RESUMEN

Variable number tandem repeats (VNTRs) account for significant genetic variation in many organisms. In humans, VNTRs have been implicated in both Mendelian and complex disorders, but are largely ignored by genomic pipelines due to the complexity of genotyping and the computational expense. We describe adVNTR-NN, a method that uses shallow neural networks to genotype a VNTR in 18 seconds on 55X whole genome data, while maintaining high accuracy. We use adVNTR-NN to genotype 10,264 VNTRs in 652 GTEx individuals. Associating VNTR length with gene expression in 46 tissues, we identify 163 "eVNTRs". Of the 22 eVNTRs in blood where independent data is available, 21 (95%) are replicated in terms of significance and direction of association. 49% of the eVNTR loci show a strong and likely causal impact on the expression of genes and 80% have maximum effect size at least 0.3. The impacted genes are involved in diseases including Alzheimer's, obesity and familial cancers, highlighting the importance of VNTRs for understanding the genetic basis of complex diseases.

Asunto(s)

Regulación de la Expresión Génica , Repeticiones de Minisatélite/genética , Alelos , Corteza Cerebral/metabolismo , Estudios de Cohortes , Sitios Genéticos , Genotipo , Humanos , Reproducibilidad de los Resultados

RESUMEN

Morphogenesis and differentiation are important stages in organ development and shape determination. However, how they are balanced and tuned during development is not fully understood. In the compound leaved tomato, an extended morphogenesis phase allows for the initiation of leaflets, resulting in the compound form. Maintaining a prolonged morphogenetic phase in early stages of compound-leaf development in tomato is dependent on delayed activity of several factors that promote differentiation, including the CIN-TCP transcription factor (TF) LA, the MYB TF CLAU and the plant hormone Gibberellin (GA), as well as on the morphogenesis-promoting activity of the plant hormone cytokinin (CK). Here, we investigated the genetic regulation of the morphogenesis-differentiation balance by studying the relationship between LA, CLAU, TKN2, CK and GA. Our genetic and molecular examination suggest that LA is expressed earlier and more broadly than CLAU and determines the developmental context of CLAU activity. Genetic interaction analysis indicates that LA and CLAU likely promote differentiation in parallel genetic pathways. These pathways converge downstream on tuning the balance between CK and GA. Comprehensive transcriptomic analyses support the genetic data and provide insights into the broader molecular basis of differentiation and morphogenesis processes in plants.

Asunto(s)

Diferenciación Celular/genética , Citocininas/genética , Giberelinas/metabolismo , Morfogénesis/genética , Citocininas/metabolismo , Regulación de la Expresión Génica de las Plantas/genética , Solanum lycopersicum/genética , Solanum lycopersicum/crecimiento & desarrollo , Solanum lycopersicum/metabolismo , Desarrollo de la Planta/genética , Hojas de la Planta/genética , Hojas de la Planta/crecimiento & desarrollo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Modificadas Genéticamente/genética , Factores de Transcripción/genética

RESUMEN

Autism spectrum disorder (ASD) is an early-onset developmental disorder characterized by deficits in communication and social interaction and restrictive or repetitive behaviours1,2. Family studies demonstrate that ASD has a substantial genetic basis with contributions both from inherited and de novo variants3,4. It has been estimated that de novo mutations may contribute to 30% of all simplex cases, in which only a single child is affected per family5. Tandem repeats (TRs), defined here as sequences of 1 to 20 base pairs in size repeated consecutively, comprise one of the major sources of de novo mutations in humans6. TR expansions are implicated in dozens of neurological and psychiatric disorders7. Yet, de novo TR mutations have not been characterized on a genome-wide scale, and their contribution to ASD remains unexplored. Here we develop new bioinformatics methods for identifying and prioritizing de novo TR mutations from sequencing data and perform a genome-wide characterization of de novo TR mutations in ASD-affected probands and unaffected siblings. We infer specific mutation events and their precise changes in repeat number, and primarily focus on more prevalent stepwise copy number changes rather than large expansions. Our results demonstrate a significant genome-wide excess of TR mutations in ASD probands. Mutations in probands tend to be larger, enriched in fetal brain regulatory regions, and are predicted to be more evolutionarily deleterious. Overall, our results highlight the importance of considering repeat variants in future studies of de novo mutations.

Asunto(s)

Trastorno del Espectro Autista/genética , Expansión de las Repeticiones de ADN/genética , Predisposición Genética a la Enfermedad , Adolescente , Adulto , Trastorno del Espectro Autista/patología , Encéfalo/metabolismo , Niño , Variaciones en el Número de Copia de ADN/genética , Femenino , Feto/metabolismo , Mutación de Línea Germinal/genética , Humanos , Análisis de los Mínimos Cuadrados , Masculino , Persona de Mediana Edad , Edad Paterna , Adulto Joven

RESUMEN

Short tandem repeats (STRs) have been implicated in a variety of complex traits in humans. However, genome-wide studies of the effects of STRs on gene expression thus far have had limited power to detect associations and provide insights into putative mechanisms. Here, we leverage whole-genome sequencing and expression data for 17 tissues from the Genotype-Tissue Expression Project to identify more than 28,000 STRs for which repeat number is associated with expression of nearby genes (eSTRs). We use fine-mapping to quantify the probability that each eSTR is causal and characterize the top 1,400 fine-mapped eSTRs. We identify hundreds of eSTRs linked with published genome-wide association study signals and implicate specific eSTRs in complex traits, including height, schizophrenia, inflammatory bowel disease and intelligence. Overall, our results support the hypothesis that eSTRs contribute to a range of human phenotypes, and our data should serve as a valuable resource for future studies of complex traits.

Asunto(s)

Regulación de la Expresión Génica , Genoma Humano , Estudio de Asociación del Genoma Completo , Repeticiones de Microsatélite/genética , Polimorfismo de Nucleótido Simple , Sitios de Carácter Cuantitativo , Estatura/genética , Biología Computacional , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Enfermedades Inflamatorias del Intestino/genética , Inteligencia/genética , Esquizofrenia/genética

RESUMEN

Tandem repeat (TR) expansions have been implicated in dozens of genetic diseases, including Huntington's Disease, Fragile X Syndrome, and hereditary ataxias. Furthermore, TRs have recently been implicated in a range of complex traits, including gene expression and cancer risk. While the human genome harbors hundreds of thousands of TRs, analysis of TR expansions has been mainly limited to known pathogenic loci. A major challenge is that expanded repeats are beyond the read length of most next-generation sequencing (NGS) datasets and are not profiled by existing genome-wide tools. We present GangSTR, a novel algorithm for genome-wide genotyping of both short and expanded TRs. GangSTR extracts information from paired-end reads into a unified model to estimate maximum likelihood TR lengths. We validate GangSTR on real and simulated data and show that GangSTR outperforms alternative methods in both accuracy and speed. We apply GangSTR to a deeply sequenced trio to profile the landscape of TR expansions in a healthy family and validate novel expansions using orthogonal technologies. Our analysis reveals that healthy individuals harbor dozens of long TR alleles not captured by current genome-wide methods. GangSTR will likely enable discovery of novel disease-associated variants not currently accessible from NGS.

Asunto(s)

Expansión de las Repeticiones de ADN , Genoma Humano , Repeticiones de Microsatélite , Análisis de Secuencia de ADN/estadística & datos numéricos , Programas Informáticos , Algoritmos , Secuencia de Bases , Conjuntos de Datos como Asunto , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Funciones de Verosimilitud , Alineación de Secuencia

RESUMEN

Whole-genome sequencing is increasingly used to identify Mendelian variants in clinical pipelines. These pipelines focus on single-nucleotide variants (SNVs) and also structural variants, while ignoring more complex repeat sequence variants. Here, we consider the problem of genotyping Variable Number Tandem Repeats (VNTRs), composed of inexact tandem duplications of short (6-100 bp) repeating units. VNTRs span 3% of the human genome, are frequently present in coding regions, and have been implicated in multiple Mendelian disorders. Although existing tools recognize VNTR carrying sequence, genotyping VNTRs (determining repeat unit count and sequence variation) from whole-genome sequencing reads remains challenging. We describe a method, adVNTR, that uses hidden Markov models to model each VNTR, count repeat units, and detect sequence variation. adVNTR models can be developed for short-read (Illumina) and single-molecule (Pacific Biosciences [PacBio]) whole-genome and whole-exome sequencing, and show good results on multiple simulated and real data sets.

Asunto(s)

Técnicas de Genotipaje/métodos , Repeticiones de Minisatélite , Genoma Humano , Humanos , Cadenas de Markov , Polimorfismo Genético

RESUMEN

Flexible maturation rates underlie part of the diversity of leaf shape, and tomato (Solanum lycopersicum) leaves are compound due to prolonged organogenic activity of the leaf margin. The CINCINNATA-teosinte branched1, cycloidea, PCF (CIN-TCP) transcription factor lanceolate (LA) restricts this organogenic activity and promotes maturation. Here, we show that tomato APETALA1/fruitfull (AP1/FUL) MADS box genes are involved in tomato leaf development and are repressed by LA. AP1/FUL expression is correlated negatively with LA activity and positively with the organogenic activity of the leaf margin. LA binds to the promoters of the AP1/FUL genes MBP20 and TM4. Overexpression of MBP20 suppressed the simple-leaf phenotype resulting from upregulation of LA activity or from downregulation of class I knotted like homeobox (KNOXI) activity. Overexpression of a dominant-negative form of MBP20 led to leaf simplification and partly suppressed the increased leaf complexity of plants with reduced LA activity or increased KNOXI activity. Tomato plants overexpressing miR319, a negative regulator of several CIN-TCP genes including LA, flower with fewer leaves via an SFT-dependent pathway, suggesting that miR319-sensitive CIN-TCPs delay flowering in tomato. These results identify a role for AP1/FUL genes in vegetative development and show that leaf and plant maturation are regulated via partially independent mechanisms.

Asunto(s)

Proteínas de Dominio MADS/genética , Hojas de la Planta/genética , Proteínas de Plantas/genética , Solanum lycopersicum/genética , Factores de Transcripción/genética , Secuencia de Aminoácidos , Perfilación de la Expresión Génica , Regulación del Desarrollo de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Proteínas Fluorescentes Verdes/genética , Proteínas Fluorescentes Verdes/metabolismo , Solanum lycopersicum/crecimiento & desarrollo , Solanum lycopersicum/metabolismo , Proteínas de Dominio MADS/metabolismo , MicroARNs/genética , MicroARNs/metabolismo , Microscopía Electrónica de Rastreo , Microscopía Fluorescente , Datos de Secuencia Molecular , Análisis de Secuencia por Matrices de Oligonucleótidos , Hojas de la Planta/crecimiento & desarrollo , Hojas de la Planta/metabolismo , Proteínas de Plantas/metabolismo , Plantas Modificadas Genéticamente , Regiones Promotoras Genéticas/genética , Unión Proteica , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Homología de Secuencia de Aminoácido , Factores de Transcripción/metabolismo

RESUMEN

During their development, leaves progress through a highly controlled yet flexible developmental program. Transcription factors from the CIN-TCP family affect leaf shape by regulating the timing of leaf maturation. Characterization of mutants in the tomato (Solanum lycopersicum) CIN-TCP gene LANCEOLATE (LA) led us to hypothesize that a threshold LA-like activity promotes leaf differentiation. Here, we examined the relationship between LA activity, leaf maturation, and final leaf size and shape. Leaves of diverse shapes from various Solanaceae species or from different positions on the tomato plant differed in the timing of growth and maturation, and these were often associated with altered LA expression dynamics. Accordingly, genetic manipulations of LA activity in tomato altered leaf growth and maturation, leading to changes in leaf size and shape. LA expression sustained until late stages of tomato leaf development, and stage-specific overexpression of miR319, a negative regulator of CIN-TCP genes, confirmed that LA-like proteins affect leaf development through these late stages. Together, our results imply that dynamic spatial and temporal leaf maturation, coordinated by LA-like genes, enables the formation of variable leaf forms.

Asunto(s)

Proteínas de Plantas/metabolismo , Solanum lycopersicum/crecimiento & desarrollo , Solanum lycopersicum/metabolismo , Solanum lycopersicum/genética , Solanum lycopersicum/ultraestructura , Microscopía Electrónica de Rastreo , Hojas de la Planta/crecimiento & desarrollo , Hojas de la Planta/metabolismo , Hojas de la Planta/ultraestructura , Proteínas de Plantas/genética , ARN Mensajero/genética

RESUMEN

Plant architecture is a predictable but flexible trait. The timing and position of organ initiation from the shoot apical meristem (SAM) contribute to the final plant form. While much progress has been made recently in understanding how the site of leaf initiation is determined, the mechanism underlying the temporal interval between leaf primordia is still largely unknown. The Arabidopsis ZRIZI (ZRZ) gene belongs to a large gene family encoding multidrug and toxic compound extrusion (MATE) transporters. Unique among plant MATE transporters identified so far, ZRZ is localized to the membrane of a small organelle, possibly the mitochondria. Plants overexpressing ZRZ in initiating leaves are short, produce leaves much faster than wild-type plants and show enhanced growth of axillary buds. These results suggest that ZRZ is involved in communicating a leaf-borne signal that determines the rate of organ initiation.

Asunto(s)

Proteínas de Arabidopsis/metabolismo , Arabidopsis/embriología , Arabidopsis/metabolismo , Proteínas de Transporte de Membrana/metabolismo , Orgánulos/metabolismo , Organogénesis , Arabidopsis/anatomía & histología , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Transporte Biológico , Perfilación de la Expresión Génica , Regulación del Desarrollo de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Genes de Plantas/genética , Proteínas de Transporte de Membrana/genética , Meristema/genética , Meristema/crecimiento & desarrollo , Especificidad de Órganos/genética , Organogénesis/genética , Fenotipo , Protoplastos/citología , Protoplastos/metabolismo , Fracciones Subcelulares/metabolismo

RESUMEN

Leaf shape diversity relies on transient morphogenetic activity in leaf margins. However, how this morphogenetic capacity is maintained is still poorly understood. Here, we uncover a role for the hormone cytokinin (CK) in the regulation of morphogenetic activity of compound leaves in tomato (Solanum lycopersicum). Manipulation of CK levels led to alterations in leaf complexity and revealed a unique potential for prolonged growth and morphogenesis in tomato leaves. We further demonstrate that the effect of CK on leaf complexity depends on proper localization of auxin signaling. Genetic analysis showed that reduction of CK levels suppresses the effect of Knotted1 like homeobox (KNOXI) proteins on leaf shape and that CK can substitute for KNOXI activity at the leaf margin, suggesting that CK mediates the activity of KNOXI proteins in the regulation of leaf shape. These results imply that CK regulates flexible leaf patterning by dynamic interaction with additional hormones and transcription factors.

Asunto(s)

Citocininas/metabolismo , Hojas de la Planta/crecimiento & desarrollo , Solanum lycopersicum/crecimiento & desarrollo , Regulación del Desarrollo de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Proteínas de Homeodominio/genética , Proteínas de Homeodominio/metabolismo , Ácidos Indolacéticos/metabolismo , Solanum lycopersicum/genética , Solanum lycopersicum/metabolismo , Hojas de la Planta/genética , Hojas de la Planta/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , ARN de Planta/genética