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1.
Nat Mater ; 18(4): 397-405, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30778227

RESUMO

The generation of organoids is one of the biggest scientific advances in regenerative medicine. Here, by lengthening the time that human pluripotent stem cells (hPSCs) were exposed to a three-dimensional microenvironment, and by applying defined renal inductive signals, we generated kidney organoids that transcriptomically matched second-trimester human fetal kidneys. We validated these results using ex vivo and in vitro assays that model renal development. Furthermore, we developed a transplantation method that utilizes the chick chorioallantoic membrane. This approach created a soft in vivo microenvironment that promoted the growth and differentiation of implanted kidney organoids, as well as providing a vascular component. The stiffness of the in ovo chorioallantoic membrane microenvironment was recapitulated in vitro by fabricating compliant hydrogels. These biomaterials promoted the efficient generation of renal vesicles and nephron structures, demonstrating that a soft environment accelerates the differentiation of hPSC-derived kidney organoids.


Assuntos
Espaço Extracelular/metabolismo , Rim/citologia , Organoides/citologia , Células-Tronco Pluripotentes/citologia , Técnicas de Cultura de Tecidos/métodos , Diferenciação Celular , Microambiente Celular , Feminino , Humanos , Cinética , Células-Tronco Pluripotentes/metabolismo , Gravidez , Terceiro Trimestre da Gravidez , Transcriptoma
2.
Stem Cells Dev ; 28(6): 370-383, 2019 03 15.
Artigo em Inglês | MEDLINE | ID: mdl-30654721

RESUMO

Osteogenic differentiation is a complex and still poorly understood biological process regulated by intrinsic cellular signals and extrinsic microenvironmental cues. Following appropriate stimuli, mesenchymal stem cells (MSCs) differentiate into osteoblasts through a tightly regulated multistep process driven by several transcription factors and characterized by the expression of a number of bone-specific proteins. In this study, we describe a novel transcription factor that we named osteoblast inducer (ObI)-1, involved in MSC differentiation toward the osteogenic lineage. ObI-1 encodes for a nuclear protein subjected to proteasomal degradation and expressed during osteoblast differentiation both in a murine multipotent mesenchymal cell line (W20-17) and in primary murine MSCs. RNA interference-mediated knockdown of ObI-1 expression significantly impairs osteoblast differentiation and matrix mineralization with reduced expression of the osteogenic markers, Runt-related transcription factor 2 (Runx2) and osteopontin. Conversely, ObI-1 overexpression enhances osteogenic differentiation and bone-specific markers expression. ObI-1 stimulates bone morphogenetic protein (BMP)-4 expression and the consequent activation of the Smad pathway; treatment with a BMP receptor type I antagonist completely abolishes ObI-1-mediated stimulation of osteogenic differentiation. Collectively, our findings suggest that ObI-1 modulates osteogenic differentiation, at least in part, through the BMP signaling pathway, increasing Runx2 activation and leading to osteoblast commitment and maturation.

3.
Microbiome ; 6(1): 218, 2018 Dec 06.
Artigo em Inglês | MEDLINE | ID: mdl-30522523

RESUMO

BACKGROUND: The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adolescent oral microbiome remains poorly studied. Here, we used a citizen science approach and 16S profiling to assess the oral microbiome of 1500 adolescents around Spain and its relationships with lifestyle, diet, hygiene, and socioeconomic and environmental parameters. RESULTS: Our results provide a detailed snapshot of the adolescent oral microbiome and how it varies with lifestyle and other factors. In addition to hygiene and dietary habits, we found that the composition of tap water was related to important changes in the abundance of several bacterial genera. This points to an important role of drinking water in shaping the oral microbiota, which has been so far poorly explored. Overall, the microbiome samples of our study can be clustered into two broad compositional patterns (stomatotypes), driven mostly by Neisseria and Prevotella, respectively. These patterns show striking similarities with those found in unrelated populations. CONCLUSIONS: We hypothesize that these stomatotypes represent two possible global optimal equilibria in the oral microbiome that reflect underlying constraints of the human oral niche. As such, they should be found across a variety of geographical regions, lifestyles, and ages.

4.
Genome Res ; 27(10): 1759-1768, 2017 10.
Artigo em Inglês | MEDLINE | ID: mdl-28855263

RESUMO

Alternative splicing (AS) generates remarkable regulatory and proteomic complexity in metazoans. However, the functions of most AS events are not known, and programs of regulated splicing remain to be identified. To address these challenges, we describe the Vertebrate Alternative Splicing and Transcription Database (VastDB), the largest resource of genome-wide, quantitative profiles of AS events assembled to date. VastDB provides readily accessible quantitative information on the inclusion levels and functional associations of AS events detected in RNA-seq data from diverse vertebrate cell and tissue types, as well as developmental stages. The VastDB profiles reveal extensive new intergenic and intragenic regulatory relationships among different classes of AS and previously unknown and conserved landscapes of tissue-regulated exons. Contrary to recent reports concluding that nearly all human genes express a single major isoform, VastDB provides evidence that at least 48% of multiexonic protein-coding genes express multiple splice variants that are highly regulated in a cell/tissue-specific manner, and that >18% of genes simultaneously express multiple major isoforms across diverse cell and tissue types. Isoforms encoded by the latter set of genes are generally coexpressed in the same cells and are often engaged by translating ribosomes. Moreover, they are encoded by genes that are significantly enriched in functions associated with transcriptional control, implying they may have an important and wide-ranging role in controlling cellular activities. VastDB thus provides an unprecedented resource for investigations of AS function and regulation.


Assuntos
Processamento Alternativo , Bases de Dados de Ácidos Nucleicos , Éxons , Redes Reguladoras de Genes , Isoformas de Proteínas , Animais , Galinhas , Humanos , Camundongos , Isoformas de Proteínas/biossíntese , Isoformas de Proteínas/genética
5.
Sci Rep ; 7: 44138, 2017 03 10.
Artigo em Inglês | MEDLINE | ID: mdl-28281571

RESUMO

Opitz trigonocephaly C syndrome (OTCS) is a rare genetic disorder characterized by craniofacial anomalies, variable intellectual and psychomotor disability, and variable cardiac defects with a high mortality rate. Different patterns of inheritance and genetic heterogeneity are known in this syndrome. Whole exome and genome sequencing of a 19-year-old girl (P7), initially diagnosed with OTCS, revealed a de novo nonsense mutation, p.Q638*, in the MAGEL2 gene. MAGEL2 is an imprinted, maternally silenced, gene located at 15q11-13, within the Prader-Willi region. Patient P7 carried the mutation in the paternal chromosome. Recently, mutations in MAGEL2 have been described in Schaaf-Yang syndrome (SHFYNG) and in severe arthrogryposis. Patient P7 bears resemblances with SHFYNG cases but has other findings not described in this syndrome and common in OTCS. We sequenced MAGEL2 in nine additional OTCS patients and no mutations were found. This study provides the first clear molecular genetic basis for an OTCS case, indicates that there is overlap between OTCS and SHFYNG syndromes, and confirms that OTCS is genetically heterogeneous. Genes encoding MAGEL2 partners, either in the retrograde transport or in the ubiquitination-deubiquitination complexes, are promising candidates as OTCS disease-causing genes.


Assuntos
Craniossinostoses , Deficiência Intelectual , Mutação de Sentido Incorreto , Proteínas , Adulto , Craniossinostoses/genética , Craniossinostoses/metabolismo , Feminino , Humanos , Deficiência Intelectual/genética , Deficiência Intelectual/metabolismo , Proteínas/genética , Proteínas/metabolismo
6.
Genome Biol ; 17(1): 251, 2016 12 14.
Artigo em Inglês | MEDLINE | ID: mdl-27964752

RESUMO

BACKGROUND: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction. RESULTS: We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species. CONCLUSIONS: The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.


Assuntos
Genética Populacional , Genoma , Lynx/genética , Animais , Espécies em Perigo de Extinção , Variação Genética , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Análise de Sequência de DNA
7.
Elife ; 52016 05 25.
Artigo em Inglês | MEDLINE | ID: mdl-27223324

RESUMO

PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate the mechanisms targeting PHF13 to chromatin, its genome wide localization and its molecular chromatin context. Size exclusion chromatography, mass spectrometry, X-ray crystallography and ChIP sequencing demonstrate that PHF13 binds chromatin in a multivalent fashion via direct interactions with H3K4me2/3 and DNA, and indirectly via interactions with PRC2 and RNA PolII. Furthermore, PHF13 depletion disrupted the interactions between PRC2, RNA PolII S5P, H3K4me3 and H3K27me3 and resulted in the up and down regulation of genes functionally enriched in transcriptional regulation, DNA binding, cell cycle, differentiation and chromatin organization. Together our findings argue that PHF13 is an H3K4me2/3 molecular reader and transcriptional co-regulator, affording it the ability to impact different chromatin processes.


Assuntos
Cromatina/metabolismo , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , DNA/metabolismo , Histonas/metabolismo , Fatores de Transcrição/química , Fatores de Transcrição/metabolismo , Animais , Linhagem Celular , Imunoprecipitação da Cromatina , Cromatografia em Gel , Cristalografia por Raios X , Regulação da Expressão Gênica , Humanos , Espectrometria de Massas , Camundongos , Ligação Proteica
8.
Genome Biol ; 17: 32, 2016 Feb 25.
Artigo em Inglês | MEDLINE | ID: mdl-26911872

RESUMO

BACKGROUND: Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes. RESULTS: We report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools. CONCLUSIONS: The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.


Assuntos
Genoma de Planta , Repetições de Microssatélites/genética , Phaseolus/genética , Transcriptoma/genética , DNA de Plantas/genética , Duplicação Gênica , Perfilação da Expressão Gênica , Genótipo , Humanos , Filogenia , Sementes/genética , Análise de Sequência de DNA
9.
PLoS Genet ; 12(1): e1005768, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26730850

RESUMO

The genome of the fission yeast Schizosaccharomyces pombe encodes 17 kinases that are essential for cell growth. These include the cell-cycle regulator Cdc2, as well as several kinases that coordinate cell growth, polarity, and morphogenesis during the cell cycle. In this study, we further characterized another of these essential kinases, Prp4, and showed that the splicing of many introns is dependent on Prp4 kinase activity. For detailed characterization, we chose the genes res1 and ppk8, each of which contains one intron of typical size and position. Splicing of the res1 intron was dependent on Prp4 kinase activity, whereas splicing of the ppk8 intron was not. Extensive mutational analyses of the 5' splice site of both genes revealed that proper transient interaction with the 5' end of snRNA U1 governs the dependence of splicing on Prp4 kinase activity. Proper transient interaction between the branch sequence and snRNA U2 was also important. Therefore, the Prp4 kinase is required for recognition and efficient splicing of introns displaying weak exon1/5' splice sites and weak branch sequences.


Assuntos
Proteínas Serina-Treonina Quinases/genética , Sítios de Splice de RNA/genética , Processamento de RNA/genética , Ribonucleoproteína Nuclear Pequena U4-U6/genética , Proteínas de Schizosaccharomyces pombe/genética , Schizosaccharomyces/genética , Proteínas de Ciclo Celular/genética , Íntrons/genética , Mutação , Fatores de Processamento de RNA , Ribonucleoproteínas Nucleares Pequenas/genética , Spliceossomos/genética , Fatores de Transcrição/genética
10.
Sci Rep ; 6(1): 18, 2016 Dec 21.
Artigo em Inglês | MEDLINE | ID: mdl-28442708

RESUMO

In contrast to the widely accepted consensus of the existence of a single RNA polymerase in bacteria, several actinomycetes have been recently shown to possess two forms of RNA polymerases due the to co-existence of two rpoB paralogs in their genome. However, the biological significance of the rpoB duplication is obscure. In this study we have determined the genome sequence of the lipoglycopeptide antibiotic A40926 producer Nonomuraea gerenzanensis ATCC 39727, an actinomycete with a large genome and two rpoB genes, i.e. rpoB(S) (the wild-type gene) and rpoB(R) (the mutant-type gene). We next analyzed the transcriptional and metabolite profiles in the wild-type gene and in two derivative strains over-expressing either rpoB(R) or a mutated form of this gene to explore the physiological role and biotechnological potential of the "mutant-type" RNA polymerase. We show that rpoB(R) controls antibiotic production and a wide range of metabolic adaptive behaviors in response to environmental pH. This may give interesting perspectives also with regard to biotechnological applications.


Assuntos
Actinomycetales/genética , Proteínas de Bactérias/genética , RNA Polimerases Dirigidas por DNA/genética , Genoma Bacteriano , Transcriptoma , Actinomycetales/metabolismo , Antibacterianos/biossíntese , Concentração de Íons de Hidrogênio , Mutação , Teicoplanina/análogos & derivados , Teicoplanina/biossíntese
11.
PLoS One ; 10(9): e0137354, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26335586

RESUMO

The human respiratory tract pathogen M. pneumoniae is one of the best characterized minimal bacterium. Until now, two main groups of clinical isolates of this bacterium have been described (types 1 and 2), differing in the sequence of the P1 adhesin gene. Here, we have sequenced the genomes of 23 clinical isolates of M. pneumoniae. Studying SNPs, non-synonymous mutations, indels and genome rearrangements of these 23 strains and 4 previously sequenced ones, has revealed new subclasses in the two main groups, some of them being associated with the country of isolation. Integrative analysis of in vitro gene essentiality and mutation rates enabled the identification of several putative virulence factors and antigenic proteins; revealing recombination machinery, glycerol metabolism and peroxide production as possible factors in the genetics and physiology of these pathogenic strains. Additionally, the transcriptomes and proteomes of two representative strains, one from each of the two main groups, have been characterized to evaluate the impact of mutations on RNA and proteins levels. This study has revealed that type 2 strains show higher expression levels of CARDS toxin, a protein recently shown to be one of the major factors of inflammation. Thus, we propose that type 2 strains could be more toxigenic than type 1 strains of M. pneumoniae.


Assuntos
Genoma Bacteriano , Mycoplasma pneumoniae/patogenicidade , Adesinas Bacterianas/genética , Variação Antigênica/genética , Antígenos de Bactérias/genética , Proteínas de Bactérias/biossíntese , Proteínas de Bactérias/genética , Toxinas Bacterianas/biossíntese , Toxinas Bacterianas/genética , Sequência de Bases , Europa (Continente)/epidemiologia , Regulação Bacteriana da Expressão Gênica , Humanos , Mutação INDEL , Japão/epidemiologia , Dados de Sequência Molecular , Mutação , Mycoplasma pneumoniae/classificação , Mycoplasma pneumoniae/genética , Mycoplasma pneumoniae/isolamento & purificação , Fases de Leitura Aberta , Pneumonia por Mycoplasma/epidemiologia , Pneumonia por Mycoplasma/microbiologia , Polimorfismo de Nucleotídeo Único , Proteoma , Transcriptoma , Tunísia/epidemiologia , Virulência/genética
12.
Nucleic Acids Res ; 43(Database issue): D618-23, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25378328

RESUMO

MyMpn (http://mympn.crg.eu) is an online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a minimal bacterium causing lower respiratory tract infections. Due to its small size, its ability to grow in vitro, and the amount of data produced over the past decades, M. pneumoniae is an interesting model organisms for the development of systems biology approaches for unicellular organisms. Our database hosts a wealth of omics-scale datasets generated by hundreds of experimental and computational analyses. These include data obtained from gene expression profiling experiments, gene essentiality studies, protein abundance profiling, protein complex analysis, metabolic reactions and network modeling, cell growth experiments, comparative genomics and 3D tomography. In addition, the intuitive web interface provides access to several visualization and analysis tools as well as to different data search options. The availability and--even more relevant--the accessibility of properly structured and organized data are of up-most importance when aiming to understand the biology of an organism on a global scale. Therefore, MyMpn constitutes a unique and valuable new resource for the large systems biology and microbiology community.


Assuntos
Bases de Dados Genéticas , Mycoplasma pneumoniae/genética , Mycoplasma pneumoniae/metabolismo , Biologia de Sistemas , Genoma Bacteriano , Internet , Metaboloma , Proteoma , Transcriptoma
13.
BMC Genomics ; 15: 384, 2014 May 19.
Artigo em Inglês | MEDLINE | ID: mdl-24884518

RESUMO

BACKGROUND: Novosphingobium sp. strain PP1Y is a marine α-proteobacterium adapted to grow at the water/fuel oil interface. It exploits the aromatic fraction of fuel oils as a carbon and energy source. PP1Y is able to grow on a wide range of mono-, poly- and heterocyclic aromatic hydrocarbons. Here, we report the complete functional annotation of the whole Novosphingobium genome. RESULTS: PP1Y genome analysis and its comparison with other Sphingomonadal genomes has yielded novel insights into the molecular basis of PP1Y's phenotypic traits, such as its peculiar ability to encapsulate and degrade the aromatic fraction of fuel oils. In particular, we have identified and dissected several highly specialized metabolic pathways involved in: (i) aromatic hydrocarbon degradation; (ii) resistance to toxic compounds; and (iii) the quorum sensing mechanism. CONCLUSIONS: In summary, the unraveling of the entire PP1Y genome sequence has provided important insight into PP1Y metabolism and, most importantly, has opened new perspectives about the possibility of its manipulation for bioremediation purposes.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Redes e Vias Metabólicas , Análise de Sequência de DNA/métodos , Sphingomonadaceae/genética , Biodegradação Ambiental , Genes Bacterianos , Filogenia , Percepção de Quorum , Sphingomonadaceae/classificação , Sphingomonadaceae/metabolismo
14.
Genes Dev ; 28(2): 182-97, 2014 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-24449271

RESUMO

The molecular mechanisms underlying specification from embryonic stem cells (ESCs) and maintenance of neural progenitor cells (NPCs) are largely unknown. Recently, we reported that the Zuotin-related factor 1 (Zrf1) is necessary for chromatin displacement of the Polycomb-repressive complex 1 (PRC1). We found that Zrf1 is required for NPC specification from ESCs and that it promotes the expression of NPC markers, including the key regulator Pax6. Moreover, Zrf1 is essential to establish and maintain Wnt ligand expression levels, which are necessary for NPC self-renewal. Reactivation of proper Wnt signaling in Zrf1-depleted NPCs restores Pax6 expression and the self-renewal capacity. ESC-derived NPCs in vitro resemble most of the characteristics of the self-renewing NPCs located in the developing embryonic cortex, which are termed radial glial cells (RGCs). Depletion of Zrf1 in vivo impairs the expression of key self-renewal regulators and Wnt ligand genes in RGCs. Thus, we demonstrate that Zrf1 plays an essential role in NPC generation and maintenance.


Assuntos
Diferenciação Celular , Proteínas de Ligação a DNA/metabolismo , Placa Neural/citologia , Placa Neural/metabolismo , Proteínas Oncogênicas/metabolismo , Células-Tronco/citologia , Células-Tronco/metabolismo , Animais , Linhagem Celular , Proteínas de Ligação a DNA/genética , Células-Tronco Embrionárias/citologia , Proteínas do Olho/genética , Regulação da Expressão Gênica no Desenvolvimento , Proteínas de Homeodomínio/genética , Humanos , Ligantes , Camundongos , Neurogênese/genética , Proteínas Oncogênicas/genética , Fator de Transcrição PAX6 , Fatores de Transcrição Box Pareados/genética , Proteínas Repressoras/genética , Transdução de Sinais , Proteínas Wnt/metabolismo
15.
EMBO J ; 32(16): 2217-30, 2013 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-23872946

RESUMO

Cellular senescence is an intrinsic defense mechanism to various cellular stresses: while still metabolically active, senescent cells stop dividing and enter a proliferation arrest. Here, we identify DPY30, a member of all mammalian histone H3K4 histone methyltransferases (HMTases), as a key regulator of the proliferation potential of human primary cells. Following depletion of DPY30, cells show a severe proliferation defect and display a senescent phenotype, including a flattened and enlarged morphology, elevated level of reactive oxygen species (ROS), increased SA-ß-galactosidase activity, and formation of senescence-associated heterochromatin foci (SAHFs). While DPY30 depletion leads to a reduced level of H3K4me3-marked active chromatin, we observed a concomitant activation of CDK inhibitors, including p16INK4a, independent of H3K4me3. ChIP experiments show that key regulators of cell-cycle progression, including ID proteins, are under direct control of DPY30. Because ID proteins are negative regulators of the transcription factors ETS1/2, depletion of DPY30 leads to the transcriptional activation of p16INK4a by ETS1/2 and thus to a senescent-like phenotype. Ectoptic re-introduction of ID protein expression can partially rescue the senescence-like phenotype induced by DPY30 depletion. Thus, our data indicate that DPY30 controls proliferation by regulating ID proteins expression, which in turn lead to senescence bypass.


Assuntos
Senescência Celular/fisiologia , Regulação da Expressão Gênica/fisiologia , Proteína 1 Inibidora de Diferenciação/metabolismo , Proteínas Nucleares/metabolismo , Transdução de Sinais/fisiologia , Western Blotting , Imunoprecipitação da Cromatina , Ensaio de Unidades Formadoras de Colônias , Citometria de Fluxo , Imunofluorescência , Técnicas de Silenciamento de Genes , Humanos , Análise em Microsséries , Proteínas Nucleares/genética , Interferência de RNA , Reação em Cadeia da Polimerase Via Transcriptase Reversa , beta-Galactosidase
16.
BMC Genomics ; 14: 123, 2013 Feb 24.
Artigo em Inglês | MEDLINE | ID: mdl-23432914

RESUMO

BACKGROUND: Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo). RESULTS: We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships. CONCLUSIONS: We show how comparative transcriptomics can be used to create useful resources for evo-devo, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these data to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies).


Assuntos
Dípteros/genética , Transcriptoma , Animais , Teorema de Bayes , Hibridização Genômica Comparativa , Dípteros/classificação , Drosophila melanogaster/genética , Desenvolvimento Embrionário/genética , Duplicação Gênica , Genômica , Filogenia , RNA/genética , RNA/metabolismo , Análise de Sequência de RNA
17.
Cell Rep ; 3(1): 60-9, 2013 Jan 31.
Artigo em Inglês | MEDLINE | ID: mdl-23273917

RESUMO

The Polycomb repressive complex 1 (PRC1) is required for decisions of stem cell fate. In mouse embryonic stem cells (ESCs), two major variations of PRC1 complex, defined by the mutually exclusive presence of Cbx7 or RYBP, have been identified. Here, we show that although the genomic localization of the Cbx7- and RYBP-containing PRC1 complexes overlaps in certain genes, it can also be mutually exclusive. At the molecular level, Cbx7 is necessary for recruitment of Ring1B to chromatin, whereas RYBP enhances the PRC1 enzymatic activity. Genes occupied by RYBP show lower levels of Ring1B and H2AK119ub and are consequently more highly transcribed than those bound by Cbx7. At the functional level, we show that genes occupied by RYBP are primarily involved in the regulation of metabolism and cell-cycle progression, whereas those bound by Cbx7 predominantly control early-lineage commitment of ESCs. Altogether, our results indicate that different PRC1 subtypes establish a complex pattern of gene regulation that regulates common and nonoverlapping aspects of ESC pluripotency and differentiation.


Assuntos
Células-Tronco Embrionárias/metabolismo , Complexo Repressor Polycomb 1/metabolismo , Proteínas do Grupo Polycomb/metabolismo , Proteínas Repressoras/metabolismo , Animais , Cromatina/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Genoma/genética , Humanos , Camundongos , Ligação Proteica , Ubiquitina-Proteína Ligases/metabolismo
18.
Genes Dev ; 26(19): 2144-53, 2012 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-22972935

RESUMO

Altered stem cell homeostasis is linked to organismal aging. However, the mechanisms involved remain poorly understood. Here we report novel alterations in hair follicle stem cells during skin aging, including increased numbers, decreased function, and an inability to tolerate stress. Performing high-throughput RNA sequencing on aging stem cells, cytokine arrays, and functional assays, we identify an age-associated imbalance in epidermal Jak-Stat signaling that inhibits stem cell function. Collectively, this study reveals a role for the aging epidermis in the disruption of cytokine and stem cell homeostasis, suggesting that stem cell decline during aging may be part of broader tumor-suppressive mechanisms.


Assuntos
Envelhecimento , Células Epidérmicas , Inflamação , Células-Tronco/citologia , Animais , Contagem de Células , Células Cultivadas , Citocinas/metabolismo , Epiderme/enzimologia , Folículo Piloso/citologia , Folículo Piloso/enzimologia , Homeostase/fisiologia , Janus Quinases/antagonistas & inibidores , Camundongos , Camundongos Endogâmicos C57BL , Fator de Transcrição STAT3/metabolismo , Transdução de Sinais , Células-Tronco/enzimologia
19.
Proc Natl Acad Sci U S A ; 109(29): 11872-7, 2012 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-22753475

RESUMO

We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site-leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.


Assuntos
Evolução Biológica , Cucumis melo/genética , Genoma de Planta/genética , Filogenia , Sequência de Bases , Mapeamento Cromossômico , Cromossomos Artificiais Bacterianos/genética , Elementos de DNA Transponíveis/genética , Resistência à Doença/genética , Genes Duplicados/genética , Genes de Plantas/genética , Genômica/métodos , Funções Verossimilhança , Modelos Genéticos , Anotação de Sequência Molecular , Dados de Sequência Molecular , Alinhamento de Sequência , Análise de Sequência de DNA
20.
Cell Stem Cell ; 10(1): 47-62, 2012 Jan 06.
Artigo em Inglês | MEDLINE | ID: mdl-22226355

RESUMO

Polycomb group proteins are essential regulators of cell fate decisions during embryogenesis. In mammals, at least five different Cbx proteins (Cbx2, Cbx4, Cbx6, Cbx7, and Cbx8) are known to associate with the core Polycomb repressive complex 1 (PRC1). Here we show that pluripotency and differentiation of mouse embryonic stem cells (ESCs) is regulated by different Cbx-associated PRC1 complexes with unique functions. Maintenance of pluripotency primarily depends on Cbx7, while lineage commitment is orchestrated by Cbx2 and Cbx4. At the molecular level, we have uncovered a Polycomb autoregulatory loop in which Cbx7 represses the expression of prodifferentiation Cbx proteins, thereby maintaining the pluripotent state. We additionally show that the occupancy of Cbx7 on promoters is completely dependent on PRC2 activity but only partially dependent on a functional PRC1 complex. Thus, Cbx proteins confer distinct target selectivity to the PRC1 complex, achieving a balance between the self-renewal and the differentiation of ESCs.


Assuntos
Diferenciação Celular/fisiologia , Células-Tronco Embrionárias/metabolismo , Células-Tronco Pluripotentes/metabolismo , Regiões Promotoras Genéticas/fisiologia , Proteínas Repressoras/metabolismo , Animais , Células-Tronco Embrionárias/citologia , Humanos , Ligases , Camundongos , Camundongos Knockout , Proteínas de Transporte da Membrana Mitocondrial , Células-Tronco Pluripotentes/citologia , Complexo Repressor Polycomb 1 , Proteínas do Grupo Polycomb , Proteínas Repressoras/genética , Ubiquitina-Proteína Ligases
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