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1.
Semin Cell Dev Biol ; 65: 60-68, 2017 05.
Artículo en Inglés | MEDLINE | ID: mdl-27751776

RESUMEN

The proneural gene, Atoh1, is necessary and in some contexts sufficient for early inner ear hair cell development. Its function is the subject of intensive research, not least because of the possibility that it could be used in therapeutic strategies to reverse hair cell loss in deafness. However, it is clear that Atoh1's function is highly context dependent. During inner ear development, Atoh1 is only able to promote hair cell differentiation at specific developmental stages. Outside the ear, Atoh1 is required for differentiation of a variety of other cell types, for example in the intestine and cerebellum. The reasons for this context dependence are poorly understood. So far, the pathways and key players that instruct Atoh1 to act as a mechanosensory cell fate determinant in the context of the inner ear are largely unknown. Here we review evidence that suggests that Atoh1 function in hair cell differentiation is modulated by interaction with other transcription factors. We particularly focus on the possible roles of Gfi1 and Pou4f3, drawing from studies in mouse, Drosophila and C. elegans.


Asunto(s)
Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/genética , Proteínas de Unión al ADN/genética , Células Ciliadas Auditivas/metabolismo , Proteínas de Homeodominio/genética , Mecanorreceptores/metabolismo , Factor de Transcripción Brn-3C/genética , Factores de Transcripción/genética , Animales , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/metabolismo , Caenorhabditis elegans/citología , Caenorhabditis elegans/crecimiento & desarrollo , Caenorhabditis elegans/metabolismo , Diferenciación Celular , Proteínas de Unión al ADN/metabolismo , Drosophila melanogaster/citología , Drosophila melanogaster/crecimiento & desarrollo , Drosophila melanogaster/metabolismo , Regulación del Desarrollo de la Expresión Génica , Células Ciliadas Auditivas/citología , Proteínas de Homeodominio/metabolismo , Mecanorreceptores/citología , Mecanotransducción Celular , Ratones , Especificidad de Órganos , Factor de Transcripción Brn-3C/metabolismo , Factores de Transcripción/metabolismo
2.
PLoS Genet ; 10(9): e1004577, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-25232951

RESUMEN

Cilia are highly conserved microtubule-based structures that perform a variety of sensory and motility functions during development and adult homeostasis. In humans, defects specifically affecting motile cilia lead to chronic airway infections, infertility and laterality defects in the genetically heterogeneous disorder Primary Ciliary Dyskinesia (PCD). Using the comparatively simple Drosophila system, in which mechanosensory neurons possess modified motile cilia, we employed a recently elucidated cilia transcriptional RFX-FOX code to identify novel PCD candidate genes. Here, we report characterization of CG31320/HEATR2, which plays a conserved critical role in forming the axonemal dynein arms required for ciliary motility in both flies and humans. Inner and outer arm dyneins are absent from axonemes of CG31320 mutant flies and from PCD individuals with a novel splice-acceptor HEATR2 mutation. Functional conservation of closely arranged RFX-FOX binding sites upstream of HEATR2 orthologues may drive higher cytoplasmic expression of HEATR2 during early motile ciliogenesis. Immunoprecipitation reveals HEATR2 interacts with DNAI2, but not HSP70 or HSP90, distinguishing it from the client/chaperone functions described for other cytoplasmic proteins required for dynein arm assembly such as DNAAF1-4. These data implicate CG31320/HEATR2 in a growing intracellular pre-assembly and transport network that is necessary to deliver functional dynein machinery to the ciliary compartment for integration into the motile axoneme.


Asunto(s)
Cilios/metabolismo , Cilios/fisiología , Proteínas/metabolismo , Animales , Dineínas Axonemales , Axonema/genética , Axonema/metabolismo , Sitios de Unión/genética , Línea Celular , Preescolar , Cilios/genética , Trastornos de la Motilidad Ciliar/genética , Trastornos de la Motilidad Ciliar/metabolismo , Drosophila/genética , Drosophila/metabolismo , Dineínas/genética , Dineínas/metabolismo , Femenino , Humanos , Síndrome de Kartagener/genética , Síndrome de Kartagener/metabolismo , Masculino , Mutación/genética , Linaje , Fenotipo , Proteínas/genética , Transcripción Genética/genética
3.
Am J Hum Genet ; 93(2): 346-56, 2013 Aug 08.
Artículo en Inglés | MEDLINE | ID: mdl-23891471

RESUMEN

Primary ciliary dyskinesia (PCD) is a ciliopathy characterized by airway disease, infertility, and laterality defects, often caused by dual loss of the inner dynein arms (IDAs) and outer dynein arms (ODAs), which power cilia and flagella beating. Using whole-exome and candidate-gene Sanger resequencing in PCD-affected families afflicted with combined IDA and ODA defects, we found that 6/38 (16%) carried biallelic mutations in the conserved zinc-finger gene BLU (ZMYND10). ZMYND10 mutations conferred dynein-arm loss seen at the ultrastructural and immunofluorescence level and complete cilia immotility, except in hypomorphic p.Val16Gly (c.47T>G) homozygote individuals, whose cilia retained a stiff and slowed beat. In mice, Zmynd10 mRNA is restricted to regions containing motile cilia. In a Drosophila model of PCD, Zmynd10 is exclusively expressed in cells with motile cilia: chordotonal sensory neurons and sperm. In these cells, P-element-mediated gene silencing caused IDA and ODA defects, proprioception deficits, and sterility due to immotile sperm. Drosophila Zmynd10 with an equivalent c.47T>G (p.Val16Gly) missense change rescued mutant male sterility less than the wild-type did. Tagged Drosophila ZMYND10 is localized primarily to the cytoplasm, and human ZMYND10 interacts with LRRC6, another cytoplasmically localized protein altered in PCD. Using a fly model of PCD, we conclude that ZMYND10 is a cytoplasmic protein required for IDA and ODA assembly and that its variants cause ciliary dysmotility and PCD with laterality defects.


Asunto(s)
Cilios/genética , Dineínas/genética , Infertilidad Masculina/genética , Síndrome de Kartagener/genética , Proteínas/genética , Sistema Respiratorio/metabolismo , Proteínas Supresoras de Tumor/genética , Animales , Axonema/genética , Axonema/metabolismo , Axonema/patología , Cilios/metabolismo , Cilios/patología , Proteínas del Citoesqueleto , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Dineínas/metabolismo , Exoma , Femenino , Regulación de la Expresión Génica , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Infertilidad Masculina/metabolismo , Infertilidad Masculina/patología , Síndrome de Kartagener/metabolismo , Síndrome de Kartagener/patología , Masculino , Ratones , Mutación , Linaje , Estructura Terciaria de Proteína , Proteínas/metabolismo , Sistema Respiratorio/patología , Proteínas Supresoras de Tumor/metabolismo
4.
PLoS Genet ; 9(12): e1003928, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-24415959

RESUMEN

Defects in cilium and centrosome function result in a spectrum of clinically-related disorders, known as ciliopathies. However, the complex molecular composition of these structures confounds functional dissection of what any individual gene product is doing under normal and disease conditions. As part of an siRNA screen for genes involved in mammalian ciliogenesis, we and others have identified the conserved centrosomal protein Azi1/Cep131 as required for cilia formation, supporting previous Danio rerio and Drosophila melanogaster mutant studies. Acute loss of Azi1 by knock-down in mouse fibroblasts leads to a robust reduction in ciliogenesis, which we rescue by expressing siRNA-resistant Azi1-GFP. Localisation studies show Azi1 localises to centriolar satellites, and traffics along microtubules becoming enriched around the basal body. Azi1 also localises to the transition zone, a structure important for regulating traffic into the ciliary compartment. To study the requirement of Azi1 during development and tissue homeostasis, Azi1 null mice were generated (Azi1(Gt/Gt)). Surprisingly, Azi1(Gt/Gt) MEFs have no discernible ciliary phenotype and moreover are resistant to Azi1 siRNA knock-down, demonstrating that a compensation mechanism exists to allow ciliogenesis to proceed despite the lack of Azi1. Cilia throughout Azi1 null mice are functionally normal, as embryonic patterning and adult homeostasis are grossly unaffected. However, in the highly specialised sperm flagella, the loss of Azi1 is not compensated, leading to striking microtubule-based trafficking defects in both the manchette and the flagella, resulting in male infertility. Our analysis of Azi1 knock-down (acute loss) versus gene deletion (chronic loss) suggests that Azi1 plays a conserved, but non-essential trafficking role in ciliogenesis. Importantly, our in vivo analysis reveals Azi1 mediates novel trafficking functions necessary for flagellogenesis. Our study highlights the importance of both acute removal of a protein, in addition to mouse knock-out studies, when functionally characterising candidates for human disease.


Asunto(s)
Cilios/genética , Infertilidad Masculina/genética , Proteínas/genética , Cola del Espermatozoide/patología , Animales , Proteínas de Ciclo Celular , Centriolos/genética , Centriolos/metabolismo , Cilios/patología , Proteínas del Citoesqueleto , Flagelos/metabolismo , Flagelos/patología , Regulación del Desarrollo de la Expresión Génica , Humanos , Infertilidad Masculina/etiología , Masculino , Ratones , Ratones Noqueados , Microtúbulos/metabolismo , Microtúbulos/patología , Proteínas/metabolismo , ARN Interferente Pequeño
5.
Semin Cell Dev Biol ; 24(5): 438-47, 2013 May.
Artículo en Inglés | MEDLINE | ID: mdl-23548731

RESUMEN

Mechanosensation is an evolutionarily ancient sensory modality seen in all main animal groups. Mechanosensation can be mediated by sensory neurons or by dedicated receptor cells that form synapses with sensory neurons. Evidence over the last 15-20 years suggests that both classes of mechanosensory cells can be specified by the atonal class of basic helix-loop-helix transcription factors. In this review we discuss recent work addressing how atonal factors specify mechanosensitive cells in vertebrates and invertebrates, and how the redeployment of these factors underlies the regeneration of mechanosensitive cells in some vertebrate groups.


Asunto(s)
Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/genética , Drosophila melanogaster/fisiología , Células Ciliadas Auditivas/fisiología , Mecanotransducción Celular , Proteínas del Tejido Nervioso/genética , Células Receptoras Sensoriales/fisiología , Vertebrados/fisiología , Factores de Edad , Animales , Secuencia de Bases , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/metabolismo , Proteínas de Drosophila , Drosophila melanogaster/crecimiento & desarrollo , Regulación del Desarrollo de la Expresión Génica , Células Ciliadas Auditivas/citología , Humanos , Datos de Secuencia Molecular , Proteínas del Tejido Nervioso/metabolismo , Células Receptoras Sensoriales/citología , Sinapsis/fisiología , Vertebrados/crecimiento & desarrollo
6.
J Anat ; 227(2): 237-42, 2015 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-26076887

RESUMEN

Much attention has been given to mammalian muscle spindles and their role in stretch-mediated muscle proprioception. Recent studies, particularly, have sought to determine the molecular mediators of stretch-evoked mechanotransduction, which these endings rely upon for functionality. Nonetheless, much about these endings remains unknown. Opportunities may be presented from consideration of extensive parallel research in stretch receptor mechanisms in arthropods. Such systems may provide a useful source of additional data and powerful tools for dissecting the complex systems of stretch transduction apparatus. At the least, such systems provide tractable exemplars of how organisms solve the problem of converting stretch stimuli to electrical output. Potentially, they may even provide molecular mechanisms and candidate molecular mediators of direct relevance to mammalian muscle spindles. Here we provide a brief overview of research on arthropod stretch receptors.


Asunto(s)
Artrópodos/fisiología , Mecanorreceptores/fisiología , Mecanotransducción Celular/fisiología , Husos Musculares/fisiología , Reflejo de Estiramiento/fisiología , Células Receptoras Sensoriales/fisiología , Animales , Propiocepción/fisiología
7.
PLoS Biol ; 9(1): e1000568, 2011 Jan 04.
Artículo en Inglés | MEDLINE | ID: mdl-21283833

RESUMEN

In neurogenesis, neural cell fate specification is generally triggered by proneural transcription factors. Whilst the role of proneural factors in fate specification is well studied, the link between neural specification and the cellular pathways that ultimately must be activated to construct specialised neurons is usually obscure. High-resolution temporal profiling of gene expression reveals the events downstream of atonal proneural gene function during the development of Drosophila chordotonal (mechanosensory) neurons. Among other findings, this reveals the onset of expression of genes required for construction of the ciliary dendrite, a key specialisation of mechanosensory neurons. We determine that atonal activates this cellular differentiation pathway in several ways. Firstly, atonal directly regulates Rfx, a well-known highly conserved ciliogenesis transcriptional regulator. Unexpectedly, differences in Rfx regulation by proneural factors may underlie variations in ciliary dendrite specialisation in different sensory neuronal lineages. In contrast, fd3F encodes a novel forkhead family transcription factor that is exclusively expressed in differentiating chordotonal neurons. fd3F regulates genes required for specialized aspects of chordotonal dendrite physiology. In addition to these intermediate transcriptional regulators, we show that atonal directly regulates a novel gene, dilatory, that is directly associated with ciliogenesis during neuronal differentiation. Our analysis demonstrates how early cell fate specification factors can regulate structural and physiological differentiation of neuronal cell types. It also suggests a model for how subtype differentiation in different neuronal lineages may be regulated by different proneural factors. In addition, it provides a paradigm for how transcriptional regulation may modulate the ciliogenesis pathway to give rise to structurally and functionally specialised ciliary dendrites.


Asunto(s)
Drosophila/metabolismo , Perfilación de la Expresión Génica , Células Receptoras Sensoriales/fisiología , Regulación hacia Arriba , Animales , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/genética , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/metabolismo , Diferenciación Celular , Línea Celular , Cilios/genética , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Drosophila/embriología , Drosophila/crecimiento & desarrollo , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Factores de Transcripción Forkhead/genética , Factores de Transcripción Forkhead/metabolismo , Genes Reporteros , Larva/crecimiento & desarrollo , Larva/metabolismo , Proteínas del Tejido Nervioso/genética , Proteínas del Tejido Nervioso/metabolismo , Factores de Transcripción del Factor Regulador X , Células Receptoras Sensoriales/ultraestructura , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
8.
J Cell Sci ; 124(Pt 15): 2622-30, 2011 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-21750193

RESUMEN

A significant number of ciliary disease genes have been found to encode proteins that localise to the basal body. By contrast, a large number of basal-body-associated proteins remain to be characterised. Here, we report the identification of a new basal body protein that is required for ciliogenesis in Drosophila. Dilatory (DILA) is a predicted coiled-coil protein homologous to vertebrate AZI1 (also known as CEP131). Mutations in dila specifically exhibit defects in ciliated cells (sensory neurons and sperm). Several features of the neuronal phenotype suggest a defect in intraflagellar transport. In sensory neuron cilia, DILA protein localises to the ciliary base, including the basal body and putative transition zone, and it interacts genetically with the ciliary coiled-coil protein, Uncoordinated. These data implicate DILA in regulating intraflagellar transport at the base of sensory cilia.


Asunto(s)
Cilios/metabolismo , Proteínas de Drosophila/metabolismo , Proteínas del Tejido Nervioso/metabolismo , Células Receptoras Sensoriales/metabolismo , Espermatozoides/metabolismo , Animales , Cilios/genética , Cilios/ultraestructura , Drosophila , Proteínas de Drosophila/genética , Inmunohistoquímica , Hibridación in Situ , Masculino , Microscopía Electrónica de Transmisión , Proteínas del Tejido Nervioso/genética , Células Receptoras Sensoriales/ultraestructura , Espermatozoides/ultraestructura
9.
Front Genet ; 13: 943197, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35873488

RESUMEN

Axonemal dynein motors are large multi-subunit complexes that drive ciliary movement. Cytoplasmic assembly of these motor complexes involves several co-chaperones, some of which are related to the R2TP co-chaperone complex. Mutations of these genes in humans cause the motile ciliopathy, Primary Ciliary Dyskinesia (PCD), but their different roles are not completely known. Two such dynein (axonemal) assembly factors (DNAAFs) that are thought to function together in an R2TP-like complex are DNAAF4 (DYX1C1) and DNAAF6 (PIH1D3). Here we investigate the Drosophila homologues, CG14921/Dnaaf4 and CG5048/Dnaaf6. Surprisingly, Drosophila Dnaaf4 is truncated such that it completely lacks a TPR domain, which in human DNAAF4 is likely required to recruit HSP90. Despite this, we provide evidence that Drosophila Dnaaf4 and Dnaaf6 proteins can associate in an R2TP-like complex that has a conserved role in dynein assembly. Both are specifically expressed and required during the development of the two Drosophila cell types with motile cilia: mechanosensory chordotonal neurons and sperm. Flies that lack Dnaaf4 or Dnaaf6 genes are viable but with impaired chordotonal neuron function and lack motile sperm. We provide molecular evidence that Dnaaf4 and Dnaaf6 are required for assembly of outer dynein arms (ODAs) and a subset of inner dynein arms (IDAs).

10.
Sci Rep ; 12(1): 13338, 2022 08 03.
Artículo en Inglés | MEDLINE | ID: mdl-35922464

RESUMEN

The Drosophila chordotonal neuron cilium is the site of mechanosensory transduction. The cilium has a 9 + 0 axoneme structure and is highly sub-compartmentalised, with proximal and distal zones harbouring different TRP channels and the proximal zone axoneme also being decorated with axonemal dynein motor complexes. The activity of the dynein complexes is essential for mechanotransduction. We investigate the localisation of TRP channels and dynein motor complexes during ciliogenesis. Differences in timing of TRP channel localisation correlate with order of construction of the two ciliary zones. Dynein motor complexes are initially not confined to their target proximal zone, but ectopic complexes beyond the proximal zone are later cleared, perhaps by retrograde transport. Differences in transient distal localisation of outer and inner dynein arm complexes (ODAs and IDAs) are consistent with previous suggestions from unicellular eukaryotes of differences in processivity during intraflagellar transport. Stable localisation depends on the targeting of their docking proteins in the proximal zone. For ODA, we characterise an ODA docking complex (ODA-DC) that is targeted directly to the proximal zone. Interestingly, the subunit composition of the ODA-DC in chordotonal neuron cilia appears to be different from the predicted ODA-DC in Drosophila sperm.


Asunto(s)
Cilios , Dineínas , Animales , Cilios/metabolismo , Drosophila/metabolismo , Dineínas/metabolismo , Masculino , Mecanotransducción Celular , Mutación , Semen/metabolismo
11.
Front Cell Dev Biol ; 10: 1016367, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36420143

RESUMEN

Although the lineage-determining ability of transcription factors is often modulated according to cellular context, the mechanisms by which such switching occurs are not well known. Using a transcriptional programming model, we found that Atoh1 is repurposed from a neuronal to an inner ear hair cell (HC) determinant by the combined activities of Gfi1 and Pou4f3. In this process, Atoh1 maintains its regulation of neuronal genes but gains ability to regulate HC genes. Pou4f3 enables Atoh1 access to genomic locations controlling the expression of sensory (including HC) genes, but Atoh1 + Pou4f3 are not sufficient for HC differentiation. Gfi1 is key to the Atoh1-induced lineage switch, but surprisingly does not alter Atoh1's binding profile. Gfi1 acts in two divergent ways. It represses the induction by Atoh1 of genes that antagonise HC differentiation, a function in keeping with its well-known repressor role in haematopoiesis. Remarkably, we find that Gfi1 also acts as a co-activator: it binds directly to Atoh1 at existing target genes to enhance its activity. These findings highlight the diversity of mechanisms by which one TF can redirect the activity of another to enable combinatorial control of cell identity.

12.
BMC Bioinformatics ; 12: 289, 2011 Jul 18.
Artículo en Inglés | MEDLINE | ID: mdl-21767381

RESUMEN

BACKGROUND: Protein-protein interaction (PPI) data are widely used to generate network models that aim to describe the relationships between proteins in biological systems. The fidelity and completeness of such networks is primarily limited by the paucity of protein interaction information and by the restriction of most of these data to just a few widely studied experimental organisms. In order to extend the utility of existing PPIs, computational methods can be used that exploit functional conservation between orthologous proteins across taxa to predict putative PPIs or 'interologs'. To date most interolog prediction efforts have been restricted to specific biological domains with fixed underlying data sources and there are no software tools available that provide a generalised framework for 'on-the-fly' interolog prediction. RESULTS: We introduce Bio::Homology::InterologWalk, a Perl module to retrieve, prioritise and visualise putative protein-protein interactions through an orthology-walk method. The module uses orthology and experimental interaction data to generate putative PPIs and optionally collates meta-data into an Interaction Prioritisation Index that can be used to help prioritise interologs for further analysis. We show the application of our interolog prediction method to the genomic interactome of the fruit fly, Drosophila melanogaster. We analyse the resulting interaction networks and show that the method proposes new interactome members and interactions that are candidates for future experimental investigation. CONCLUSIONS: Our interolog prediction tool employs the Ensembl Perl API and PSICQUIC enabled protein interaction data sources to generate up to date interologs 'on-the-fly'. This represents a significant advance on previous methods for interolog prediction as it allows the use of the latest orthology and protein interaction data for all of the genomes in Ensembl. The module outputs simple text files, making it easy to customise the results by post-processing, allowing the putative PPI datasets to be easily integrated into existing analysis workflows. The Bio::Homology::InterologWalk module, sample scripts and full documentation are freely available from the Comprehensive Perl Archive Network (CPAN) under the GNU Public license.


Asunto(s)
Proteínas de Drosophila/metabolismo , Drosophila melanogaster/metabolismo , Mapeo de Interacción de Proteínas , Proteómica/métodos , Programas Informáticos , Animales , Proteínas de Drosophila/genética , Drosophila melanogaster/química , Genoma de los Insectos
13.
Biol Open ; 10(10)2021 10 15.
Artículo en Inglés | MEDLINE | ID: mdl-34553759

RESUMEN

Ciliary motility is powered by a suite of highly conserved axoneme-specific dynein motor complexes. In humans, the impairment of these motors through mutation results in the disease primary ciliary dyskinesia (PCD). Studies in Drosophila have helped to validate several PCD genes whose products are required for cytoplasmic pre-assembly of axonemal dynein motors. Here we report the characterisation of the Drosophila orthologue of the less-known assembly factor DNAAF3. This gene, CG17669 (Dnaaf3), is expressed exclusively in developing mechanosensory chordotonal (Ch) neurons and the cells that generate spermatozoa, The only two Drosophila cell types bearing cilia/flagella containing dynein motors. Mutation of Dnaaf3 results in larvae that are deaf and adults that are uncoordinated, indicating defective Ch neuron function. The mutant Ch neuron cilia of the antenna specifically lack dynein arms, while Ca imaging in larvae reveals a complete loss of Ch neuron response to vibration stimulus, confirming that mechanotransduction relies on ciliary dynein motors. Mutant males are infertile with immotile sperm whose flagella lack dynein arms and show axoneme disruption. Analysis of proteomic changes suggest a reduction in heavy chains of all axonemal dynein forms, consistent with an impairment of dynein pre-assembly.


Asunto(s)
Dineínas Axonemales/genética , Trastornos de la Motilidad Ciliar/genética , Proteínas de Drosophila/genética , Drosophila/genética , Proteínas Asociadas a Microtúbulos/genética , Animales , Axonema/genética , Cilios/genética , Femenino , Flagelos/genética , Masculino , Mecanotransducción Celular/genética , Mutación
14.
BMC Bioinformatics ; 11: 590, 2010 Dec 03.
Artículo en Inglés | MEDLINE | ID: mdl-21129181

RESUMEN

BACKGROUND: One of the most commonly performed tasks when analysing high throughput gene expression data is to use clustering methods to classify the data into groups. There are a large number of methods available to perform clustering, but it is often unclear which method is best suited to the data and how to quantify the quality of the classifications produced. RESULTS: Here we describe an R package containing methods to analyse the consistency of clustering results from any number of different clustering methods using resampling statistics. These methods allow the identification of the the best supported clusters and additionally rank cluster members by their fidelity within the cluster. These metrics allow us to compare the performance of different clustering algorithms under different experimental conditions and to select those that produce the most reliable clustering structures. We show the application of this method to simulated data, canonical gene expression experiments and our own novel analysis of genes involved in the specification of the peripheral nervous system in the fruitfly, Drosophila melanogaster. CONCLUSIONS: Our package enables users to apply the merged consensus clustering methodology conveniently within the R programming environment, providing both analysis and graphical display functions for exploring clustering approaches. It extends the basic principle of consensus clustering by allowing the merging of results between different methods to provide an averaged clustering robustness. We show that this extension is useful in correcting for the tendency of clustering algorithms to treat outliers differently within datasets. The R package, clusterCons, is freely available at CRAN and sourceforge under the GNU public licence.


Asunto(s)
Perfilación de la Expresión Génica/métodos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Análisis por Conglomerados , Bases de Datos Genéticas , Reconocimiento de Normas Patrones Automatizadas
15.
BMC Dev Biol ; 10: 34, 2010 Mar 26.
Artículo en Inglés | MEDLINE | ID: mdl-20346138

RESUMEN

BACKGROUND: bHLH transcription factors play many roles in neural development. cousin of atonal (cato) encodes one such factor that is expressed widely in the developing sensory nervous system of Drosophila. However, nothing definitive was known of its function owing to the lack of specific mutations. RESULTS: We characterised the expression pattern of cato in detail using newly raised antibodies and GFP reporter gene constructs. Expression is predominantly in sensory lineages that depend on the atonal and amos proneural genes. In lineages that depend on the scute proneural gene, cato is expressed later and seems to be particularly associated with the type II neurons. Consistent with this, we find evidence that cato is a direct target gene of Atonal and Amos, but not of Scute. We generated two specific mutations of cato. Mutant embryos show several defects in chordotonal sensory lineages, most notably the duplication of the sensory neuron, which appears to be caused by an extra cell division. In addition, we show that cato is required to form the single chordotonal organ that persists in atonal mutant embryos. CONCLUSIONS: We conclude that although widely expressed in the developing PNS, cato is expressed and regulated very differently in different sensory lineages. Mutant phenotypes correlate with cato's major expression in the chordotonal sensory lineage. In these cells, we propose that it plays roles in sense organ precursor maintenance and/or identity, and in controlling the number of cell divisions in the neuronal branch of the lineage arising from these precursors.


Asunto(s)
Drosophila melanogaster/embriología , Drosophila melanogaster/metabolismo , Animales , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/genética , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/metabolismo , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Proteínas del Tejido Nervioso/metabolismo , Neurogénesis , Sistema Nervioso Periférico/metabolismo , Células Receptoras Sensoriales/metabolismo
16.
Sci Rep ; 10(1): 7431, 2020 05 04.
Artículo en Inglés | MEDLINE | ID: mdl-32366993

RESUMEN

Age-related hearing loss (ARHL) is a threat to future human wellbeing. Multiple factors contributing to the terminal auditory decline have been identified; but a unified understanding of ARHL - or the homeostatic maintenance of hearing before its breakdown - is missing. We here present an in-depth analysis of homeostasis and ageing in the antennal ears of the fruit fly Drosophila melanogaster. We show that Drosophila, just like humans, display ARHL. By focusing on the phase of dynamic stability prior to the eventual hearing loss we discovered a set of evolutionarily conserved homeostasis genes. The transcription factors Onecut (closest human orthologues: ONECUT2, ONECUT3), Optix (SIX3, SIX6), Worniu (SNAI2) and Amos (ATOH1, ATOH7, ATOH8, NEUROD1) emerged as key regulators, acting upstream of core components of the fly's molecular machinery for auditory transduction and amplification. Adult-specific manipulation of homeostatic regulators in the fly's auditory neurons accelerated - or protected against - ARHL.


Asunto(s)
Envejecimiento , Antenas de Artrópodos/fisiología , Drosophila melanogaster/fisiología , Pérdida Auditiva/genética , Audición/genética , Homeostasis , Neuronas/fisiología , Animales , Proteínas de Drosophila/genética , Femenino , Genotipo , Proteínas de Homeodominio/genética , Humanos , Masculino , Ratones , Factores de Crecimiento Nervioso/genética , Proteínas del Tejido Nervioso/genética , Interferencia de ARN , Análisis de Secuencia de ARN , Sonido , Factores de Tiempo , Transactivadores/genética , Factores de Transcripción/genética , Transcriptoma
17.
Dev Cell ; 7(5): 687-96, 2004 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-15525530

RESUMEN

In Drosophila, commitment of a cell to a sense organ precursor (SOP) fate requires bHLH proneural transcription factor upregulation, a process that depends in most cases on the interplay of proneural gene autoregulation and inhibitory Notch signaling. A subset of SOPs are selected by a recruitment pathway involving EGFR signaling to ectodermal cells expressing the proneural gene atonal. We show that EGFR signaling drives recruitment by directly facilitating atonal autoregulation. Pointed, the transcription factor that mediates EGFR signaling, and Atonal protein itself bind cooperatively to adjacent conserved binding sites in an atonal enhancer. Recruitment is therefore contingent on the combined presence of Atonal protein (providing competence) and EGFR signaling (triggering recruitment). Thus, autoregulation is the nodal control point targeted by signaling. This exemplifies a simple and general mechanism for regulating the transition from competence to cell fate commitment whereby a cell signal directly targets the autoregulation of a selector gene.


Asunto(s)
Drosophila/embriología , Receptores ErbB/metabolismo , Regulación del Desarrollo de la Expresión Génica , Órganos de los Sentidos/embriología , Transducción de Señal , Animales , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico , Sitios de Unión , Proteínas de Unión al ADN/metabolismo , Drosophila/genética , Proteínas de Drosophila , Ensayo de Cambio de Movilidad Electroforética , Elementos de Facilitación Genéticos , Glutatión Transferasa/metabolismo , Proteínas Fluorescentes Verdes/metabolismo , Inmunohistoquímica , Proteínas de la Membrana/metabolismo , Modelos Biológicos , Modelos Moleculares , Proteínas del Tejido Nervioso , Proteínas Proto-Oncogénicas/metabolismo , Receptores Notch , Proteínas Recombinantes de Fusión/metabolismo , Factores de Transcripción/metabolismo , Regulación hacia Arriba
18.
Genes Cells ; 13(9): 915-29, 2008 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-18681894

RESUMEN

The question of how proneural bHLH transcription factors recognize and regulate their target genes is still relatively poorly understood. We previously showed that Scute (Sc) and Atonal (Ato) target genes have different cognate E box motifs, suggesting that specific DNA interactions contribute to differences in their target gene specificity. Here we show that Sc and Ato proteins (in combination with Daughterless) can activate reporter gene expression via their cognate E boxes in a non-neuronal cell culture system, suggesting that the proteins have strong intrinsic abilities to recognize different E box motifs in the absence of specialized cofactors. Functional comparison of E boxes from several target genes and site-directed mutagenesis of E box motifs suggests that specificity and activity require further sequence elements flanking both sides of the previously identified E box motifs. Moreover, the proneural cofactor, Senseless, can augment the function of Sc and Ato on their cognate E boxes and therefore may contribute to proneural specificity.


Asunto(s)
Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/metabolismo , Proteínas de Drosophila/metabolismo , Elementos E-Box/genética , Proteínas Nucleares/metabolismo , Factores de Transcripción/metabolismo , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Animales , Animales Modificados Genéticamente , Secuencia de Bases , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/genética , Sitios de Unión/genética , Células Cultivadas , Drosophila/citología , Drosophila/embriología , Drosophila/genética , Drosophila/metabolismo , Proteínas de Drosophila/genética , Embrión no Mamífero , Genes de Insecto , Genes Reporteros , Proteínas Fluorescentes Verdes/metabolismo , Secuencias Hélice-Asa-Hélice/genética , Inmunohistoquímica , Luciferasas/metabolismo , Datos de Secuencia Molecular , Proteínas Nucleares/genética , Sensibilidad y Especificidad , Factores de Transcripción/genética , Transfección
19.
Front Genet ; 10: 24, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-30774648

RESUMEN

The motile cilium/flagellum is an ancient eukaryotic organelle. The molecular machinery of ciliary motility comprises a variety of cilium-specific dynein motor complexes along with other complexes that regulate their activity. Assembling the motors requires the function of dedicated "assembly factors" and transport processes. In humans, mutation of any one of at least 40 different genes encoding components of the motility apparatus causes Primary Ciliary Dyskinesia (PCD), a disease of defective ciliary motility. Recently, Drosophila has emerged as a model for motile cilia biology and motile ciliopathies. This is somewhat surprising as most Drosophila cells lack cilia, and motile cilia are confined to just two specialized cell types: the sperm flagellum with a 9+2 axoneme and the ciliated dendrite of auditory/proprioceptive (chordotonal, Ch) neurons with a 9+0 axoneme. To determine the utility of Drosophila as a model for motile cilia, we survey the Drosophila genome for ciliary motility gene homologs, and assess their expression and function. We find that the molecules of cilium motility are well conserved in Drosophila. Most are readily characterized by their restricted cell-type specific expression patterns and phenotypes. There are also striking differences between the two motile ciliated cell types. Notably, sperm and Ch neuron cilia express and require entirely different outer dynein arm variants-the first time this has been clearly established in any organism. These differences might reflect the specialized functions for motility in the two cilium types. Moreover, the Ch neuron cilia lack the critical two-headed inner arm dynein (I1/f) but surprisingly retain key regulatory proteins previously associated with it. This may have implications for other motile 9+0 cilia, including vertebrate embryonic nodal cilia required for left-right axis asymmetry. We discuss the possibility that cell-type specificity in ciliary motility machinery might occur in humans, and therefore underlie some of the phenotypic variation observed in PCD caused by different gene mutations. Our work lays the foundation for the increasing use of Drosophila as an excellent model for new motile ciliary gene discovery and validation, for understanding motile cilium function and assembly, as well as understanding the nature of genetic defects underlying human motile ciliopathies.

20.
J Neuroendocrinol ; 31(12): e12807, 2019 12.
Artículo en Inglés | MEDLINE | ID: mdl-31679160

RESUMEN

The interaction of animals with conspecifics, termed social behaviour, has a major impact on the survival of many vertebrate species. Neuropeptide hormones modulate the underlying physiology that governs social interactions, and many findings concerning the neuroendocrine mechanisms of social behaviours have been extrapolated from animal models to humans. Neurones expressing neuropeptides show similar distribution patterns within the hypothalamic nucleus, even when evolutionarily distant species are compared. During evolution, hypothalamic neuropeptides and releasing hormones have retained not only their structures, but also their biological functions, including their effects on behaviour. Here, we review the current understanding of the mechanisms of social behaviours in several classes of animals, such as worms, insects and fish, as well as laboratory, wild and domesticated mammals.


Asunto(s)
Hipotálamo/fisiología , Neuropéptidos/fisiología , Conducta Social , Animales
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