RESUMEN
Despite a wealth of molecular knowledge, quantitative laws for accurate prediction of biological phenomena remain rare. Alternative pre-mRNA splicing is an important regulated step in gene expression frequently perturbed in human disease. To understand the combined effects of mutations during evolution, we quantified the effects of all possible combinations of exonic mutations accumulated during the emergence of an alternatively spliced human exon. This revealed that mutation effects scale non-monotonically with the inclusion level of an exon, with each mutation having maximum effect at a predictable intermediate inclusion level. This scaling is observed genome-wide for cis and trans perturbations of splicing, including for natural and disease-associated variants. Mathematical modeling suggests that competition between alternative splice sites is sufficient to cause this non-linearity in the genotype-phenotype map. Combining the global scaling law with specific pairwise interactions between neighboring mutations allows accurate prediction of the effects of complex genotype changes involving >10 mutations.
Asunto(s)
Empalme Alternativo/genética , Empalme del ARN/genética , Receptor fas/genética , Animales , Exones/genética , Técnicas Genéticas , Genética , Genotipo , Humanos , Intrones/genética , Ratones , Modelos Teóricos , Mutación/genética , Fenotipo , Precursores del ARN/metabolismo , Sitios de Empalme de ARN/genética , ARN Mensajero/metabolismoRESUMEN
Many processes can cause the same nucleotide change in a genome, making the identification of the mechanisms causing mutations a difficult challenge. Here, we show that clustered mutations provide a more precise fingerprint of mutagenic processes. Of nine clustered mutation signatures identified from >1,000 tumor genomes, three relate to variable APOBEC activity and three are associated with tobacco smoking. An additional signature matches the spectrum of translesion DNA polymerase eta (POLH). In lymphoid cells, these mutations target promoters, consistent with AID-initiated somatic hypermutation. In solid tumors, however, they are associated with UV exposure and alcohol consumption and target the H3K36me3 chromatin of active genes in a mismatch repair (MMR)-dependent manner. These regions normally have a low mutation rate because error-free MMR also targets H3K36me3 chromatin. Carcinogens and error-prone repair therefore redistribute mutations to the more important regions of the genome, contributing a substantial mutation load in many tumors, including driver mutations.
Asunto(s)
Reparación de la Incompatibilidad de ADN , Mutación , Neoplasias/genética , Desaminasas APOBEC , Citidina Desaminasa , Citosina Desaminasa/genética , ADN Polimerasa Dirigida por ADN/genética , Humanos , Neoplasias Hepáticas/inducido químicamente , Neoplasias Hepáticas/genética , Melanoma/genética , Mutagénesis , Fumar/efectos adversos , Rayos Ultravioleta/efectos adversosRESUMEN
Thousands of proteins have been validated genetically as therapeutic targets for human diseases1. However, very few have been successfully targeted, and many are considered 'undruggable'. This is particularly true for proteins that function via protein-protein interactions-direct inhibition of binding interfaces is difficult and requires the identification of allosteric sites. However, most proteins have no known allosteric sites, and a comprehensive allosteric map does not exist for any protein. Here we address this shortcoming by charting multiple global atlases of inhibitory allosteric communication in KRAS. We quantified the effects of more than 26,000 mutations on the folding of KRAS and its binding to six interaction partners. Genetic interactions in double mutants enabled us to perform biophysical measurements at scale, inferring more than 22,000 causal free energy changes. These energy landscapes quantify how mutations tune the binding specificity of a signalling protein and map the inhibitory allosteric sites for an important therapeutic target. Allosteric propagation is particularly effective across the central ß-sheet of KRAS, and multiple surface pockets are genetically validated as allosterically active, including a distal pocket in the C-terminal lobe of the protein. Allosteric mutations typically inhibit binding to all tested effectors, but they can also change the binding specificity, revealing the regulatory, evolutionary and therapeutic potential to tune pathway activation. Using the approach described here, it should be possible to rapidly and comprehensively identify allosteric target sites in many proteins.
Asunto(s)
Sitio Alostérico , Pliegue de Proteína , Proteínas Proto-Oncogénicas p21(ras) , Humanos , Regulación Alostérica/efectos de los fármacos , Regulación Alostérica/genética , Sitio Alostérico/efectos de los fármacos , Sitio Alostérico/genética , Mutación , Unión Proteica , Proteínas Proto-Oncogénicas p21(ras)/antagonistas & inhibidores , Proteínas Proto-Oncogénicas p21(ras)/química , Proteínas Proto-Oncogénicas p21(ras)/genética , Proteínas Proto-Oncogénicas p21(ras)/metabolismo , Reproducibilidad de los Resultados , Especificidad por Sustrato/efectos de los fármacos , Especificidad por Sustrato/genética , TermodinámicaRESUMEN
Synonymous mutations change the sequence of a gene without directly altering the sequence of the encoded protein. Here, we present evidence that these "silent" mutations frequently contribute to human cancer. Selection on synonymous mutations in oncogenes is cancer-type specific, and although the functional consequences of cancer-associated synonymous mutations may be diverse, they recurrently alter exonic motifs that regulate splicing and are associated with changes in oncogene splicing in tumors. The p53 tumor suppressor (TP53) also has recurrent synonymous mutations, but, in contrast to those in oncogenes, these are adjacent to splice sites and inactivate them. We estimate that between one in two and one in five silent mutations in oncogenes have been selected, equating to ~6%- 8% of all selected single-nucleotide changes in these genes. In addition, our analyses suggest that dosage-sensitive oncogenes have selected mutations in their 3' UTRs.
Asunto(s)
Mutación , Neoplasias/genética , Oncogenes , Sitios de Empalme de ARN , Regiones no Traducidas 3' , Secuencia de Bases , Genes p53 , Humanos , Empalme del ARNRESUMEN
Allosteric communication between distant sites in proteins is central to biological regulation but still poorly characterized, limiting understanding, engineering and drug development1-6. An important reason for this is the lack of methods to comprehensively quantify allostery in diverse proteins. Here we address this shortcoming and present a method that uses deep mutational scanning to globally map allostery. The approach uses an efficient experimental design to infer en masse the causal biophysical effects of mutations by quantifying multiple molecular phenotypes-here we examine binding and protein abundance-in multiple genetic backgrounds and fitting thermodynamic models using neural networks. We apply the approach to two of the most common protein interaction domains found in humans, an SH3 domain and a PDZ domain, to produce comprehensive atlases of allosteric communication. Allosteric mutations are abundant, with a large mutational target space of network-altering 'edgetic' variants. Mutations are more likely to be allosteric closer to binding interfaces, at glycine residues and at specific residues connecting to an opposite surface within the PDZ domain. This general approach of quantifying mutational effects for multiple molecular phenotypes and in multiple genetic backgrounds should enable the energetic and allosteric landscapes of many proteins to be rapidly and comprehensively mapped.
Asunto(s)
Sitio Alostérico , Dominios PDZ , Proteínas , Regulación Alostérica/genética , Dominios PDZ/genética , Unión Proteica/genética , Proteínas/química , TermodinámicaRESUMEN
Accurate models describing the relationship between genotype and phenotype are necessary in order to understand and predict how mutations to biological sequences affect the fitness and evolution of living organisms. The apparent abundance of epistasis (genetic interactions), both between and within genes, complicates this task and how to build mechanistic models that incorporate epistatic coefficients (genetic interaction terms) is an open question. The Walsh-Hadamard transform represents a rigorous computational framework for calculating and modeling epistatic interactions at the level of individual genotypic values (known as genetical, biological or physiological epistasis), and can therefore be used to address fundamental questions related to sequence-to-function encodings. However, one of its main limitations is that it can only accommodate two alleles (amino acid or nucleotide states) per sequence position. In this paper we provide an extension of the Walsh-Hadamard transform that allows the calculation and modeling of background-averaged epistasis (also known as ensemble epistasis) in genetic landscapes with an arbitrary number of states per position (20 for amino acids, 4 for nucleotides, etc.). We also provide a recursive formula for the inverse matrix and then derive formulae to directly extract any element of either matrix without having to rely on the computationally intensive task of constructing or inverting large matrices. Finally, we demonstrate the utility of our theory by using it to model epistasis within both simulated and empirical multiallelic fitness landscapes, revealing that both pairwise and higher-order genetic interactions are enriched between physically interacting positions.
Asunto(s)
Epistasis Genética , Modelos Genéticos , Epistasis Genética/genética , Biología Computacional/métodos , Algoritmos , Mutación/genética , GenotipoRESUMEN
The nonsense-mediated mRNA decay (NMD) pathway degrades some but not all mRNAs bearing premature termination codons (PTCs). Decades of work have elucidated the molecular mechanisms of NMD. More recently, statistical analyses of large genomic datasets have allowed the importance of known and novel 'rules of NMD' to be tested and combined into methods that accurately predict whether PTC-containing mRNAs are degraded or not. We discuss these genomic approaches and how they can be applied to identify diseases and individuals that may benefit from inhibition or activation of NMD. We also discuss the importance of NMD for gene editing and tumor evolution, and how inhibiting NMD may be an effective strategy to increase the efficacy of cancer immunotherapy.
Asunto(s)
Empalme Alternativo/genética , Enfermedades Genéticas Congénitas/genética , Neoplasias/genética , Degradación de ARNm Mediada por Codón sin Sentido/genética , Codón sin Sentido/genética , Humanos , ARN Mensajero/genéticaRESUMEN
Why are genes harmful when they are overexpressed? By testing possible causes of overexpression phenotypes in yeast, we identify intrinsic protein disorder as an important determinant of dosage sensitivity. Disordered regions are prone to make promiscuous molecular interactions when their concentration is increased, and we demonstrate that this is the likely cause of pathology when genes are overexpressed. We validate our findings in two animals, Drosophila melanogaster and Caenorhabditis elegans. In mice and humans the same properties are strongly associated with dosage-sensitive oncogenes, such that mass-action-driven molecular interactions may be a frequent cause of cancer. Dosage-sensitive genes are tightly regulated at the transcriptional, RNA, and protein levels, which may serve to prevent harmful increases in protein concentration under physiological conditions. Mass-action-driven interaction promiscuity is a single theoretical framework that can be used to understand, predict, and possibly treat the effects of increased gene expression in evolution and disease.
Asunto(s)
Expresión Génica , Proteínas/metabolismo , Proteínas/toxicidad , Animales , Caenorhabditis elegans/genética , Caenorhabditis elegans/metabolismo , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Humanos , Ratones , Neoplasias/metabolismo , ARN Mensajero/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismoRESUMEN
A central question in genetics and evolution is the extent to which the outcomes of mutations change depending on the genetic context in which they occur1-3. Pairwise interactions between mutations have been systematically mapped within4-18 and between 19 genes, and have been shown to contribute substantially to phenotypic variation among individuals 20 . However, the extent to which genetic interactions themselves are stable or dynamic across genotypes is unclear21, 22. Here we quantify more than 45,000 genetic interactions between the same 87 pairs of mutations across more than 500 closely related genotypes of a yeast tRNA. Notably, all pairs of mutations interacted in at least 9% of genetic backgrounds and all pairs switched from interacting positively to interacting negatively in different genotypes (false discovery rate < 0.1). Higher-order interactions are also abundant and dynamic across genotypes. The epistasis in this tRNA means that all individual mutations switch from detrimental to beneficial, even in closely related genotypes. As a consequence, accurate genetic prediction requires mutation effects to be measured across different genetic backgrounds and the use of higher-order epistatic terms.
Asunto(s)
Evolución Molecular , Mutación , ARN de Transferencia/genética , Saccharomyces cerevisiae/genética , Epistasis Genética , Aptitud Genética , Genotipo , Filogenia , Alineación de SecuenciaRESUMEN
Genetically identical individuals that grow in the same environment often show substantial phenotypic variation within populations of organisms as diverse as bacteria, nematodes, rodents and humans. With some exceptions, the causes are poorly understood. Here we show that isogenic Caenorhabditis elegans nematodes vary in their size at hatching, speed of development, growth rate, starvation resistance, fecundity, and also in the rate of development of their germline relative to that of somatic tissues. We show that the primary cause of this variation is the age of an individual's mother, with the progeny of young mothers exhibiting several phenotypic impairments. We identify age-dependent changes in the maternal provisioning of the lipoprotein complex vitellogenin to embryos as the molecular mechanism that underlies the variation in multiple traits throughout the life of an animal. The production of sub-optimal progeny by young mothers may reflect a trade-off between the competing fitness traits of a short generation time and the survival and fecundity of the progeny.
Asunto(s)
Envejecimiento/fisiología , Variación Biológica Poblacional , Caenorhabditis elegans/fisiología , Madres , Fenotipo , Vitelogeninas/metabolismo , Animales , Variación Biológica Poblacional/genética , Tamaño Corporal , Caenorhabditis elegans/embriología , Caenorhabditis elegans/genética , Caenorhabditis elegans/crecimiento & desarrollo , Yema de Huevo/metabolismo , Femenino , Fertilidad , Perfilación de la Expresión Génica , Células Germinativas/fisiología , Masculino , InaniciónRESUMEN
The folding of genomic DNA from the beads-on-a-string-like structure of nucleosomes into higher-order assemblies is crucially linked to nuclear processes. Here we calculate 3D structures of entire mammalian genomes using data from a new chromosome conformation capture procedure that allows us to first image and then process single cells. The technique enables genome folding to be examined at a scale of less than 100 kb, and chromosome structures to be validated. The structures of individual topological-associated domains and loops vary substantially from cell to cell. By contrast, A and B compartments, lamina-associated domains and active enhancers and promoters are organized in a consistent way on a genome-wide basis in every cell, suggesting that they could drive chromosome and genome folding. By studying genes regulated by pluripotency factor and nucleosome remodelling deacetylase (NuRD), we illustrate how the determination of single-cell genome structure provides a new approach for investigating biological processes.
Asunto(s)
Ensamble y Desensamble de Cromatina , Genoma , Imagen Molecular/métodos , Nucleosomas/química , Análisis de la Célula Individual/métodos , Animales , Factor de Unión a CCCTC , Proteínas de Ciclo Celular/metabolismo , Ensamble y Desensamble de Cromatina/genética , Proteínas Cromosómicas no Histona/metabolismo , Cromosomas de los Mamíferos/química , Cromosomas de los Mamíferos/genética , Cromosomas de los Mamíferos/metabolismo , ADN/química , ADN/genética , ADN/metabolismo , Elementos de Facilitación Genéticos , Fase G1 , Regulación de la Expresión Génica , Redes Reguladoras de Genes , Genoma/genética , Haploidia , Complejo Desacetilasa y Remodelación del Nucleosoma Mi-2/metabolismo , Ratones , Modelos Moleculares , Conformación Molecular , Imagen Molecular/normas , Células Madre Embrionarias de Ratones/citología , Células Madre Embrionarias de Ratones/metabolismo , Nucleosomas/genética , Nucleosomas/metabolismo , Regiones Promotoras Genéticas , Proteínas Represoras/metabolismo , Reproducibilidad de los Resultados , Análisis de la Célula Individual/normas , CohesinasRESUMEN
The same mutation can have different effects in different individuals. One important reason for this is that the outcome of a mutation can depend on the genetic context in which it occurs. This dependency is known as epistasis. In recent years, there has been a concerted effort to quantify the extent of pairwise and higher-order genetic interactions between mutations through deep mutagenesis of proteins and RNAs. This research has revealed two major components of epistasis: nonspecific genetic interactions caused by nonlinearities in genotype-to-phenotype maps, and specific interactions between particular mutations. Here, we provide an overview of our current understanding of the mechanisms causing epistasis at the molecular level, the consequences of genetic interactions for evolution and genetic prediction, and the applications of epistasis for understanding biology and determining macromolecular structures.
Asunto(s)
Epistasis Genética , Modelos Genéticos , Animales , Evolución Molecular , Humanos , Mutación , Polimorfismo Genético , Conformación Proteica , Pliegue de Proteína , Dominios y Motivos de Interacción de ProteínasRESUMEN
Cancer genome sequencing has revealed considerable variation in somatic mutation rates across the human genome, with mutation rates elevated in heterochromatic late replicating regions and reduced in early replicating euchromatin. Multiple mechanisms have been suggested to underlie this, but the actual cause is unknown. Here we identify variable DNA mismatch repair (MMR) as the basis of this variation. Analysing â¼17 million single-nucleotide variants from the genomes of 652 tumours, we show that regional autosomal mutation rates at megabase resolution are largely stable across cancer types, with differences related to changes in replication timing and gene expression. However, mutations arising after the inactivation of MMR are no longer enriched in late replicating heterochromatin relative to early replicating euchromatin. Thus, differential DNA repair and not differential mutation supply is the primary cause of the large-scale regional mutation rate variation across the human genome.
Asunto(s)
Reparación de la Incompatibilidad de ADN/genética , Genoma Humano/genética , Tasa de Mutación , Línea Celular , Momento de Replicación del ADN/genética , Regulación Neoplásica de la Expresión Génica/genética , Humanos , Mutagénesis/genética , Neoplasias/genética , Neoplasias/patologíaRESUMEN
The development of a multicellular organism and physiological responses require massive coordinated changes in gene expression across several cell and tissue types. Polymorphic regions of the genome that influence gene expression levels have been identified by expression quantitative trait locus (eQTL) mapping in many species, including loci that have cell-dependent, tissue-dependent and age-dependent effects. However, there has been no comprehensive characterization of how polymorphisms influence the complex dynamic patterns of gene expression that occur during development and in physiology. Here we describe an efficient experimental design to infer gene expression dynamics from single expression profiles in different genotypes, and apply it to characterize the effect of local (cis) and distant (trans) genetic variation on gene expression at high temporal resolution throughout a 12-hour period of the development of Caenorhabditis elegans. Taking dynamic variation into account identifies >50% more cis-eQTLs, including more than 900 that alter the dynamics of expression during this period. Local sequence polymorphisms extensively affect the timing, rate, magnitude and shape of expression changes. Indeed, many local sequence variants both increase and decrease gene expression, depending on the time-point profiled. Expression dynamics during this 12-hour period are also influenced extensively in trans by distal loci. In particular, several trans loci influence genes with quite diverse dynamic expression patterns, but they do so primarily during a common time interval. Trans loci can therefore act as modifiers of expression during a particular period of development. This study provides the first characterization, to our knowledge, of the effect of local and distant genetic variation on the dynamics of gene expression throughout an extensive time period. Moreover, the approach developed here should facilitate the genetic dissection of other dynamic processes, including potentially development, physiology and disease progression in humans.
Asunto(s)
Caenorhabditis elegans/embriología , Caenorhabditis elegans/genética , Regulación del Desarrollo de la Expresión Génica/genética , Variación Genética/genética , Animales , Perfilación de la Expresión Génica , Genes de Helminto/genética , Sitios de Carácter Cuantitativo/genética , Factores de TiempoRESUMEN
To what extent can variation in phenotypic traits such as disease risk be accurately predicted in individuals? In this Review, I highlight recent studies in model organisms that are relevant both to the challenge of accurately predicting phenotypic variation from individual genome sequences ('whole-genome reverse genetics') and for understanding why, in many cases, this may be impossible. These studies argue that only by combining genetic knowledge with in vivo measurements of biological states will it be possible to make accurate genetic predictions for individual humans.
Asunto(s)
Genoma Humano , Genotipo , Fenotipo , Animales , Mapeo Cromosómico , Epistasis Genética , Interacción Gen-Ambiente , Variación Genética , HumanosRESUMEN
Cancer genome sequencing provides the first direct information on how mutation rates vary across the human genome in somatic cells. Testing diverse genetic and epigenetic features, here we show that mutation rates in cancer genomes are strikingly related to chromatin organization. Indeed, at the megabase scale, a single featurelevels of the heterochromatin-associated histone modification H3K9me3can account for more than 40% of mutation-rate variation, and a combination of features can account for more than 55%. The strong association between mutation rates and chromatin organization is upheld in samples from different tissues and for different mutation types. This suggests that the arrangement of the genome into heterochromatin- and euchromatin-like domains is a dominant influence on regional mutation-rate variation in human somatic cells.
Asunto(s)
Eucromatina/genética , Heterocromatina/genética , Tasa de Mutación , Neoplasias/genética , Neoplasias/patología , Animales , Islas de CpG/genética , Epigénesis Genética , Genoma Humano/genética , Histonas/química , Histonas/metabolismo , Humanos , Leucemia/genética , Neoplasias Pulmonares/genética , Masculino , Melanoma/genética , Metilación , Mutagénesis/genética , Pan troglodytes/genética , Polimorfismo de Nucleótido Simple/genética , Análisis de Componente Principal , Neoplasias de la Próstata/genética , Carcinoma Pulmonar de Células Pequeñas/genéticaRESUMEN
Many mutations, including those that cause disease, only have a detrimental effect in a subset of individuals. The reasons for this are usually unknown, but may include additional genetic variation and environmental risk factors. However, phenotypic discordance remains even in the absence of genetic variation, for example between monozygotic twins, and incomplete penetrance of mutations is frequent in isogenic model organisms in homogeneous environments. Here we propose a model for incomplete penetrance based on genetic interaction networks. Using Caenorhabditis elegans as a model system, we identify two compensation mechanisms that vary among individuals and influence mutation outcome. First, feedback induction of an ancestral gene duplicate differs across individuals, with high expression masking the effects of a mutation. This supports the hypothesis that redundancy is maintained in genomes to buffer stochastic developmental failure. Second, during normal embryonic development we find that there is substantial variation in the induction of molecular chaperones such as Hsp90 (DAF-21). Chaperones act as promiscuous buffers of genetic variation, and embryos with stronger induction of Hsp90 are less likely to be affected by an inherited mutation. Simultaneously quantifying the variation in these two independent responses allows the phenotypic outcome of a mutation to be more accurately predicted in individuals. Our model and methodology provide a framework for dissecting the causes of incomplete penetrance. Further, the results establish that inter-individual variation in both specific and more general buffering systems combine to determine the outcome inherited mutations in each individual.
Asunto(s)
Caenorhabditis elegans/genética , Redes Reguladoras de Genes/genética , Mutación/genética , Animales , Caenorhabditis elegans/embriología , Proteínas de Caenorhabditis elegans/biosíntesis , Proteínas de Caenorhabditis elegans/genética , Retroalimentación Fisiológica , Regulación del Desarrollo de la Expresión Génica , Genes Duplicados/genética , Proteínas HSP90 de Choque Térmico/biosíntesis , Proteínas HSP90 de Choque Térmico/genética , Modelos Genéticos , Penetrancia , Procesos EstocásticosRESUMEN
It has long been known that methylated cytosines deaminate at higher rates than unmodified cytosines and constitute mutational hotspots in mammalian genomes. The repertoire of naturally occurring cytosine modifications, however, extends beyond 5-methylcytosine to include its oxidation derivatives, notably 5-hydroxymethylcytosine. The effects of these modifications on sequence evolution are unknown. Here, we combine base-resolution maps of methyl- and hydroxymethylcytosine in human and mouse with population genomic, divergence and somatic mutation data to show that hydroxymethylated and methylated cytosines show distinct patterns of variation and evolution. Surprisingly, hydroxymethylated sites are consistently associated with elevated C to G transversion rates at the level of segregating polymorphisms, fixed substitutions, and somatic mutations in tumors. Controlling for multiple potential confounders, we find derived C to G SNPs to be 1.43-fold (1.22-fold) more common at hydroxymethylated sites compared to methylated sites in human (mouse). Increased C to G rates are evident across diverse functional and sequence contexts and, in cancer genomes, correlate with the expression of Tet enzymes and specific components of the mismatch repair pathway (MSH2, MSH6, and MBD4). Based on these and other observations we suggest that hydroxymethylation is associated with a distinct mutational burden and that the mismatch repair pathway is implicated in causing elevated transversion rates at hydroxymethylated cytosines.
Asunto(s)
5-Metilcitosina/metabolismo , Islas de CpG/genética , Citosina/análogos & derivados , Citosina/metabolismo , Animales , Metilación de ADN/genética , Humanos , Ratones , Mutación/genéticaRESUMEN
Chromatin regulators are widely expressed proteins with diverse roles in gene expression, nuclear organization, cell cycle regulation, pluripotency, physiology and development, and are frequently mutated in human diseases such as cancer. Their inhibition often results in pleiotropic effects that are difficult to study using conventional approaches. We have developed a semi-automated nuclear tracking algorithm to quantify the divisions, movements and positions of all nuclei during the early development of Caenorhabditis elegans and have used it to systematically study the effects of inhibiting chromatin regulators. The resulting high dimensional datasets revealed that inhibition of multiple regulators, including F55A3.3 (encoding FACT subunit SUPT16H), lin-53 (RBBP4/7), rba-1 (RBBP4/7), set-16 (MLL2/3), hda-1 (HDAC1/2), swsn-7 (ARID2), and let-526 (ARID1A/1B) affected cell cycle progression and caused chromosome segregation defects. In contrast, inhibition of cir-1 (CIR1) accelerated cell division timing in specific cells of the AB lineage. The inhibition of RNA polymerase II also accelerated these division timings, suggesting that normal gene expression is required to delay cell cycle progression in multiple lineages in the early embryo. Quantitative analyses of the dataset suggested the existence of at least two functionally distinct SWI/SNF chromatin remodeling complex activities in the early embryo, and identified a redundant requirement for the egl-27 and lin-40 MTA orthologs in the development of endoderm and mesoderm lineages. Moreover, our dataset also revealed a characteristic rearrangement of chromatin to the nuclear periphery upon the inhibition of multiple general regulators of gene expression. Our systematic, comprehensive and quantitative datasets illustrate the power of single cell-resolution quantitative tracking and high dimensional phenotyping to investigate gene function. Furthermore, the results provide an overview of the functions of essential chromatin regulators during the early development of an animal.
Asunto(s)
Proteínas de Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/citología , Caenorhabditis elegans/embriología , Cromatina/metabolismo , Desarrollo Embrionario , Análisis de la Célula Individual/métodos , Animales , Caenorhabditis elegans/genética , Ciclo Celular , Linaje de la Célula , Núcleo Celular/metabolismo , Segregación Cromosómica , Embrión no Mamífero/citología , Embrión no Mamífero/metabolismo , Desarrollo Embrionario/genética , Endodermo/citología , Endodermo/embriología , Regulación del Desarrollo de la Expresión Génica , Genes de Helminto , Humanos , Mesodermo/citología , Mesodermo/embriología , Interferencia de ARNRESUMEN
Cancers, like many diseases, are normally caused by combinations of genetic alterations rather than by changes affecting single genes. It is well established that the genetic alterations that drive cancer often interact epistatically, having greater or weaker consequences in combination than expected from their individual effects. In a stringent statistical analysis of data from > 3,000 tumors, we find that the co-occurrence and mutual exclusivity relationships between cancer driver alterations change quite extensively in different types of cancer. This cannot be accounted for by variation in tumor heterogeneity or unrecognized cancer subtypes. Rather, it suggests that how genomic alterations interact cooperatively or partially redundantly to driver cancer changes in different types of cancers. This re-wiring of epistasis across cell types is likely to be a basic feature of genetic architecture, with important implications for understanding the evolution of multicellularity and human genetic diseases. In addition, if this plasticity of epistasis across cell types is also true for synthetic lethal interactions, a synthetic lethal strategy to kill cancer cells may frequently work in one type of cancer but prove ineffective in another.