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1.
Cell ; 162(5): 1051-65, 2015 Aug 27.
Artículo en Inglés | MEDLINE | ID: mdl-26300125

RESUMEN

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.


Asunto(s)
Cromatina/metabolismo , Cromosomas Humanos/metabolismo , Proyecto Genoma Humano , Línea Celular , Cromosomas Humanos/química , Estudios de Cohortes , Femenino , Redes Reguladoras de Genes , Estudio de Asociación del Genoma Completo , Histonas/metabolismo , Humanos , Linfocitos/metabolismo , Masculino , Sitios de Carácter Cuantitativo , Elementos Reguladores de la Transcripción
2.
Nature ; 583(7818): 737-743, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32728247

RESUMEN

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.


Asunto(s)
Proteínas de Ciclo Celular/metabolismo , Cromatina/química , Cromatina/genética , Proteínas Cromosómicas no Histona/metabolismo , Genoma Humano/genética , Anotación de Secuencia Molecular , Empalme Alternativo/genética , Diferenciación Celular/genética , Línea Celular , Células/metabolismo , Cromatina/metabolismo , Secuenciación de Inmunoprecipitación de Cromatina , Elementos de Facilitación Genéticos/genética , Regulación de la Expresión Génica , Humanos , Conformación Molecular , Regiones Promotoras Genéticas/genética , Cohesinas
3.
Mol Cell ; 58(4): 586-97, 2015 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-26000844

RESUMEN

The human genome sequence has profoundly altered our understanding of biology, human diversity, and disease. The path from the first draft sequence to our nascent era of personal genomes and genomic medicine has been made possible only because of the extraordinary advancements in DNA sequencing technologies over the past 10 years. Here, we discuss commonly used high-throughput sequencing platforms, the growing array of sequencing assays developed around them, as well as the challenges facing current sequencing platforms and their clinical application.


Asunto(s)
Genoma Humano/genética , Genómica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Microbiota/genética , Transcriptoma/genética , Humanos , Neoplasias/genética , Medicina de Precisión/métodos
4.
Nat Methods ; 13(11): 953-958, 2016 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-27723755

RESUMEN

Paired DNA and RNA profiling is increasingly employed in genomics research to uncover molecular mechanisms of disease and to explore personal genotype and phenotype correlations. Here, we introduce Simul-seq, a technique for the production of high-quality whole-genome and transcriptome sequencing libraries from small quantities of cells or tissues. We apply the method to laser-capture-microdissected esophageal adenocarcinoma tissue, revealing a highly aneuploid tumor genome with extensive blocks of increased homozygosity and corresponding increases in allele-specific expression. Among this widespread allele-specific expression, we identify germline polymorphisms that are associated with response to cancer therapies. We further leverage this integrative data to uncover expressed mutations in several known cancer genes as well as a recurrent mutation in the motor domain of KIF3B that significantly affects kinesin-microtubule interactions. Simul-seq provides a new streamlined approach for generating comprehensive genome and transcriptome profiles from limited quantities of clinically relevant samples.


Asunto(s)
ADN/genética , Perfilación de la Expresión Génica/métodos , ARN Mensajero/genética , Análisis de Secuencia de ADN/métodos , Análisis de Secuencia de ARN/métodos , Neoplasias Esofágicas/genética , Biblioteca de Genes , Genoma Humano/genética , Humanos , Cinesinas/genética , Masculino , Mutación , Transcriptoma , Transposasas/genética
5.
BMC Genet ; 14: 40, 2013 May 09.
Artículo en Inglés | MEDLINE | ID: mdl-23659281

RESUMEN

BACKGROUND: Mice homozygous for the juvenile alopecia mutation (jal) display patches of hair loss that appear as soon as hair develops in the neonatal period and persist throughout life. Although a report initially describing this mouse variant suggested that jal maps to mouse Chromosome 13, our preliminary mapping analysis did not support that claim. RESULTS: To map jal to a particular mouse chromosome, we produced a 103-member intraspecific backcross panel that segregated for jal, and typed it for 93 PCR-scorable, microsatellite markers that are located throughout the mouse genome. Only markers from the centromeric tip of Chromosome 2 failed to segregate independently from jal, suggesting that jal resides in that region. To more precisely define jal's location, we characterized a second, 374-member backcross panel for the inheritance of five microsatellite markers from proximal Chromosome 2. This analysis restricted jal's position between D2Mit359 and D2Mit80, an interval that includes Il2ra (for interleukin 2 receptor, alpha chain), a gene that is known to be associated with alopecia areata in humans. Complementation testing with an engineered null allele of Il2ra, however, showed that jal is a mutation in a distinct gene. To further refine the location of jal, the 374-member panel was typed for a set of four single-nucleotide markers located between D2Mit359 and D2Mit80, identifying a 0.55 Mb interval where jal must lie. This span includes ten genes-only one of which, Gata3 (for GATA binding protein 3)-is known to be expressed in skin. Complementation testing between jal and a Gata3 null allele produced doubly heterozygous, phenotypically mutant offspring. CONCLUSIONS: The results presented indicate that the jal mutation is a mutant allele of the Gata3 gene on mouse Chromosome 2. We therefore recommend that the jal designation be changed to Gata3jal, and suggest that this mouse variant may provide an animal model for at least some forms of focal alopecia that have their primary defect in the hair follicle and lack an inflammatory component.


Asunto(s)
Alelos , Alopecia/genética , Mapeo Cromosómico , Factor de Transcripción GATA3/genética , Mutación , Animales , Secuencia de Bases , Cartilla de ADN , Prueba de Complementación Genética , Subunidad alfa del Receptor de Interleucina-2/genética , Ratones , Ratones Endogámicos , Reacción en Cadena de la Polimerasa
6.
PLoS One ; 17(8): e0272703, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35943990

RESUMEN

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex chronic multi-systemic disease characterized by extreme fatigue that is not improved by rest, and worsens after exertion, whether physical or mental. Previous studies have shown ME/CFS-associated alterations in the immune system and mitochondria. We used transmission electron microscopy (TEM) to investigate the morphology and ultrastructure of unstimulated and stimulated ME/CFS immune cells and their intracellular organelles, including mitochondria. PBMCs from four participants were studied: a pair of identical twins discordant for moderate ME/CFS, as well as two age- and gender- matched unrelated subjects-one with an extremely severe form of ME/CFS and the other healthy. TEM analysis of CD3/CD28-stimulated T cells suggested a significant increase in the levels of apoptotic and necrotic cell death in T cells from ME/CFS patients (over 2-fold). Stimulated Tcells of ME/CFS patients also had higher numbers of swollen mitochondria. We also found a large increase in intracellular giant lipid droplet-like organelles in the stimulated PBMCs from the extremely severe ME/CFS patient potentially indicative of a lipid storage disorder. Lastly, we observed a slight increase in platelet aggregation in stimulated cells, suggestive of a possible role of platelet activity in ME/CFS pathophysiology and disease severity. These results indicate extensive morphological alterations in the cellular and mitochondrial phenotypes of ME/CFS patients' immune cells and suggest new insights into ME/CFS biology.


Asunto(s)
Síndrome de Fatiga Crónica , Síndrome de Fatiga Crónica/metabolismo , Humanos , Leucocitos Mononucleares/metabolismo , Microscopía Electrónica de Transmisión , Fenotipo , Proyectos Piloto
7.
Exp Dermatol ; 19(6): 527-32, 2010 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-20201958

RESUMEN

Please cite this paper as: The mouse frizzy (fr) and rat 'hairless' (fr(CR)) mutations are natural variants of protease serine S1 family member 8 (Prss8). Experimental Dermatology 2010; 19: 527-532. Abstract: We have previously suggested (based on genetic mapping analysis) that the allelic 'fuzzy' and 'hairless' mutations in the rat are likely orthologues of the mouse frizzy mutation (fr). Here, we analysed three large intraspecific backcross panels that segregated for mouse fr to restrict this locus to a 0.6-Mb region that includes fewer than 30 genes. DNA sequencing of one of these candidates known to be expressed in skin, protease serine S1 family member 8 (Prss8), revealed a T to A transversion associated with the fr allele that would result in a valine to aspartate substitution at residue 170 in the gene product. To test whether this missense mutation might be the molecular basis of this frizzy variant, we crossed fr/fr mice with mice that carried a recessive perinatal lethal mutation in Prss8. Hybrid offspring that inherited both fr and the Prss8 null allele displayed abnormal hair and skin, showing that these two mutations are allelic, and suggesting strongly that the T to A mutation in Prss8 is responsible for the mutant frizzy phenotype. Sequence analysis of all Prss8 coding regions in the 'hairless' rat identified a 12-bp deletion in the third exon, indicating that mouse fr and the rat 'hairless' mutations are indeed orthologues. However, this analysis failed to detect any alterations to Prss8 coding sequences in the allelic 'fuzzy' rat variant.


Asunto(s)
Enfermedades del Cabello/genética , Mutación/genética , Serina Endopeptidasas/genética , Animales , Mapeo Cromosómico , Cromosomas de los Mamíferos/genética , Intercambio Genético/genética , Femenino , Prueba de Complementación Genética , Enfermedades del Cabello/patología , Folículo Piloso/patología , Endogamia , Masculino , Ratones , Ratones Endogámicos BALB C , Ratones Endogámicos C57BL , Ratones Mutantes , Mutación Missense/genética , Polimorfismo de Nucleótido Simple/genética , Ratas , Ratas sin Pelo , Ratas Endogámicas BN , Ratas Mutantes , Análisis de Secuencia de ADN , Eliminación de Secuencia/genética , Piel/patología , Vibrisas/patología
8.
Nat Genet ; 47(7): 710-6, 2015 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-26053494

RESUMEN

Aberrant regulation of gene expression in cancer can promote survival and proliferation of cancer cells. Here we integrate whole-genome sequencing data from The Cancer Genome Atlas (TCGA) for 436 patients from 8 cancer subtypes with ENCODE and other regulatory annotations to identify point mutations in regulatory regions. We find evidence for positive selection of mutations in transcription factor binding sites, consistent with these sites regulating important cancer cell functions. Using a new method that adjusts for sample- and genomic locus-specific mutation rates, we identify recurrently mutated sites across individuals with cancer. Mutated regulatory sites include known sites in the TERT promoter and many new sites, including a subset in proximity to cancer-related genes. In reporter assays, two new sites display decreased enhancer activity upon mutation. These data demonstrate that many regulatory regions contain mutations under selective pressure and suggest a greater role for regulatory mutations in cancer than previously appreciated.


Asunto(s)
Neoplasias/genética , Regiones Promotoras Genéticas , Secuencia de Bases , Sitios de Unión , Secuencia Conservada , Regulación Neoplásica de la Expresión Génica , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Genoma Humano , Humanos , Anotación de Secuencia Molecular , Mutación
9.
BMC Res Notes ; 6: 189, 2013 May 09.
Artículo en Inglés | MEDLINE | ID: mdl-23656696

RESUMEN

BACKGROUND: Mice homozygous for the spontaneous wooly mutation (abbreviated wly) are recognized as early as 3-4 weeks of age by the rough or matted appearance of their coats. Previous genetic analysis has placed wly in a 5.9 Mb interval on Chromosome 11 that contains over 200 known genes. Assignment of wly to one of these genes is needed in order to provide probes that would ultimately facilitate a complete molecular analysis of that gene's role in the normal and disrupted development of the mammalian integument. RESULTS: Here, a large intraspecific backcross family was used to genetically map wly to a smaller (0.8 Mb) span on mouse Chromosome 11 that includes fewer than 20 genes. DNA sequencing of the coding regions in two of these candidates known to be expressed in skin has revealed a 955 bp, wly-specific deletion. This deletion, which lies within the coordinates of both Slc5a10 [for solute carrier family 5 (sodium/glucose cotransporter), member 10] and Fam83g (for family with sequence similarity 83, member G), alters the splicing of mutant Fam83g transcripts only, and is predicted to result in a severely truncated (probably non-functional) protein product. CONCLUSION: We suggest that this mutation in Fam83g is the likely basis of the mouse wooly phenotype.


Asunto(s)
Mapeo Cromosómico , Mutación , Proteínas/genética , Secuencia de Aminoácidos , Animales , Secuencia de Bases , Cruzamientos Genéticos , Cartilla de ADN , Meiosis/genética , Ratones , Sondas Moleculares , Datos de Secuencia Molecular , Fenotipo , Homología de Secuencia de Aminoácido
10.
Science ; 342(6159): 750-2, 2013 Nov 08.
Artículo en Inglés | MEDLINE | ID: mdl-24136358

RESUMEN

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.


Asunto(s)
Cromatina/genética , Cromatina/metabolismo , Regulación de la Expresión Génica , Predisposición Genética a la Enfermedad/genética , Sitios de Unión , Factor de Unión a CCCTC , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Línea Celular Tumoral , Proteínas Cromosómicas no Histona/genética , Proteínas Cromosómicas no Histona/metabolismo , Elementos de Facilitación Genéticos/genética , Variación Genética , Histonas/genética , Histonas/metabolismo , Humanos , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Cohesinas
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