regulatory network and predict that primed enhancers in PAH PAECs are activated by the differentially active TFs, resulting in an aberrant response to endothelial signals, which could lead to disturbed angiogenesis and endothelial-to-mesenchymal-transition. We validate these predictions for a selection of target genes in PAECs stimulated with TGF-ß, VEGF or serotonin. Our study highlights the role of chromatin state and enhancers in disease-relevant cell types of PAH.


Assuntos
Elementos Facilitadores Genéticos , Redes Reguladoras de Genes , Hipertensão Arterial Pulmonar/genética , Artéria Pulmonar/patologia , Remodelação Vascular/genética , Adulto , Biópsia , Estudos de Casos e Controles , Células Cultivadas , Cromatina/metabolismo , Células Endoteliais/patologia , Endotélio Vascular/citologia , Epigênese Genética , Transição Epitelial-Mesenquimal/genética , Feminino , Código das Histonas/genética , Histonas/genética , Humanos , Lactente , Pulmão/irrigação sanguínea , Masculino , Pessoa de Meia-Idade , Cultura Primária de Células , Hipertensão Arterial Pulmonar/patologia , Artéria Pulmonar/citologia , RNA-Seq , Serotonina/metabolismo , Fatores de Transcrição/metabolismo , Fator de Crescimento Transformador beta/metabolismo , Fator A de Crescimento do Endotélio Vascular/metabolismo , Adulto Jovem
18.
Cell Stem Cell ; 20(4): 490-504.e5, 2017 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-28017794

RESUMO

In familial pulmonary arterial hypertension (FPAH), the autosomal dominant disease-causing BMPR2 mutation is only 20% penetrant, suggesting that genetic variation provides modifiers that alleviate the disease. Here, we used comparison of induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) from three families with unaffected mutation carriers (UMCs), FPAH patients, and gender-matched controls to investigate this variation. Our analysis identified features of UMC iPSC-ECs related to modifiers of BMPR2 signaling or to differentially expressed genes. FPAH-iPSC-ECs showed reduced adhesion, survival, migration, and angiogenesis compared to UMC-iPSC-ECs and control cells. The "rescued" phenotype of UMC cells was related to an increase in specific BMPR2 activators and/or a reduction in inhibitors, and the improved cell adhesion could be attributed to preservation of related signaling. The improved survival was related to increased BIRC3 and was independent of BMPR2. Our findings therefore highlight protective modifiers for FPAH that could help inform development of future treatment strategies.


Assuntos
Receptores de Proteínas Morfogenéticas Ósseas Tipo II/genética , Células Endoteliais/citologia , Hipertensão Pulmonar/genética , Hipertensão Pulmonar/prevenção & controle , Células-Tronco Pluripotentes Induzidas/citologia , Mutação/genética , Sequência de Bases , Proteína Morfogenética Óssea 4/farmacologia , Adesão Celular/efeitos dos fármacos , Movimento Celular/efeitos dos fármacos , Forma Celular/efeitos dos fármacos , Sobrevivência Celular/efeitos dos fármacos , Células Endoteliais/efeitos dos fármacos , Células Endoteliais/metabolismo , Edição de Genes , Regulação da Expressão Gênica/efeitos dos fármacos , Heterozigoto , Humanos , Hipertensão Pulmonar/patologia , Células-Tronco Pluripotentes Induzidas/efeitos dos fármacos , Células-Tronco Pluripotentes Induzidas/metabolismo , Neovascularização Fisiológica/efeitos dos fármacos , Neovascularização Fisiológica/genética , Fosforilação/efeitos dos fármacos , Análise de Sequência de RNA , Transdução de Sinais/efeitos dos fármacos , Proteínas Smad/metabolismo , Proteínas Quinases p38 Ativadas por Mitógeno/metabolismo
19.
Nat Biotechnol ; 31(11): 1009-14, 2013 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-24108091

RESUMO

Global RNA studies have become central to understanding biological processes, but methods such as microarrays and short-read sequencing are unable to describe an entire RNA molecule from 5' to 3' end. Here we use single-molecule long-read sequencing technology from Pacific Biosciences to sequence the polyadenylated RNA complement of a pooled set of 20 human organs and tissues without the need for fragmentation or amplification. We show that full-length RNA molecules of up to 1.5 kb can readily be monitored with little sequence loss at the 5' ends. For longer RNA molecules more 5' nucleotides are missing, but complete intron structures are often preserved. In total, we identify ∼14,000 spliced GENCODE genes. High-confidence mappings are consistent with GENCODE annotations, but >10% of the alignments represent intron structures that were not previously annotated. As a group, transcripts mapping to unannotated regions have features of long, noncoding RNAs. Our results show the feasibility of deep sequencing full-length RNA from complex eukaryotic transcriptomes on a single-molecule level.


Assuntos
Perfilação da Expressão Gênica/métodos , Análise de Sequência de RNA/métodos , Transcriptoma , DNA Complementar/química , DNA Complementar/genética , Humanos , Íntrons , Cadeias de Markov , RNA Mensageiro/química , RNA Mensageiro/genética , Alinhamento de Sequência
20.
Science ; 342(6159): 750-2, 2013 Nov 08.
Artigo em Inglês | MEDLINE | ID: mdl-24136358

RESUMO

The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.


Assuntos
Cromatina/genética , Cromatina/metabolismo , Regulação da Expressão Gênica , Predisposição Genética para Doença/genética , Sítios de Ligação , Fator de Ligação a CCCTC , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Linhagem Celular Tumoral , Proteínas Cromossômicas não Histona/genética , Proteínas Cromossômicas não Histona/metabolismo , Elementos Facilitadores Genéticos/genética , Variação Genética , Histonas/genética , Histonas/metabolismo , Humanos , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Coesinas
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