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Phytocannabinoids with seven-carbon alkyl chains (phorols) have gained a lot of attention, as they are commonly believed to be more potent versions of typical cannabinoids with shorter alkyl chains. At the time of this article, cannabidiphorol (CBDP) and tetrahydrocannabiphorol (THCP) can both be purchased in the North American market, even though their biological activities are nearly unknown. To investigate their relative potency, we conducted in vitro receptor-binding experiments with CBDP (cannabinoid CB1/CB2 receptor antagonism, serotonin 5HT-1A agonism, dopamine D2S (short form) agonism, and mu-opioid negative allosteric modulation) and compared the observed activity with that of CBD. To our knowledge, this is the first publication to investigate CBDP's receptor activity in vitro. A similar activity profile was observed for both CBD and CBDP, with the only notable difference at the CB2 receptor. Contrary to common expectations, CBD was found to be a slightly more potent CB2 antagonist than CBDP (p < 0.05). At the highest tested concentration, CBD demonstrated antagonist activity with a 33% maximum response of SR144528 (selective CB2 antagonist/inverse agonist). CBDP at the same concentration produced a weaker antagonist activity. A radioligand binding assay revealed that among cannabinoid and serotonin receptors, CB2 is likely the main biological target of CBDP. However, both CBD and CBDP were found to be significantly less potent than SR144528. The interaction of CBDP with the mu-opioid receptor (MOR) produced unexpected results. Although the cannabidiol family is considered to be a set of negative allosteric modulators (NAMs) of opioid receptors, we observed a significant increase in met-enkephalin-induced mu-opioid internalization when cells were incubated with 3 µM of CBDP and 1 µM met-enkephalin, a type of activity expected from positive allosteric modulators (PAMs). To provide a structural explanation for the observed PAM effect, we conducted molecular docking simulations. These simulations revealed the co-binding potential of CBDP (or CBD) and met-enkephalin to the MOR.
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Receptor Cannabinoide CB2 , Humanos , Receptor Cannabinoide CB2/metabolismo , Cannabidiol/farmacología , Cannabidiol/metabolismo , Cannabidiol/química , Receptores Opioides mu/metabolismo , Receptores Opioides mu/agonistas , Receptor Cannabinoide CB1/metabolismo , Receptor Cannabinoide CB1/antagonistas & inhibidores , Unión Proteica , Cannabinoides/metabolismo , Cannabinoides/farmacología , Cannabinoides/química , Dronabinol/farmacología , Dronabinol/análogos & derivados , Dronabinol/química , Dronabinol/metabolismo , Receptores de Dopamina D2/metabolismo , AnimalesRESUMEN
Monitor lizards are unique among ectothermic reptiles in that they have high aerobic capacity and distinctive cardiovascular physiology resembling that of endothermic mammals. Here, we sequence the genome of the Komodo dragon Varanus komodoensis, the largest extant monitor lizard, and generate a high-resolution de novo chromosome-assigned genome assembly for V. komodoensis using a hybrid approach of long-range sequencing and single-molecule optical mapping. Comparing the genome of V. komodoensis with those of related species, we find evidence of positive selection in pathways related to energy metabolism, cardiovascular homoeostasis, and haemostasis. We also show species-specific expansions of a chemoreceptor gene family related to pheromone and kairomone sensing in V. komodoensis and other lizard lineages. Together, these evolutionary signatures of adaptation reveal the genetic underpinnings of the unique Komodo dragon sensory and cardiovascular systems, and suggest that selective pressure altered haemostasis genes to help Komodo dragons evade the anticoagulant effects of their own saliva. The Komodo dragon genome is an important resource for understanding the biology of monitor lizards and reptiles worldwide.
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Sistema Cardiovascular , Lagartos , Aclimatación , Animales , CromosomasRESUMEN
Some of the fastest evolving regions of the human genome are conserved noncoding elements with many human-specific DNA substitutions. These human accelerated regions (HARs) are enriched nearby regulatory genes, and several HARs function as developmental enhancers. To investigate if this evolutionary signature is unique to humans, we quantified evidence of accelerated substitutions in conserved genomic elements across multiple lineages and applied this approach simultaneously to the genomes of five apes: human, chimpanzee, gorilla, orangutan, and gibbon. We find roughly similar numbers and genomic distributions of lineage-specific accelerated regions (linARs) in all five apes. In particular, apes share an enrichment of linARs in regulatory DNA nearby genes involved in development, especially transcription factors and other regulators. Many developmental loci harbor clusters of nonoverlapping linARs from multiple apes, suggesting that accelerated evolution in each species affected distinct regulatory elements that control a shared set of developmental pathways. Our statistical tests distinguish between GC-biased and unbiased accelerated substitution rates, allowing us to quantify the roles of different evolutionary forces in creating linARs. We find evidence of GC-biased gene conversion in each ape, but unbiased acceleration consistent with positive selection or loss of constraint is more common in all five lineages. It therefore appears that similar evolutionary processes created independent accelerated regions in the genomes of different apes, and that these lineage-specific changes to conserved noncoding sequences may have differentially altered expression of a core set of developmental genes across ape evolution.
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Evolución Molecular , Hominidae/genética , Algoritmos , Animales , Simulación por Computador , Conversión Génica , Hominidae/crecimiento & desarrollo , Humanos , Modelos Genéticos , Selección GenéticaRESUMEN
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is an important tool for studying gene regulatory proteins, such as transcription factors and histones. Peak calling is one of the first steps in the analysis of these data. Peak calling consists of two sub-problems: identifying candidate peaks and testing candidate peaks for statistical significance. We surveyed 30 methods and identified 12 features of the two sub-problems that distinguish methods from each other. We picked six methods GEM, MACS2, MUSIC, BCP, Threshold-based method (TM) and ZINBA] that span this feature space and used a combination of 300 simulated ChIP-seq data sets, 3 real data sets and mathematical analyses to identify features of methods that allow some to perform better than the others. We prove that methods that explicitly combine the signals from ChIP and input samples are less powerful than methods that do not. Methods that use windows of different sizes are more powerful than the ones that do not. For statistical testing of candidate peaks, methods that use a Poisson test to rank their candidate peaks are more powerful than those that use a Binomial test. BCP and MACS2 have the best operating characteristics on simulated transcription factor binding data. GEM has the highest fraction of the top 500 peaks containing the binding motif of the immunoprecipitated factor, with 50% of its peaks within 10 base pairs of a motif. BCP and MUSIC perform best on histone data. These findings provide guidance and rationale for selecting the best peak caller for a given application.
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Análisis de Secuencia de ADN , Algoritmos , Sitios de Unión , Inmunoprecipitación de Cromatina , Secuenciación de Nucleótidos de Alto Rendimiento , Histonas , Análisis de Secuencia por Matrices de Oligonucleótidos , Factores de TranscripciónRESUMEN
Transcription factors (TFs) are thought to function with partners to achieve specificity and precise quantitative outputs. In the developing heart, heterotypic TF interactions, such as between the T-box TF TBX5 and the homeodomain TF NKX2-5, have been proposed as a mechanism for human congenital heart defects. We report extensive and complex interdependent genomic occupancy of TBX5, NKX2-5, and the zinc finger TF GATA4 coordinately controlling cardiac gene expression, differentiation, and morphogenesis. Interdependent binding serves not only to co-regulate gene expression but also to prevent TFs from distributing to ectopic loci and activate lineage-inappropriate genes. We define preferential motif arrangements for TBX5 and NKX2-5 cooperative binding sites, supported at the atomic level by their co-crystal structure bound to DNA, revealing a direct interaction between the two factors and induced DNA bending. Complex interdependent binding mechanisms reveal tightly regulated TF genomic distribution and define a combinatorial logic for heterotypic TF regulation of differentiation.
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Factor de Transcripción GATA4/metabolismo , Proteínas de Homeodominio/metabolismo , Miocardio/citología , Organogénesis , Proteínas de Dominio T Box/metabolismo , Factores de Transcripción/metabolismo , Animales , Diferenciación Celular , Cristalografía por Rayos X , Embrión de Mamíferos/metabolismo , Proteína Homeótica Nkx-2.5 , Proteínas de Homeodominio/genética , Ratones , Ratones Transgénicos , Modelos Moleculares , Miocardio/metabolismo , Regiones Promotoras Genéticas , Dominios y Motivos de Interacción de Proteínas , Proteínas de Dominio T Box/genética , Factores de Transcripción/genéticaRESUMEN
Mammals have evolved remarkably different sensory, reproductive, metabolic, and skeletal systems. To explore the genetic basis for these differences, we developed a comparative genomics approach to scan whole-genome multiple sequence alignments to identify regions that evolved rapidly in an ancestral lineage but are conserved within extant species. This pattern suggests that ancestral changes in function were maintained in descendants. After applying this test to therian mammals, we identified 4,797 accelerated regions, many of which are noncoding and located near developmental transcription factors. We then used mouse transgenic reporter assays to test if noncoding accelerated regions are enhancers and to determine how therian-specific substitutions affect their activity in vivo. We discovered enhancers with expression specific to the therian version in brain regions involved in the hormonal control of milk ejection, uterine contractions, blood pressure, temperature, and visual processing. This work underscores the idea that changes in developmental gene expression are important for mammalian evolution, and it pinpoints candidate genes for unique aspects of mammalian biology.
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Elementos de Facilitación Genéticos , Evolución Molecular , Proteínas de Homeodominio/genética , Mamíferos/genética , Animales , Encéfalo/metabolismo , Secuencia Conservada/genética , Regulación del Desarrollo de la Expresión Génica , Genómica , RatonesRESUMEN
Next-generation sequencing technology enables the identification of thousands of gene regulatory sequences in many cell types and organisms. We consider the problem of testing if two such sequences differ in their number of binding site motifs for a given transcription factor (TF) protein. Binding site motifs impart regulatory function by providing TFs the opportunity to bind to genomic elements and thereby affect the expression of nearby genes. Evolutionary changes to such functional DNA are hypothesized to be major contributors to phenotypic diversity within and between species; but despite the importance of TF motifs for gene expression, no method exists to test for motif loss or gain. Assuming that motif counts are Binomially distributed, and allowing for dependencies between motif instances in evolutionarily related sequences, we derive the probability mass function of the difference in motif counts between two nucleotide sequences. We provide a method to numerically estimate this distribution from genomic data and show through simulations that our estimator is accurate. Finally, we introduce the R package motifDiverge that implements our methodology and illustrate its application to gene regulatory enhancers identified by a mouse developmental time course experiment. While this study was motivated by analysis of regulatory motifs, our results can be applied to any problem involving two correlated Bernoulli trials.
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We propose that data mining and network analysis utilizing public databases can identify and quantify relationships between scientific discoveries and major advances in medicine (cures). Further development of such approaches could help to increase public understanding and governmental support for life science research and could enhance decision making in the quest for cures.
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Investigación Biomédica/economía , Minería de Datos , Publicaciones , Animales , Disciplinas de las Ciencias Biológicas/economía , Ensayos Clínicos como Asunto , Toma de Decisiones , Descubrimiento de Drogas , Humanos , National Institutes of Health (U.S.)/economía , Estados Unidos , United States Food and Drug Administration/economíaRESUMEN
RNA-seq is widely used to determine differential expression of genes or transcripts as well as identify novel transcripts, identify allele-specific expression, and precisely measure translation of transcripts. Thoughtful experimental design and choice of analysis tools are critical to ensure high-quality data and interpretable results. Important considerations for experimental design include number of replicates, whether to collect paired-end or single-end reads, sequence length, and sequencing depth. Common analysis steps in all RNA-seq experiments include quality control, read alignment, assigning reads to genes or transcripts, and estimating gene or transcript abundance. Our aims are two-fold: to make recommendations for common components of experimental design and assess tool capabilities for each of these steps. We also test tools designed to detect differential expression, since this is the most widespread application of RNA-seq. We hope that these analyses will help guide those who are new to RNA-seq and will generate discussion about remaining needs for tool improvement and development.
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Análisis de Secuencia de ARN , Reacción en Cadena de la Polimerasa , Control de Calidad , Empalme del ARN , ARN Mensajero/genéticaRESUMEN
The chicken has long served as an important model organism in many fields, and continues to aid our understanding of animal development. Functional genomics studies aimed at probing the mechanisms that regulate development require high-quality genomes and transcript annotations. The quality of these resources has improved dramatically over the last several years, but many isoforms and genes have yet to be identified. We hope to contribute to the process of improving these resources with the data presented here: a set of long cDNA sequencing reads, and a curated set of new genes and transcript isoforms not currently represented in the most up-to-date genome annotation currently available to the community of researchers who rely on the chicken genome.
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Pollos/genética , Genómica/métodos , Animales , Embrión de Pollo , ADN Complementario/genética , Corazón/embriología , ARN Mensajero/genéticaRESUMEN
BACKGROUND: Large-scale annotation efforts have improved our ability to coarsely predict regulatory elements throughout vertebrate genomes. However, it is unclear how complex spatiotemporal patterns of gene expression driven by these elements emerge from the activity of short, transcription factor binding sequences. RESULTS: We describe a comprehensive promoter extension assay in which the regulatory potential of all 6 base-pair (bp) sequences was tested in the context of a minimal promoter. To enable this large-scale screen, we developed algorithms that use a reverse-complement aware decomposition of the de Bruijn graph to design a library of DNA oligomers incorporating every 6-bp sequence exactly once. Our library multiplexes all 4,096 unique 6-mers into 184 double-stranded 15-bp oligomers, which is sufficiently compact for in vivo testing. We injected each multiplexed construct into zebrafish embryos and scored GFP expression in 15 tissues at two developmental time points. Twenty-seven constructs produced consistent expression patterns, with the majority doing so in only one tissue. Functional sequences are enriched near biologically relevant genes, match motifs for developmental transcription factors, and are required for enhancer activity. By concatenating tissue-specific functional sequences, we generated completely synthetic enhancers for the notochord, epidermis, spinal cord, forebrain and otic lateral line, and show that short regulatory sequences do not always function modularly. CONCLUSIONS: This work introduces a unique in vivo catalog of short, functional regulatory sequences and demonstrates several important principles of regulatory element organization. Furthermore, we provide resources for designing compact, reverse-complement aware k-mer libraries.
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Regulación del Desarrollo de la Expresión Génica , Oligonucleótidos/genética , Especificidad de Órganos/genética , Secuencias Reguladoras de Ácidos Nucleicos/genética , Biología Sintética/métodos , Pez Cebra/genética , Animales , Secuencia de Bases , Disección , Embrión no Mamífero/metabolismo , Elementos de Facilitación Genéticos , Ontología de Genes , Datos de Secuencia Molecular , Motivos de Nucleótidos/genética , Pez Cebra/embriologíaRESUMEN
BACKGROUND: We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing. RESULTS: Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. CONCLUSIONS: Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.
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Adaptación Fisiológica/genética , Genoma/genética , Modelos Genéticos , Filogenia , Tortugas/genética , Animales , Composición de Base/genética , Evolución Molecular , Femenino , Congelación , Humanos , Hipoxia/genética , Hipoxia/fisiopatología , Sistema Inmunológico/metabolismo , Isocoras/genética , Funciones de Verosimilitud , Longevidad/genética , Masculino , MicroARNs/genética , MicroARNs/metabolismo , Anotación de Secuencia Molecular , Familia de Multigenes , Seudogenes/genética , Estándares de Referencia , Secuencias Repetitivas de Ácidos Nucleicos/genética , Selección Genética , Procesos de Determinación del Sexo , TemperaturaRESUMEN
Heart development is exquisitely sensitive to the precise temporal regulation of thousands of genes that govern developmental decisions during differentiation. However, we currently lack a detailed understanding of how chromatin and gene expression patterns are coordinated during developmental transitions in the cardiac lineage. Here, we interrogated the transcriptome and several histone modifications across the genome during defined stages of cardiac differentiation. We find distinct chromatin patterns that are coordinated with stage-specific expression of functionally related genes, including many human disease-associated genes. Moreover, we discover a novel preactivation chromatin pattern at the promoters of genes associated with heart development and cardiac function. We further identify stage-specific distal enhancer elements and find enriched DNA binding motifs within these regions that predict sets of transcription factors that orchestrate cardiac differentiation. Together, these findings form a basis for understanding developmentally regulated chromatin transitions during lineage commitment and the molecular etiology of congenital heart disease.
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Epigénesis Genética , Redes Reguladoras de Genes , Miocardio/citología , Animales , Diferenciación Celular , Cromatina/metabolismo , Células Madre Embrionarias/metabolismo , Elementos de Facilitación Genéticos , Corazón/embriología , Humanos , Ratones , Factores de Transcripción/metabolismo , TranscriptomaRESUMEN
This report of independent genome sequences of two natural populations of Drosophila melanogaster (37 from North America and 6 from Africa) provides unique insight into forces shaping genomic polymorphism and divergence. Evidence of interactions between natural selection and genetic linkage is abundant not only in centromere- and telomere-proximal regions, but also throughout the euchromatic arms. Linkage disequilibrium, which decays within 1 kbp, exhibits a strong bias toward coupling of the more frequent alleles and provides a high-resolution map of recombination rate. The juxtaposition of population genetics statistics in small genomic windows with gene structures and chromatin states yields a rich, high-resolution annotation, including the following: (1) 5'- and 3'-UTRs are enriched for regions of reduced polymorphism relative to lineage-specific divergence; (2) exons overlap with windows of excess relative polymorphism; (3) epigenetic marks associated with active transcription initiation sites overlap with regions of reduced relative polymorphism and relatively reduced estimates of the rate of recombination; (4) the rate of adaptive nonsynonymous fixation increases with the rate of crossing over per base pair; and (5) both duplications and deletions are enriched near origins of replication and their density correlates negatively with the rate of crossing over. Available demographic models of X and autosome descent cannot account for the increased divergence on the X and loss of diversity associated with the out-of-Africa migration. Comparison of the variation among these genomes to variation among genomes from D. simulans suggests that many targets of directional selection are shared between these species.
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Drosophila melanogaster/genética , Ligamiento Genético , Variación Genética , Genoma , África , Animales , Centrómero/genética , Cromatina/genética , Mapeo Cromosómico , Drosophila melanogaster/fisiología , Genética de Población , Desequilibrio de Ligamiento , Selección Genética , Especificidad de la Especie , Telómero/genética , Regiones no Traducidas/genética , Cromosoma X/genéticaRESUMEN
The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering â¼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for â¼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.
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Evolución Molecular , Genoma Humano/genética , Genoma/genética , Mamíferos/genética , Animales , Enfermedad , Exones/genética , Genómica , Salud , Humanos , Anotación de Secuencia Molecular , Filogenia , ARN/clasificación , ARN/genética , Selección Genética/genética , Alineación de Secuencia , Análisis de Secuencia de ADNRESUMEN
BACKGROUND: The molecular basis and characteristics of familial non-medullary thyroid cancer are poorly understood. In this study, we performed microRNA (miRNA) profiling of familial and sporadic papillary thyroid cancer tumor samples. METHODOLOGY/PRINCIPAL FINDINGS: Genome wide miRNA profiling of sporadic and familial papillary thyroid cancer was performed. Differentially expressed miRNAs were validated by quantitative RT-PCR. Ectopic expression of miR-886-3p in thyroid cancer lines was performed to identify pathways targeted by the miRNA, as well as, to determine its effect on tumor cell biology. We found four differentially expressed miRNAs between familial and sporadic papillary thyroid cancer tumor samples. MiR-886-3p and miR-20a were validated to be differentially expressed by 3- and 4-fold, respectively. Pathway analysis of genome-wide expression data on cells overexpressing miR-886-3p and target prediction analysis showed genes involved in DNA replication and focal adhesion pathways were regulated by miR-886-3p. Overexpression of miR-886-3p in thyroid cancer cell lines significantly inhibited cellular proliferation, the number and size of spheroids and cellular migration. Additionally, overexpression of miR-886-3p increased the number of cells in S phase. CONCLUSIONS/SIGNIFICANCE: Our findings for the first time suggest that miR-886-3p plays an important role in thyroid cancer tumor cell biology and regulates genes involved in DNA replication and focal adhesion. Thus, miR-886-3p may play a role in the initiation and or progression of papillary thyroid cancer.
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Movimiento Celular/genética , MicroARNs/genética , MicroARNs/metabolismo , Precursores del ARN/genética , Precursores del ARN/metabolismo , Neoplasias de la Tiroides/genética , Neoplasias de la Tiroides/metabolismo , Secuencia de Bases , Carcinoma , Carcinoma Medular/congénito , Carcinoma Papilar , Ciclo Celular/genética , Línea Celular Tumoral , Proliferación Celular , Replicación del ADN/genética , Regulación hacia Abajo , Femenino , Adhesiones Focales/genética , Perfilación de la Expresión Génica , Genómica , Humanos , Masculino , Neoplasia Endocrina Múltiple Tipo 2a , Síndromes Neoplásicos Hereditarios , Esferoides Celulares/metabolismo , Esferoides Celulares/patología , Cáncer Papilar Tiroideo , Neoplasias de la Tiroides/patologíaRESUMEN
Assignment of alleles to haplotypes for nearly all the variants on all chromosomes can be performed by genetic analysis of a nuclear family with three or more children. Whole-genome sequence data enable deterministic phasing of nearly all sequenced alleles by permitting assignment of recombinations to precise chromosomal positions and specific meioses. We demonstrate this process of genetic phasing on two families each with four children. We generate haplotypes for all of the children and their parents; these haplotypes span all genotyped positions, including rare variants. Misassignments of phase between variants (switch errors) are nearly absent. Our algorithm can also produce multimegabase haplotypes for nuclear families with just two children and can handle families with missing individuals. We implement our algorithm in a suite of software scripts (Haploscribe). Haplotypes and family genome sequences will become increasingly important for personalized medicine and for fundamental biology.
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Algoritmos , Cromosomas Humanos/genética , Variación Genética , Haplotipos/genética , Patrón de Herencia/genética , Modelos Genéticos , Programas Informáticos , Humanos , Mutación/genética , Linaje , Análisis de Secuencia de ADN/métodosRESUMEN
Transcription factor binding site(s) (TFBS) gain and loss (i.e., turnover) is a well-documented feature of cis-regulatory module (CRM) evolution, yet little attention has been paid to the evolutionary force(s) driving this turnover process. The predominant view, motivated by its widespread occurrence, emphasizes the importance of compensatory mutation and genetic drift. Positive selection, in contrast, although it has been invoked in specific instances of adaptive gene expression evolution, has not been considered as a general alternative to neutral compensatory evolution. In this study we evaluate the two hypotheses by analyzing patterns of single nucleotide polymorphism in the TFBS of well-characterized CRM in two closely related Drosophila species, Drosophila melanogaster and Drosophila simulans. An important feature of the analysis is classification of TFBS mutations according to the direction of their predicted effect on binding affinity, which allows gains and losses to be evaluated independently along the two phylogenetic lineages. The observed patterns of polymorphism and divergence are not compatible with neutral evolution for either class of mutations. Instead, multiple lines of evidence are consistent with contributions of positive selection to TFBS gain and loss as well as purifying selection in its maintenance. In discussion, we propose a model to reconcile the finding of selection driving TFBS turnover with constrained CRM function over long evolutionary time.
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Sitios de Unión/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/metabolismo , Drosophila/metabolismo , Unión Proteica/genética , Selección Genética , Factores de Transcripción/metabolismo , Animales , Evolución Biológica , Bases de Datos Genéticas , Drosophila/genética , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Regulación de la Expresión Génica , Modelos Genéticos , Mutación , Filogenia , Polimorfismo Genético , Análisis de Secuencia de ADN , Especificidad de la Especie , Factores de Transcripción/genéticaRESUMEN
BACKGROUND: The authors are interested in identifying molecular markers that can aid in the diagnosis of adrenocortical carcinoma (ACC). The aim of this study was to identify microRNAs (miRNAs or miRs) that are differentially expressed in malignant adrenocortical tumors as compared with benign tumors and assess their potential as diagnostic predictors. METHODS: Differentially expressed miRNAs were identified using microarray profiling of adrenocortical tumors and validated by quantitative real-time RT-PCR. RESULTS: Microarray profiling in benign and primary malignant adrenocortical tumors revealed several significant differences between these histological groups. By using directed quantitative RT-PCR analysis on a subset of these differentially expressed miRNAs, the authors determined that miRs -100, -125b, and -195 were significantly down-regulated, whereas miR-483-5p was significantly up-regulated in malignant as compared with benign tumors. Furthermore, the current study shows that miR-483-5p expression can accurately categorize tumors as benign or malignant. CONCLUSIONS: The authors identified 4 miRNAs that are dysregulated in adrenocortical carcinoma. The high expression of one of these, miR-483-5p, appears to be a defining characteristic of adrenocortical malignancies, and can thus be used to accurately distinguish between benign and malignant adrenocortical tumors.
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Neoplasias de la Corteza Suprarrenal/genética , Factor 3 de Iniciación Eucariótica/análisis , Perfilación de la Expresión Génica , MicroARNs/análisis , Factor II del Crecimiento Similar a la Insulina/metabolismo , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Estudios de Validación como AsuntoRESUMEN
The developmental mechanisms through which the cerebral cortex increased in size and complexity during primate evolution are essentially unknown. To uncover genetic networks active in the developing cerebral cortex, we combined three-dimensional reconstruction of human fetal brains at midgestation and whole genome expression profiling. This novel approach enabled transcriptional characterization of neurons from accurately defined cortical regions containing presumptive Broca and Wernicke language areas, as well as surrounding associative areas. We identified hundreds of genes displaying differential expression between the two regions, but no significant difference in gene expression between left and right hemispheres. Validation by qRTPCR and in situ hybridization confirmed the robustness of our approach and revealed novel patterns of area- and layer-specific expression throughout the developing cortex. Genes differentially expressed between cortical areas were significantly associated with fast-evolving non-coding sequences harboring human-specific substitutions that could lead to divergence in their repertoires of transcription factor binding sites. Strikingly, while some of these sequences were accelerated in the human lineage only, many others were accelerated in chimpanzee and/or mouse lineages, indicating that genes important for cortical development may be particularly prone to changes in transcriptional regulation across mammals. Genes differentially expressed between cortical regions were also enriched for transcriptional targets of FoxP2, a key gene for the acquisition of language abilities in humans. Our findings point to a subset of genes with a unique combination of cortical areal expression and evolutionary patterns, suggesting that they play important roles in the transcriptional network underlying human-specific neural traits.