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Abstract
The role of centrioles changes as a function of the cell cycle. Centrioles promote formation of spindle poles in mitosis and act as basal bodies to assemble primary cilia in interphase. Stringent regulations govern conversion between these two states. Although the molecular mechanisms have not been fully elucidated, recent findings have begun to shed light on pathways that regulate the conversion of centrioles to basal bodies and vice versa. Emerging studies also provide insights into how defects in the balance between centrosome and cilia function could promote ciliopathies and cancer.
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Affiliation(s)
- Tetsuo Kobayashi
- Department of Pathology, School of Medicine, New York University Cancer Institute, New York, NY 10016, USA
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52
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zur Lage PI, Simpson TI, Jarman A. Linking specification to differentiation: From proneural genes to the regulation of ciliogenesis. Fly (Austin) 2011; 5:322-6. [PMID: 21558799 DOI: 10.4161/fly.5.4.16159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Much of developmental biology is concerned with the processes by which cells become committed to particular fates in a regulated fashion, whereas cell biology addresses, among other things, the variety of differentiated forms and functions that cells can acquire. One open question is how the regulators of the former process lead to attainment of the latter. 'High-level' regulators of cell fate specification include the proneural factors, which drive cells to commit as precursors in the sensory nervous system. Recent research has concentrated on the gene expression events downstream of proneural factor function. Here we summarise this research and describe our own research that has provided clear links between a proneural factor, atonal, and the cell biological programme of ciliogenesis, which is a central aspect of sensory neuron differentiation.
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Affiliation(s)
- Petra I zur Lage
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
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53
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Ptenb mediates gastrulation cell movements via Cdc42/AKT1 in zebrafish. PLoS One 2011; 6:e18702. [PMID: 21494560 PMCID: PMC3073981 DOI: 10.1371/journal.pone.0018702] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 03/15/2011] [Indexed: 01/12/2023] Open
Abstract
Phosphatidylinositol 3-kinase (PI3 kinase) mediates gastrulation cell migration in zebrafish via its regulation of PIP2/PIP3 balance. Although PI3 kinase counter enzyme PTEN has also been reported to be essential for gastrulation, its role in zebrafish gastrulation has been controversial due to the lack of gastrulation defects in pten-null mutants. To clarify this issue, we knocked down a pten isoform, ptenb by using anti-sense morpholino oligos (MOs) in zebrafish embryos and found that ptenb MOs inhibit convergent extension by affecting cell motility and protrusion during gastrulation. The ptenb MO-induced convergence defect could be rescued by a PI3-kinase inhibitor, LY294002 and by overexpressing dominant negative Cdc42. Overexpression of human constitutively active akt1 showed similar convergent extension defects in zebrafish embryos. We also observed a clear enhancement of actin polymerization in ptenb morphants under cofocal microscopy and in actin polymerization assay. These results suggest that Ptenb by antagonizing PI3 kinase and its downstream Akt1 and Cdc42 to regulate actin polymerization that is critical for proper cell motility and migration control during gastrulation in zebrafish.
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54
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Eberl DF, Kernan MJ. Recording sound-evoked potentials from the Drosophila antennal nerve. Cold Spring Harb Protoc 2011; 2011:prot5576. [PMID: 21363940 DOI: 10.1101/pdb.prot5576] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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55
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Cachero S, Simpson TI, zur Lage PI, Ma L, Newton FG, Holohan EE, Armstrong JD, Jarman AP. The gene regulatory cascade linking proneural specification with differentiation in Drosophila sensory neurons. PLoS Biol 2011; 9:e1000568. [PMID: 21283833 PMCID: PMC3023811 DOI: 10.1371/journal.pbio.1000568] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 11/05/2010] [Indexed: 12/20/2022] Open
Abstract
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.
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Affiliation(s)
- Sebastián Cachero
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - T. Ian Simpson
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Petra I. zur Lage
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Lina Ma
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Fay G. Newton
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Eimear E. Holohan
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - J. Douglas Armstrong
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew P. Jarman
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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56
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Schachter H, Boulianne G. Life is sweet! A novel role for N-glycans in Drosophila lifespan. Fly (Austin) 2011; 5:18-24. [PMID: 21057214 DOI: 10.4161/fly.5.1.13920] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
N-glycans are post-translational modifications in which the sugar chain is covalently linked to protein by a GlcNAcβ1-N-asparagine linkage. Drosophila melanogaster and other invertebrates, but not vertebrates, synthesize large amounts of "paucimannose" N-glycans that contain only three or four mannose residues. The enzyme UDP-GlcNAc:α3-D-mannoside β1,2-N-acetylglucosaminyltransferase I (GnTI, encoded by the Mgat1 gene) controls the synthesis of paucimannose N-glycans. Either deletion or neuron-specific knockdown of Mgat1 in wild type flies results in pronounced defects in locomotion, structural defects in the adult central nervous system and a severely reduced lifespan. We have recently shown that neuronal expression of a wild-type Mgat1 transgene in Mgat1-null flies rescues the structural defects in the brain (fused β-lobes) and the shortened lifespan and, surprisingly, results in a dramatic 135% increase in mean lifespan relative to genetically identical controls that do not express the transgene. In this review, we discuss various approaches that can be used to determine the roles of paucimannose N-glycans in Drosophila longevity and in the adult CNS.
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Affiliation(s)
- Harry Schachter
- Program in Molecular Structure and Function, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
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57
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Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A 2010; 107:21931-6. [PMID: 21106759 DOI: 10.1073/pnas.1016071107] [Citation(s) in RCA: 2904] [Impact Index Per Article: 207.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Developmental programs are controlled by transcription factors and chromatin regulators, which maintain specific gene expression programs through epigenetic modification of the genome. These regulatory events at enhancers contribute to the specific gene expression programs that determine cell state and the potential for differentiation into new cell types. Although enhancer elements are known to be associated with certain histone modifications and transcription factors, the relationship of these modifications to gene expression and developmental state has not been clearly defined. Here we interrogate the epigenetic landscape of enhancer elements in embryonic stem cells and several adult tissues in the mouse. We find that histone H3K27ac distinguishes active enhancers from inactive/poised enhancer elements containing H3K4me1 alone. This indicates that the amount of actively used enhancers is lower than previously anticipated. Furthermore, poised enhancer networks provide clues to unrealized developmental programs. Finally, we show that enhancers are reset during nuclear reprogramming.
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58
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Abstract
In animals, RFX transcription factors govern ciliogenesis by binding to an X-box motif in the promoters of ciliogenic genes. In Caenorhabditis elegans, the sole RFX transcription factor (TF) daf-19 null mutant lacks all sensory cilia, fails to express many ciliogenic genes, and is defective in many sensory behaviors, including male mating. The daf-19c isoform is expressed in all ciliated sensory neurons and is necessary and sufficient for activating X-box containing ciliogenesis genes. Here, we describe the daf-19(n4132) mutant that is defective in expression of the sensory polycystic kidney disease (PKD) gene battery and male mating behavior, without affecting expression of ciliogenic genes or ciliogenesis. daf-19(n4132) disrupts expression of a new isoform, daf-19m (for function in male mating). daf-19m is expressed in male-specific PKD and core IL2 neurons via internal promoters and remote enhancer elements located in introns of the daf-19 genomic locus. daf-19m genetically programs the sensory functions of a subset of ciliated neurons, independent of daf-19c. In the male-specific HOB neuron, DAF-19(M) acts downstream of the zinc finger TF EGL-46, indicating that a TF cascade controls the PKD gene battery in this cell-type specific context. We conclude that the RFX TF DAF-19 regulates ciliogenesis via X-box containing ciliogenic genes and controls ciliary specialization by regulating non-X-box containing sensory genes. This study reveals a more extensive role for RFX TFs in generating fully functional cilia.
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59
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Transcriptional control of genes involved in ciliogenesis: a first step in making cilia. Biol Cell 2010; 102:499-513. [PMID: 20690903 DOI: 10.1042/bc20100035] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cilia and flagella have essential functions in a wide range of organisms. Cilia assembly is dynamic during development and different types of cilia are found in multicellular organisms. How this dynamic and specific assembly is regulated remains an important question in cilia biology. In metazoans, the regulation of the overall expression level of key components necessary for cilia assembly or function is an important way to achieve ciliogenesis control. The FOXJ1 (forkhead box J1) and RFX (regulatory factor X) family of transcription factors have been shown to be important players in controlling ciliary gene expression. They fulfill a complementary and synergistic function by regulating specific and common target genes. FOXJ1 is essential to allow for the assembly of motile cilia in vertebrates through the regulation of genes specific to motile cilia or necessary for basal body apical transport, whereas RFX proteins are necessary to assemble both primary and motile cilia in metazoans, in particular, by regulating genes involved in intraflagellar transport. Recently, different transcription factors playing specific roles in cilia biogenesis and physiology have also been discovered. All these factors are subject to complex regulation to allow for the dynamic and specific regulation of ciliogenesis in metazoans.
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60
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Hsu YC, Liao WC, Kao CY, Chiu IM. Regulation of FGF1 gene promoter through transcription factor RFX1. J Biol Chem 2010; 285:13885-95. [PMID: 20189986 PMCID: PMC2859551 DOI: 10.1074/jbc.m109.081463] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 01/20/2010] [Indexed: 12/11/2022] Open
Abstract
Fibroblast growth factor 1 (FGF1) has been suggested to have an important role in cell growth, proliferation, and neurogenesis. Human FGF1 gene 1B promoter (-540 to +31)-driven green fluorescence (F1BGFP) has been shown to monitor endogenous FGF1 expression. F1BGFP could also be used to isolate neural stem/progenitor cells from embryonic, neonatal, and adult mouse brains or to isolate glioblastoma stem cells (GBM-SCs) from human glioblastoma tissues. Here, we present evidence that transcription factor RFX1 could bind the 18-bp cis-elements (-484 to -467) of the F1B promoter, modulate F1BGFP expression and endogenous FGF1 expression, and further regulate the maintenance of GBM-SCs. These observations were substantiated by using yeast one-hybrid assay, electrophoretic mobility shift assay, chromatin immunoprecipitation assay, gain- and loss-of-function assays, and neurosphere assays. Overexpression of RFX1 was shown to down-regulate FGF-1B mRNA expression and neurosphere formation in human glioblastoma cells, whereas RNA interference knockdown of RFX1 demonstrated the opposite effects. Our findings provide insight into FGF1 gene regulation and suggest that the roles of FGF1 and RFX1 in the maintenance of GBM-SCs. RFX1 may negatively regulate the self-renewal of GBM-SCs through modulating FGF-1B and FGF1 expression levels by binding the 18-bp cis-elements of the F1B promoter.
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Affiliation(s)
- Yi-Chao Hsu
- From the Division of Regenerative Medicine, Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Miaoli County 35053, Taiwan
| | - Wei-Chih Liao
- From the Division of Regenerative Medicine, Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Miaoli County 35053, Taiwan
- the Graduate Program of Biotechnology in Medicine, Institute of Biotechnology, and Department of Life Sciences, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chien-Yu Kao
- From the Division of Regenerative Medicine, Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Miaoli County 35053, Taiwan
- the Graduate Program of Biotechnology in Medicine, Institute of Biotechnology, and Department of Life Sciences, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ing-Ming Chiu
- From the Division of Regenerative Medicine, Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Miaoli County 35053, Taiwan
- the Graduate Program of Biotechnology in Medicine, Institute of Biotechnology, and Department of Life Sciences, National Tsing Hua University, Hsinchu 30013, Taiwan
- the Department of Internal Medicine and Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, and
- the Department of Life Sciences, National Chung Hsing University, Taichung 250, Taiwan
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61
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Purvis TL, Hearn T, Spalluto C, Knorz VJ, Hanley KP, Sanchez-Elsner T, Hanley NA, Wilson DI. Transcriptional regulation of the Alström syndrome gene ALMS1 by members of the RFX family and Sp1. Gene 2010; 460:20-9. [PMID: 20381594 PMCID: PMC2913254 DOI: 10.1016/j.gene.2010.03.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 02/17/2010] [Accepted: 03/31/2010] [Indexed: 01/26/2023]
Abstract
Mutations in the human gene ALMS1 cause Alström syndrome, a disorder characterised by neurosensory degeneration, metabolic defects and cardiomyopathy. ALMS1 encodes a centrosomal protein implicated in the assembly and maintenance of primary cilia. Expression of ALMS1 varies between tissues and recent data suggest that its transcription is modulated during adipogenesis and growth arrest. However the ALMS1 promoter has not been defined. This study focused on identifying and characterising the ALMS1 proximal promoter, initially by using 5' RACE to map transcription start sites. Luciferase reporter assay and EMSA data strongly suggest that ALMS1 transcription is regulated by the ubiquitous factor Sp1. In addition, reporter assay, EMSA, chromatin immunoprecipitation and RNA interference data indicate that ALMS1 transcription is regulated by regulatory factor X (RFX) proteins. These transcription factors are cell-type restricted in their expression profile and known to regulate genes of the ciliogenic pathway. We show binding of RFX proteins to an evolutionarily conserved X-box in the ALMS1 proximal promoter and present evidence that these proteins are responsible for ALMS1 transcription during growth arrest induced by low serum conditions. In summary, this work provides the first data on transcription factors regulating general and context-specific transcription of the disease-associated gene ALMS1.
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Affiliation(s)
- Tracey L Purvis
- Centre for Human Development, Stem Cells and Regeneration, Human Genetics Division, University of Southampton, UK
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62
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Hearing in Drosophila requires TilB, a conserved protein associated with ciliary motility. Genetics 2010; 185:177-88. [PMID: 20215474 DOI: 10.1534/genetics.110.114009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Cilia were present in the earliest eukaryotic ancestor and underlie many biological processes ranging from cell motility and propulsion of extracellular fluids to sensory physiology. We investigated the contribution of the touch insensitive larva B (tilB) gene to cilia function in Drosophila melanogaster. Mutants of tilB exhibit dysfunction in sperm flagella and ciliated dendrites of chordotonal organs that mediate hearing and larval touch sensitivity. Mutant sperm axonemes as well as sensory neuron dendrites of Johnston's organ, the fly's auditory organ, lack dynein arms. Through deficiency mapping and sequencing candidate genes, we identified tilB mutations in the annotated gene CG14620. A genomic CG14620 transgene rescued deafness and male sterility of tilB mutants. TilB is a 395-amino-acid protein with a conserved N-terminal leucine-rich repeat region at residues 16-164 and a coiled-coil domain at residues 171-191. A tilB-Gal4 transgene driving fluorescently tagged TilB proteins elicits cytoplasmic expression in embryonic chordotonal organs, in Johnston's organ, and in sperm flagella. TilB does not appear to affect tubulin polyglutamylation or polyglycylation. The phenotypes and expression of tilB indicate function in cilia construction or maintenance, but not in intraflagellar transport. This is also consistent with phylogenetic association of tilB homologs with presence of genes encoding axonemal dynein arm components. Further elucidation of tilB functional mechanisms will provide greater understanding of cilia function and will facilitate understanding ciliary diseases.
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63
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The RFX protein RfxA is an essential regulator of growth and morphogenesis in Penicillium marneffei. EUKARYOTIC CELL 2010; 9:578-91. [PMID: 20118209 DOI: 10.1128/ec.00226-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fungi are small eukaryotes capable of undergoing multiple complex developmental programs. The opportunistic human pathogen Penicillium marneffei is a dimorphic fungus, displaying vegetative (proliferative) multicellular hyphal growth at 25 degrees C and unicellular yeast growth at 37 degrees C. P. marneffei also undergoes asexual development into differentiated multicellular conidiophores bearing uninucleate spores. These morphogenetic processes require regulated changes in cell polarity establishment, cell cycle dynamics, and nuclear migration. The RFX (regulatory factor X) proteins are a family of transcriptional regulators in eukaryotes. We sought to determine how the sole P. marneffei RFX protein, RfxA, contributes to the regulation of morphogenesis. Attempts to generate a haploid rfxA deletion strain were unsuccessful, but we did isolate an rfxA(+)/rfxADelta heterozygous diploid strain. The role of RfxA was assessed using conditional overexpression, RNA interference (RNAi), and the production of dominant interfering alleles. Reduced RfxA function resulted in defective mitoses during growth at 25 degrees C and 37 degrees C. This was also observed for the heterozygous diploid strain during growth at 37 degrees C. In contrast, overexpression of rfxA caused growth arrest during conidial germination. The data show that rfxA must be precisely regulated for appropriate nuclear division and to maintain genome integrity. Perturbations in rfxA expression also caused defects in cellular proliferation and differentiation. The data suggest a role for RfxA in linking cellular division with morphogenesis, particularly during conidiation and yeast growth, where the uninucleate state of these cell types necessitates coupling of nuclear and cellular division tighter than that observed during multinucleate hyphal growth.
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64
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Soyer J, Flasse L, Raffelsberger W, Beucher A, Orvain C, Peers B, Ravassard P, Vermot J, Voz ML, Mellitzer G, Gradwohl G. Rfx6 is an Ngn3-dependent winged helix transcription factor required for pancreatic islet cell development. Development 2010; 137:203-12. [PMID: 20040487 DOI: 10.1242/dev.041673] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The transcription factor neurogenin 3 (Neurog3 or Ngn3) controls islet cell fate specification in multipotent pancreatic progenitor cells in the mouse embryo. However, our knowledge of the genetic programs implemented by Ngn3, which control generic and islet subtype-specific properties, is still fragmentary. Gene expression profiling in isolated Ngn3-positive progenitor cells resulted in the identification of the uncharacterized winged helix transcription factor Rfx6. Rfx6 is initially expressed broadly in the gut endoderm, notably in Pdx1-positive cells in the developing pancreatic buds, and then becomes progressively restricted to the endocrine lineage, suggesting a dual function in both endoderm development and islet cell differentiation. Rfx6 is found in postmitotic islet progenitor cells in the embryo and is maintained in all developing and adult islet cell types. Rfx6 is dependent on Ngn3 and acts upstream of or in parallel with NeuroD, Pax4 and Arx transcription factors during islet cell differentiation. In zebrafish, the Rfx6 ortholog is similarly found in progenitors and hormone expressing cells of the islet lineage. Loss-of-function studies in zebrafish revealed that rfx6 is required for the differentiation of glucagon-, ghrelin- and somatostatin-expressing cells, which, in the absence of rfx6, are blocked at the progenitor stage. By contrast, beta cells, whose number is only slightly reduced, were no longer clustered in a compact islet. These data unveil Rfx6 as a novel regulator of islet cell development.
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Affiliation(s)
- Josselin Soyer
- Institute of Genetics and Molecular and Cell Biology (IGBMC), Inserm U-964, CNRS UMR7104, University of Strasbourg, Illkirch, France
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65
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Ashique AM, Choe Y, Karlen M, May SR, Phamluong K, Solloway MJ, Ericson J, Peterson AS. The Rfx4 transcription factor modulates Shh signaling by regional control of ciliogenesis. Sci Signal 2009; 2:ra70. [PMID: 19887680 DOI: 10.1126/scisignal.2000602] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Regulatory factor X (Rfx) homologs regulate the transcription of genes necessary for ciliogenesis in invertebrates and vertebrates. Primary cilia are necessary for Hedgehog signaling and regulation of the activity of the transcriptional regulators known as Gli proteins, which are targets of Hedgehog signaling. Here, we describe an Rfx4(L298P) mouse mutant with distinct dorsoventral patterning defects in the ventral spinal cord and telencephalon due to aberrant Sonic hedgehog (Shh) signaling and Gli3 activity. We find that Ift172, which encodes an intraflagellar transport protein necessary for ciliogenesis, is a direct transcriptional target of Rfx4, and the decrease in its expression in the developing telencephalon and spinal cord of Rfx4(L298P) mutants correlates with defects in patterning and cilia formation. Our data indicate that Rfx4 is a regionally specific transcriptional regulator of ciliogenesis and thus is also a regionally specific modulator of Shh signaling during development of the central nervous system.
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Affiliation(s)
- Amir M Ashique
- Department of Molecular Biology, Genentech, South San Francisco, CA 94080, USA
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66
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Stevens NR, Dobbelaere J, Wainman A, Gergely F, Raff JW. Ana3 is a conserved protein required for the structural integrity of centrioles and basal bodies. ACTA ACUST UNITED AC 2009; 187:355-63. [PMID: 19948479 PMCID: PMC2779252 DOI: 10.1083/jcb.200905031] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recent studies have identified a conserved "core" of proteins that are required for centriole duplication. A small number of additional proteins have recently been identified as potential duplication factors, but it is unclear whether any of these proteins are components of the core duplication machinery. In this study, we investigate the function of one of these proteins, Drosophila melanogaster Ana3. We show that Ana3 is present in centrioles and basal bodies, but its behavior is distinct from that of the core duplication proteins. Most importantly, we find that Ana3 is required for the structural integrity of both centrioles and basal bodies and for centriole cohesion, but it is not essential for centriole duplication. We show that Ana3 has a mammalian homologue, Rotatin, that also localizes to centrioles and basal bodies and appears to be essential for cilia function. Thus, Ana3 defines a conserved family of centriolar proteins and plays an important part in ensuring the structural integrity of centrioles and basal bodies.
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67
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El Zein L, Ait-Lounis A, Morlé L, Thomas J, Chhin B, Spassky N, Reith W, Durand B. RFX3 governs growth and beating efficiency of motile cilia in mouse and controls the expression of genes involved in human ciliopathies. J Cell Sci 2009; 122:3180-9. [PMID: 19671664 DOI: 10.1242/jcs.048348] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cilia are cellular organelles that play essential physiological and developmental functions in various organisms. They can be classified into two categories, primary cilia and motile cilia, on the basis of their axonemal architecture. Regulatory factor X (RFX) transcription factors have been shown to be involved in the assembly of primary cilia in Caenorhabditis elegans, Drosophila and mice. Here, we have taken advantage of a novel primary-cell culture system derived from mouse brain to show that RFX3 is also necessary for biogenesis of motile cilia. We found that the growth and beating efficiencies of motile cilia are impaired in multiciliated Rfx3(-/-) cells. RFX3 was required for optimal expression of the FOXJ1 transcription factor, a key player in the differentiation program of motile cilia. Furthermore, we demonstrate for the first time that RFX3 regulates the expression of axonemal dyneins involved in ciliary motility by binding directly to the promoters of their genes. In conclusion, RFX proteins not only regulate genes involved in ciliary assembly, but also genes that are involved in ciliary motility and that are associated with ciliopathies such as primary ciliary dyskinesia in humans.
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68
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Intraflagellar transport and the generation of dynamic, structurally and functionally diverse cilia. Trends Cell Biol 2009; 19:306-16. [DOI: 10.1016/j.tcb.2009.04.002] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 04/21/2009] [Accepted: 04/22/2009] [Indexed: 01/25/2023]
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69
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Feng C, Xu W, Zuo Z. Knockout of the regulatory factor X1 gene leads to early embryonic lethality. Biochem Biophys Res Commun 2009; 386:715-7. [PMID: 19559676 DOI: 10.1016/j.bbrc.2009.06.111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 06/21/2009] [Indexed: 11/30/2022]
Abstract
The biological function of regulatory factor X1 (RFX1), the prototype member of the transcription factor RFX family, is not clear. We have used gene trap technique to disrupt the expression of RFX1 in mice. Although, heterozygous RFX1(+/-) mice appear normal and fertile, homozygous RFX1(-/-) embryos died at an early stage (most likely before embryonic day 2.5). Our results indicate that RFX1 regulates expression of genes that are essential for early embryonic development/survival and that RFX1 function can not be compensated by other RFX1 family members.
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Affiliation(s)
- Chenzhuo Feng
- Department of Anesthesiology, School of Medicine, University of Virginia, Charlottesville, VA, USA
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Huh MS, Todd MAM, Picketts DJ. SCO-ping out the mechanisms underlying the etiology of hydrocephalus. Physiology (Bethesda) 2009; 24:117-26. [PMID: 19364914 DOI: 10.1152/physiol.00039.2008] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The heterogeneous nature of congenital hydrocephalus has hampered our understanding of the molecular basis of this common clinical problem. However, disease gene identification and characterization of multiple transgenic mouse models has highlighted the importance of the subcommissural organ (SCO) and the ventricular ependymal (vel) cells. Here, we review how altered development and function of the SCO and vel cells contributes to hydrocephalus.
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Affiliation(s)
- Michael S Huh
- Regenerative Medicine Program, Ottawa Health Research Institute, Canada
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71
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Rotureau B, Morales MA, Bastin P, Späth GF. The flagellum-mitogen-activated protein kinase connection in Trypanosomatids: a key sensory role in parasite signalling and development? Cell Microbiol 2009; 11:710-8. [DOI: 10.1111/j.1462-5822.2009.01295.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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72
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Dennis MY, Paracchini S, Scerri TS, Prokunina-Olsson L, Knight JC, Wade-Martins R, Coggill P, Beck S, Green ED, Monaco AP. A common variant associated with dyslexia reduces expression of the KIAA0319 gene. PLoS Genet 2009; 5:e1000436. [PMID: 19325871 PMCID: PMC2653637 DOI: 10.1371/journal.pgen.1000436] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 02/24/2009] [Indexed: 11/19/2022] Open
Abstract
Numerous genetic association studies have implicated the KIAA0319 gene on human chromosome 6p22 in dyslexia susceptibility. The causative variant(s) remains unknown but may modulate gene expression, given that (1) a dyslexia-associated haplotype has been implicated in the reduced expression of KIAA0319, and (2) the strongest association has been found for the region spanning exon 1 of KIAA0319. Here, we test the hypothesis that variant(s) responsible for reduced KIAA0319 expression resides on the risk haplotype close to the gene's transcription start site. We identified seven single-nucleotide polymorphisms on the risk haplotype immediately upstream of KIAA0319 and determined that three of these are strongly associated with multiple reading-related traits. Using luciferase-expressing constructs containing the KIAA0319 upstream region, we characterized the minimal promoter and additional putative transcriptional regulator regions. This revealed that the minor allele of rs9461045, which shows the strongest association with dyslexia in our sample (max p-value = 0.0001), confers reduced luciferase expression in both neuronal and non-neuronal cell lines. Additionally, we found that the presence of this rs9461045 dyslexia-associated allele creates a nuclear protein-binding site, likely for the transcriptional silencer OCT-1. Knocking down OCT-1 expression in the neuronal cell line SHSY5Y using an siRNA restores KIAA0319 expression from the risk haplotype to nearly that seen from the non-risk haplotype. Our study thus pinpoints a common variant as altering the function of a dyslexia candidate gene and provides an illustrative example of the strategic approach needed to dissect the molecular basis of complex genetic traits. Dyslexia, or reading disability, is a common disorder caused by both genetic and environmental factors. Genetic studies have implicated a number of genes as candidates for playing a role in dyslexia. We functionally characterized one such gene (KIAA0319) to identify variant(s) that might affect gene expression and contribute to the disorder. We discovered a variant residing outside of the protein-coding region of KIAA0319 that reduces expression of the gene. This variant creates a binding site for the transcription factor OCT-1. Previous studies have shown that OCT-1 binding to a specific DNA sequence upstream of a gene can reduce the expression of that gene. In this case, reduced KIAA0319 expression could lead to improper development of regions of the brain involved in reading ability. This is the first study to identify a functional variant implicated in dyslexia. More broadly, our study illustrates the steps that can be utilized for identifying mutations causing other complex genetic disorders.
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Affiliation(s)
- Megan Y. Dennis
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Silvia Paracchini
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Thomas S. Scerri
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland, United States of America
| | - Julian C. Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Richard Wade-Martins
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
| | - Penny Coggill
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Eric D. Green
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (EDG); (APM)
| | - Anthony P. Monaco
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (EDG); (APM)
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Yu X, Ng CP, Habacher H, Roy S. Foxj1 transcription factors are master regulators of the motile ciliogenic program. Nat Genet 2008; 40:1445-53. [PMID: 19011630 DOI: 10.1038/ng.263] [Citation(s) in RCA: 336] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 08/28/2008] [Indexed: 11/09/2022]
Abstract
Motile cilia induce fluid movement through their rhythmic beating activity. In mammals, the transcription factor Foxj1 has been implicated in motile cilia formation. Here we show that a zebrafish Foxj1 homolog, foxj1a, is a target of Hedgehog signaling in the floor plate. Loss of Foxj1a compromises the assembly of motile cilia that decorate floor plate cells. Besides the floor plate, foxj1a is expressed in Kupffer's vesicle and pronephric ducts, where it also promotes ciliary differentiation. We show that Foxj1a activates a constellation of genes essential for motile cilia formation and function, and that its activity is sufficient for ectopic development of cilia that resemble motile cilia. We also document that a paralogous gene, foxj1b, is expressed in the otic vesicle and seems to regulate motile cilia formation in this tissue. Our findings identify a dedicated master regulatory role for Foxj1 in the transcriptional program that controls the production of motile cilia.
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Affiliation(s)
- Xianwen Yu
- Institute of Molecular and Cell Biology, Cancer and Developmental Cell Biology Division, Proteos, Singapore
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74
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Senti G, Swoboda P. Distinct isoforms of the RFX transcription factor DAF-19 regulate ciliogenesis and maintenance of synaptic activity. Mol Biol Cell 2008; 19:5517-28. [PMID: 18843046 DOI: 10.1091/mbc.e08-04-0416] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Neurons form elaborate subcellular structures such as dendrites, axons, cilia, and synapses to receive signals from their environment and to transmit them to the respective target cells. In the worm Caenorhabditis elegans, lack of the RFX transcription factor DAF-19 leads to the absence of cilia normally found on 60 sensory neurons. We now describe and functionally characterize three different isoforms of DAF-19. The short isoform DAF-19C is specifically expressed in ciliated sensory neurons and sufficient to rescue all cilia-related phenotypes of daf-19 mutants. In contrast, the long isoforms DAF-19A/B function in basically all nonciliated neurons. We discovered behavioral and cellular phenotypes in daf-19 mutants that depend on the isoforms daf-19a/b. These novel synaptic maintenance phenotypes are reminiscent of synaptic decline seen in many human neurodegenerative disorders. The C. elegans daf-19 mutant worms can thus serve as a molecular model for the mechanisms of functional neuronal decline.
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Affiliation(s)
- Gabriele Senti
- Department of Biosciences and Nutrition, Karolinska Institute, S-14157 Huddinge, Sweden
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75
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Revealing the anti-HRP epitope in Drosophila and Caenorhabditis. Glycoconj J 2008; 26:385-95. [PMID: 18726691 DOI: 10.1007/s10719-008-9155-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 05/19/2008] [Accepted: 05/27/2008] [Indexed: 10/21/2022]
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76
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Abstract
Because life is often unpredictable, dynamic, and complex, all animals have evolved remarkable abilities to cope with changes in their external environment and internal physiology. This regulatory plasticity leads to shifts in behavior and metabolism, as well as to changes in development, growth, and reproduction, which is thought to improve the chances of survival and reproductive success. In favorable environments, the nematode Caenorhabditis elegans develops rapidly to reproductive maturity, but in adverse environments, animals arrest at the dauer diapause, a long-lived stress resistant stage. A molecular and genetic analysis of dauer formation has revealed key insights into how sensory and dietary cues are coupled to conserved endocrine pathways, including insulin/IGF, TGF-beta, serotonergic, and steroid hormone signal transduction, which govern the choice between reproduction and survival. These and other pathways reveal a molecular basis for metazoan plasticity in response to extrinsic and intrinsic signals.
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Affiliation(s)
- Nicole Fielenbach
- Huffington Center on Aging, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Adam Antebi
- Huffington Center on Aging, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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77
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Aftab S, Semenec L, Chu JSC, Chen N. Identification and characterization of novel human tissue-specific RFX transcription factors. BMC Evol Biol 2008; 8:226. [PMID: 18673564 PMCID: PMC2533330 DOI: 10.1186/1471-2148-8-226] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 08/01/2008] [Indexed: 02/06/2023] Open
Abstract
Background Five regulatory factor X (RFX) transcription factors (TFs)–RFX1-5–have been previously characterized in the human genome, which have been demonstrated to be critical for development and are associated with an expanding list of serious human disease conditions including major histocompatibility (MHC) class II deficiency and ciliaophathies. Results In this study, we have identified two additional RFX genes–RFX6 and RFX7–in the current human genome sequences. Both RFX6 and RFX7 are demonstrated to be winged-helix TFs and have well conserved RFX DNA binding domains (DBDs), which are also found in winged-helix TFs RFX1-5. Phylogenetic analysis suggests that the RFX family in the human genome has undergone at least three gene duplications in evolution and the seven human RFX genes can be clearly categorized into three subgroups: (1) RFX1-3, (2) RFX4 and RFX6, and (3) RFX5 and RFX7. Our functional genomics analysis suggests that RFX6 and RFX7 have distinct expression profiles. RFX6 is expressed almost exclusively in the pancreatic islets, while RFX7 has high ubiquitous expression in nearly all tissues examined, particularly in various brain tissues. Conclusion The identification and further characterization of these two novel RFX genes hold promise for gaining critical insight into development and many disease conditions in mammals, potentially leading to identification of disease genes and biomarkers.
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Affiliation(s)
- Syed Aftab
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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78
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Giansanti MG, Bucciarelli E, Bonaccorsi S, Gatti M. Drosophila SPD-2 is an essential centriole component required for PCM recruitment and astral-microtubule nucleation. Curr Biol 2008; 18:303-9. [PMID: 18291647 DOI: 10.1016/j.cub.2008.01.058] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 01/04/2008] [Accepted: 01/24/2008] [Indexed: 12/12/2022]
Abstract
SPD-2 is a C. elegans centriolar protein required for both centriole duplication and pericentriolar material (PCM) recruitment [1-4]. SPD-2 is conserved in Drosophila (DSpd-2) and is a component of the fly centriole [5-7]. The analysis of a P element-induced hypomorphic mutation has shown that DSpd-2 is primarily required for PCM recruitment at the sperm centriole but is dispensable for both centriole duplication and aster formation [5]. Here we show that null mutations carrying early stop codons in the DSpd-2 coding sequence suppress astral microtubule (MT) nucleation in both neuroblasts (NBs) and spermatocytes. These mutations also disrupt proper Miranda localization in dividing NBs, as previously observed in mutants lacking astral MTs [8-10]. Spermatocyte analysis revealed that DSpd-2 is enriched at both the centrioles and the PCM and is required for the maintenance of cohesion between the two centrioles but not for centriole duplication. We found that DSpd-2 localization at the centrosome requires the wild-type activity of Asl but is independent of the function of D-PLP, Cnn, gamma-tubulin, DGrip91, and D-TACC. Conversely, DSpd-2 mutants displayed normal centrosomal accumulations of Asl and D-PLP, strongly reduced amounts of Cnn, gamma-tubulin, and DGrip91, and diffuse localization of D-TACC. These results indicate that DSpd-2 functions in a very early step of the PCM recruitment pathway.
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Affiliation(s)
- Maria Grazia Giansanti
- Dipartimento di Genetica e Biologia Molecolare, Università di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
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79
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Barreau C, Benson E, Gudmannsdottir E, Newton F, White-Cooper H. Post-meiotic transcription in Drosophila testes. Development 2008; 135:1897-902. [DOI: 10.1242/dev.021949] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Post-meiotic transcription was accepted to be essentially absent from Drosophila spermatogenesis. We identify 24 Drosophila genes whose mRNAs are most abundant in elongating spermatids. By single-cyst quantitative RT-PCR, we demonstrate post-meiotic transcription of these genes. We conclude that transcription stops in Drosophila late primary spermatocytes, then is reactivated by two pathways for a few loci just before histone-to-transition protein-to-protamine chromatin remodelling in spermiogenesis. These mRNAs localise to a small region at the distal elongating end of the spermatid bundles, thus they represent a new class of sub-cellularly localised mRNAs. Mutants for a post-meiotically transcribed gene (scotti), are male sterile, and show spermatid individualisation defects, indicating a function in late spermiogenesis.
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Affiliation(s)
- Carine Barreau
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Elizabeth Benson
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Elin Gudmannsdottir
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Fay Newton
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Helen White-Cooper
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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80
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Raya Á, Izpisúa Belmonte JC. Insights into the establishment of left–right asymmetries in vertebrates. ACTA ACUST UNITED AC 2008; 84:81-94. [DOI: 10.1002/bdrc.20122] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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81
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Laurençon A, Dubruille R, Efimenko E, Grenier G, Bissett R, Cortier E, Rolland V, Swoboda P, Durand B. Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species. Genome Biol 2008; 8:R195. [PMID: 17875208 PMCID: PMC2375033 DOI: 10.1186/gb-2007-8-9-r195] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Revised: 09/14/2007] [Accepted: 09/17/2007] [Indexed: 01/02/2023] Open
Abstract
An RFX-binding site is shown to be conserved in the promoters of a subset of ciliary genes and a subsequent screen for this site in two Drosophila species identified novel RFX target genes that are involved in sensory ciliogenesis. Background Regulatory factor X (RFX) transcription factors play a key role in ciliary assembly in nematode, Drosophila and mouse. Using the tremendous advantages of comparative genomics in closely related species, we identified novel genes regulated by dRFX in Drosophila. Results We first demonstrate that a subset of known ciliary genes in Caenorhabditis elegans and Drosophila are regulated by dRFX and have a conserved RFX binding site (X-box) in their promoters in two highly divergent Drosophila species. We then designed an X-box consensus sequence and carried out a genome wide computer screen to identify novel genes under RFX control. We found 412 genes that share a conserved X-box upstream of the ATG in both species, with 83 genes presenting a more restricted consensus. We analyzed 25 of these 83 genes, 16 of which are indeed RFX target genes. Two of them have never been described as involved in ciliogenesis. In addition, reporter construct expression analysis revealed that three of the identified genes encode proteins specifically localized in ciliated endings of Drosophila sensory neurons. Conclusion Our X-box search strategy led to the identification of novel RFX target genes in Drosophila that are involved in sensory ciliogenesis. We also established a highly valuable Drosophila cilia and basal body dataset. These results demonstrate the accuracy of the X-box screen and will be useful for the identification of candidate genes for human ciliopathies, as several human homologs of RFX target genes are known to be involved in diseases, such as Bardet-Biedl syndrome.
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Affiliation(s)
- Anne Laurençon
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
| | - Raphaëlle Dubruille
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
- University of Massachusetts Medical School, Department of Neurobiology, Worcester, MA 01605, USA
| | - Evgeni Efimenko
- Karolinska Institute, Department of Biosciences and Nutrition, Södertörn University College, School of Life Sciences, S-14189 Huddinge, Sweden
| | - Guillaume Grenier
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
| | - Ryan Bissett
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
- University of Glasgow, Glasgow Biomedical Research Centre, Wellcome Centre for Molecular Parasitology and Infection and Immunity, Glasgow G12 8TA, UK
| | - Elisabeth Cortier
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
| | - Vivien Rolland
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
| | - Peter Swoboda
- Karolinska Institute, Department of Biosciences and Nutrition, Södertörn University College, School of Life Sciences, S-14189 Huddinge, Sweden
| | - Bénédicte Durand
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
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Bae YK, Barr MM. Sensory roles of neuronal cilia: cilia development, morphogenesis, and function in C. elegans. FRONTIERS IN BIOSCIENCE : A JOURNAL AND VIRTUAL LIBRARY 2008; 13:5959-74. [PMID: 18508635 PMCID: PMC3124812 DOI: 10.2741/3129] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In the free-living nematode Caenorhabditis elegans, cilia are found on the dendritic endings of sensory neurons. C. elegans cilia are classified as 'primary' or 'sensory' according to the '9+0' axonemal ultrastructure (nine doublet outer microtubules with no central microtubule pair) and lack of motility, characteristics of '9+2' cilia. The C. elegans ciliated nervous system allows the animal to perceive environmental stimuli and make appropriate developmental, physiological, and behavioral decisions. In vertebrates, the biological significance of primary cilia had been largely neglected. Recent findings have placed primary/sensory cilia in the center of cellular signaling and developmental processes. Studies using genetic model organisms such as C. elegans identified the link between ciliary dysfunction and human ciliopathies. Future studies in the worm will address important basic questions regarding ciliary development, morphogenesis, specialization, and signaling functions.
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Affiliation(s)
- Young-Kyung Bae
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
- Department of Genetics and The Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Maureen M. Barr
- Department of Genetics and The Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854, USA
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83
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Zhang D, Zeldin DC, Blackshear PJ. Regulatory factor X4 variant 3: a transcription factor involved in brain development and disease. J Neurosci Res 2008; 85:3515-22. [PMID: 17510980 PMCID: PMC2367213 DOI: 10.1002/jnr.21356] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Regulatory factor X4 variant 3 (RFX4_v3) is a recently identified transcription factor specifically expressed in the brain. Gene disruption in mice demonstrated that interruption of a single allele (heterozygous, +/-) prevented formation of the subcommissural organ (SCO), resulting in congenital hydrocephalus, whereas interruption of two alleles (homozygous, -/-) caused fatal failure of dorsal midline brain structure formation. These mutagenesis studies implicated RFX4_v3 in early brain development as well as the genesis of the SCO. Rfx4_v3 deficiency presumably causes abnormalities in brain by altering the expression levels of many genes that are crucial for brain morphogenesis, such as the signaling components in the Wnt, bone morphogenetic protein, and retinoic acid pathways. RFX4_v3 might affect these critical signaling pathways in brain development. Cx3cl1, a chemokine gene highly expressed in brain, was identified as a direct target for RFX4_v3, indicating that RFX4_v3 possesses trans-acting activity to stimulate gene expression. Rfx4_v3 is highly expressed in the suprachiasmatic nucleus and might be involved in regulating the circadian clock. One haplotype in RFX4_v3 gene is linked to a higher risk of bipolar disorder, suggesting that this protein might contribute to the pathogenesis of the disease. This Mini-Review describes our current knowledge about RFX4_v3, an important protein that appears to be involved in many aspects of brain development and disease.
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Affiliation(s)
- Donghui Zhang
- Laboratory of Neurobiology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
- Laboratory of Respiratory Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Darryl C. Zeldin
- Laboratory of Respiratory Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
- Office of Clinical Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Perry J. Blackshear
- Laboratory of Neurobiology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
- Office of Clinical Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
- Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina
- *Correspondence to: Dr. Perry J. Blackshear, A2-05 NIEHS, 111 Alexander Dr., Research Triangle Park, NC 27709. E-mail:
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84
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Wingert RA, Selleck R, Yu J, Song HD, Chen Z, Song A, Zhou Y, Thisse B, Thisse C, McMahon AP, Davidson AJ. The cdx genes and retinoic acid control the positioning and segmentation of the zebrafish pronephros. PLoS Genet 2007; 3:1922-38. [PMID: 17953490 PMCID: PMC2042002 DOI: 10.1371/journal.pgen.0030189] [Citation(s) in RCA: 252] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Accepted: 09/11/2007] [Indexed: 12/11/2022] Open
Abstract
Kidney function depends on the nephron, which comprises a blood filter, a tubule that is subdivided into functionally distinct segments, and a collecting duct. How these regions arise during development is poorly understood. The zebrafish pronephros consists of two linear nephrons that develop from the intermediate mesoderm along the length of the trunk. Here we show that, contrary to current dogma, these nephrons possess multiple proximal and distal tubule domains that resemble the organization of the mammalian nephron. We examined whether pronephric segmentation is mediated by retinoic acid (RA) and the caudal (cdx) transcription factors, which are known regulators of segmental identity during development. Inhibition of RA signaling resulted in a loss of the proximal segments and an expansion of the distal segments, while exogenous RA treatment induced proximal segment fates at the expense of distal fates. Loss of cdx function caused abrogation of distal segments, a posterior shift in the position of the pronephros, and alterations in the expression boundaries of raldh2 and cyp26a1, which encode enzymes that synthesize and degrade RA, respectively. These results suggest that the cdx genes act to localize the activity of RA along the axis, thereby determining where the pronephros forms. Consistent with this, the pronephric-positioning defect and the loss of distal tubule fate were rescued in embryos doubly-deficient for cdx and RA. These findings reveal a novel link between the RA and cdx pathways and provide a model for how pronephric nephrons are segmented and positioned along the embryonic axis.
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Affiliation(s)
- Rebecca A Wingert
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Rori Selleck
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jing Yu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Huai-Dong Song
- Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Second Medical University, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Second Medical University, Shanghai, China
| | - Anhua Song
- Department of Medicine, Division of Hematology/Oncology, Children's Hospital, Boston, Massachusetts, United States of America
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Yi Zhou
- Department of Medicine, Division of Hematology/Oncology, Children's Hospital, Boston, Massachusetts, United States of America
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Bernard Thisse
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Christine Thisse
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Andrew P McMahon
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Alan J Davidson
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
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85
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Xu S, Witmer PD, Lumayag S, Kovacs B, Valle D. MicroRNA (miRNA) Transcriptome of Mouse Retina and Identification of a Sensory Organ-specific miRNA Cluster. J Biol Chem 2007; 282:25053-66. [PMID: 17597072 DOI: 10.1074/jbc.m700501200] [Citation(s) in RCA: 382] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although microRNAs (miRNAs) provide a newly recognized level of regulation of gene expression, the miRNA transcriptome of the retina and the contributions of miRNAs to retinal development and function are largely unknown. To begin to understand the functions of miRNAs in retina, we compared miRNA expression profiles in adult mouse retina, brain, and heart by microarray analysis. Our results show that at least 78 miRNAs are expressed in adult mouse retina, 21 of which are potentially retina-specific. Among these, we identified a polycistronic, sensory organ-specific paralogous miRNA cluster that includes miR-96, miR-182, and miR-183 on mouse chromosome 6qA3 with conservation of synteny to human chromosome 7q32.2. In situ hybridization showed that members of this cluster are expressed in photoreceptors, retinal bipolar and amacrine cells. Consistent with their genomic organization, these miRNAs have a similar expression pattern during development with abundance increasing postnatally and peaking in adult retina. Target prediction and in vitro functional studies showed that MITF, a transcription factor required for the establishment and maintenance of retinal pigmented epithelium, is a direct target of miR-96 and miR-182. Additionally, to identify miRNAs potentially involved in circadian rhythm regulation of the retina, we performed miRNA expression profiling with retinal RNA harvested at noon (Zeitgeber time 5) and midnight (Zeitgeber time 17) and identified a subgroup of 12 miRNAs, including members of the miR-183/96/182 cluster with diurnal variation in expression pattern. Our results suggest that miR-96 and miR-182 are involved in circadian rhythm regulation, perhaps by modulating the expression of adenylyl cyclase VI (ADCY6).
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Affiliation(s)
- Shunbin Xu
- Department of Ophthalmology and Neurological Sciences, Rush University Medical Center, Chicago, Illinois 60302, USA
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86
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Matsumoto A, Ukai-Tadenuma M, Yamada RG, Houl J, Uno KD, Kasukawa T, Dauwalder B, Itoh TQ, Takahashi K, Ueda R, Hardin PE, Tanimura T, Ueda HR. A functional genomics strategy reveals clockwork orange as a transcriptional regulator in the Drosophila circadian clock. Genes Dev 2007; 21:1687-700. [PMID: 17578908 PMCID: PMC1899476 DOI: 10.1101/gad.1552207] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Drosophila circadian clock consists of integrated autoregulatory feedback loops, making the clock difficult to elucidate without comprehensively identifying the network components in vivo. Previous studies have adopted genome-wide screening for clock-controlled genes using high-density oligonucleotide arrays that identified hundreds of clock-controlled genes. In an attempt to identify the core clock genes among these candidates, we applied genome-wide functional screening using an RNA interference (RNAi) system in vivo. Here we report the identification of novel clock gene candidates including clockwork orange (cwo), a transcriptional repressor belonging to the basic helix-loop-helix ORANGE family. cwo is rhythmically expressed and directly regulated by CLK-CYC through canonical E-box sequences. A genome-wide search for its target genes using the Drosophila genome tiling array revealed that cwo forms its own negative feedback loop and directly suppresses the expression of other clock genes through the E-box sequence. Furthermore, this negative transcriptional feedback loop contributes to sustaining a high-amplitude circadian oscillation in vivo. Based on these results, we propose that the competition between cyclic CLK-CYC activity and the adjustable threshold imposed by CWO keeps E-box-mediated transcription within the controllable range of its activity, thereby rendering a Drosophila circadian clock capable of generating high-amplitude oscillation.
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Affiliation(s)
- Akira Matsumoto
- Center for Research and Advancement in Higher Education, Kyushu University, Ropponmatu, Fukuoka 810-8560, Japan
- E-MAIL ; FAX 81-92-726-4641
| | - Maki Ukai-Tadenuma
- Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Jerry Houl
- Department of Biology and Center for Research on Biological Clocks, Texas A&M University, College Station, Texas 77843, USA
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
| | - Kenichiro D. Uno
- Functional Genomics Unit, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takeya Kasukawa
- Functional Genomics Unit, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Brigitte Dauwalder
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
| | - Taichi Q. Itoh
- Department of Biology, Faculty of Science, Kyushu University, Ropponmatu, Fukuoka 810-8560, Japan
| | - Kuniaki Takahashi
- Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Ryu Ueda
- Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Paul E. Hardin
- Department of Biology and Center for Research on Biological Clocks, Texas A&M University, College Station, Texas 77843, USA
| | - Teiichi Tanimura
- Department of Biology, Faculty of Science, Kyushu University, Ropponmatu, Fukuoka 810-8560, Japan
| | - Hiroki R. Ueda
- Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Functional Genomics Unit, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Department of Bioscience, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Corresponding authors.E-MAIL ; FAX 81-78-306-3194
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87
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Kadener S, Stoleru D, McDonald M, Nawathean P, Rosbash M. Clockwork Orange is a transcriptional repressor and a new Drosophila circadian pacemaker component. Genes Dev 2007; 21:1675-86. [PMID: 17578907 PMCID: PMC1899475 DOI: 10.1101/gad.1552607] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Many organisms use circadian clocks to keep temporal order and anticipate daily environmental changes. In Drosophila, the master clock gene Clock promotes the transcription of several key target genes. Two of these gene products, PER and TIM, repress CLK-CYC-mediated transcription. To recognize additional direct CLK target genes, we designed a genome-wide approach and identified clockwork orange (cwo) as a new core clock component. cwo encodes a transcriptional repressor that synergizes with PER and inhibits CLK-mediated activation. Consistent with this function, the mRNA profiles of CLK direct target genes in cwo mutant flies manifest high trough values and low amplitude oscillations. Because behavioral rhythmicity fails to persist in constant darkness (DD) with little or no effect on average mRNA levels in flies lacking cwo, transcriptional oscillation amplitude appears to be linked to rhythmicity. Moreover, the mutant flies are long period, consistent with the late repression indicated by the RNA profiles. These findings suggest that CWO acts preferentially in the late night to help terminate CLK-CYC-mediated transcription of direct target genes including cwo itself. The presence of mammalian homologs with circadian expression features (Dec1 and Dec2) suggests that a similar feedback mechanism exists in mammalian clocks.
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Affiliation(s)
- Sebastian Kadener
- Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Dan Stoleru
- Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
- Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Michael McDonald
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Pipat Nawathean
- Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
- Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Michael Rosbash
- Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
- Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02454, USA
- Corresponding author.E-MAIL ; FAX (781) 736-3164
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88
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Kernan MJ. Mechanotransduction and auditory transduction in Drosophila. Pflugers Arch 2007; 454:703-20. [PMID: 17436012 DOI: 10.1007/s00424-007-0263-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 03/22/2007] [Indexed: 11/28/2022]
Abstract
Insects are utterly reliant on sensory mechanotransduction, the process of converting physical stimuli into neuronal receptor potentials. The senses of proprioception, touch, and hearing are involved in almost every aspect of an adult insect's complex behavioral repertoire and are mediated by a diverse array of specialized sensilla and sensory neurons. The physiology and morphology of several of these have been described in detail; genetic approaches in Drosophila, combining behavioral screens and sensory electrophysiology with forward and reverse genetic techniques, have now revealed specific proteins involved in their differentiation and operation. These include three different TRP superfamily ion channels that are required for transduction in tactile bristles, chordotonal stretch receptors, and polymodal nociceptors. Transduction also depends on the normal differentiation and mechanical integrity of the modified cilia that form the neuronal sensory endings, the accessory structures that transmit stimuli to them and, in bristles, a specialized receptor lymph and transepithelial potential. Flies hear near-field sounds with a vibration-sensitive, antennal chordotonal organ. Biomechanical analyses of wild-type antennae reveal non-linear, active mechanical properties that increase their sensitivity to weak stimuli. The effects of mechanosensory and ciliary mutations on antennal mechanics show that the sensory cilia are the active motor elements and indicate distinct roles for TRPN and TRPV channels in auditory transduction and amplification.
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Affiliation(s)
- Maurice J Kernan
- Department of Neurobiology and Behavior and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-5230, USA.
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89
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Ait-Lounis A, Baas D, Barras E, Benadiba C, Charollais A, Nlend Nlend R, Liègeois D, Meda P, Durand B, Reith W. Novel function of the ciliogenic transcription factor RFX3 in development of the endocrine pancreas. Diabetes 2007; 56:950-9. [PMID: 17229940 DOI: 10.2337/db06-1187] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The transcription factor regulatory factor X (RFX)-3 regulates the expression of genes required for the growth and function of cilia. We show here that mouse RFX3 is expressed in developing and mature pancreatic endocrine cells during embryogenesis and in adults. RFX3 expression already is evident in early Ngn3-positive progenitors and is maintained in all major pancreatic endocrine cell lineages throughout their development. Primary cilia of hitherto unknown function present on these cells consequently are reduced in number and severely stunted in Rfx3(-/-) mice. This ciliary abnormality is associated with a developmental defect leading to a uniquely altered cellular composition of the islets of Langerhans. Just before birth, Rfx3(-/-) islets contain considerably less insulin-, glucagon-, and ghrelin-producing cells, whereas pancreatic polypeptide-positive cells are markedly increased in number. In adult mice, the defect leads to small and disorganized islets, reduced insulin production, and impaired glucose tolerance. These findings suggest that RFX3 participates in the mechanisms that govern pancreatic endocrine cell differentiation and that the presence of primary cilia on islet cells may play a key role in this process.
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Affiliation(s)
- Aouatef Ait-Lounis
- Department of Pathology and Immunology, University of Geneva Medical School, 1 Rue Michel-Servet, CH-1211, Geneva, Switzerland
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90
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Baas D, Meiniel A, Benadiba C, Bonnafe E, Meiniel O, Reith W, Durand B. A deficiency in RFX3 causes hydrocephalus associated with abnormal differentiation of ependymal cells. Eur J Neurosci 2007; 24:1020-30. [PMID: 16930429 DOI: 10.1111/j.1460-9568.2006.05002.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ciliated ependymal cells play central functions in the control of cerebrospinal fluid homeostasis in the mammalian brain, and defects in their differentiation or ciliated properties can lead to hydrocephalus. Regulatory factor X (RFX) transcription factors regulate genes required for ciliogenesis in the nematode, drosophila and mammals. We show here that Rfx3-deficient mice suffer from hydrocephalus without stenosis of the aqueduct of Sylvius. RFX3 is expressed strongly in the ciliated ependymal cells of the subcommissural organ (SCO), choroid plexuses (CP) and ventricular walls during embryonic and postnatal development. Ultrastructural analysis revealed that the hydrocephalus is associated with a general defect in CP differentiation and with severe agenesis of the SCO. The specialized ependymal cells of the CP show an altered epithelial organization, and the SCO cells lose their characteristic ultrastructural features and adopt aspects more typical of classical ependymal cells. These differentiation defects are associated with changes in the number of cilia, although no obvious ultrastructural defects of these cilia can be observed in adult mice. Moreover, agenesis of the SCO is associated with downregulation of SCO-spondin expression as early as E14.5 of embryonic development. These results demonstrate that RFX3 is necessary for ciliated ependymal cell differentiation in the mouse.
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Affiliation(s)
- D Baas
- CGMC UMR 5534 CNRS, Université Claude Bernard Lyon-1, 69622 Villeurbanne, France
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91
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Feistel K, Blum M. Three types of cilia including a novel 9+4 axoneme on the notochordal plate of the rabbit embryo. Dev Dyn 2007; 235:3348-58. [PMID: 17061268 DOI: 10.1002/dvdy.20986] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Motile monocilia play a pivotal role in left-right axis determination in mouse and zebrafish embryos. Cilia with 9+0 axonemes localize to the distal indentation of the mouse egg cylinder ("node"), while Kupffer's vesicle cilia in zebrafish show 9+2 arrangements. Here we studied cilia in a prototype mammalian embryo, the rabbit, which develops via a flat blastodisc. Transcription of ciliary marker genes Foxj1, Rfx3, lrd, polaris, and Kif3a initiated in Hensen's node and persisted in the nascent notochord. Cilia emerged on cells leaving Hensen's node anteriorly to form the notochordal plate. Cilia lengthened to about 5 mum and polarized from an initially central position to the posterior pole of cells. Electron-microscopic analysis revealed 9+0 and 9+2 cilia and a novel 9+4 axoneme intermingled in a salt-and-pepper-like fashion. Our data suggest that despite a highly conserved ciliogenic program, which initiates in the organizer, axonemal structures may vary widely within the vertebrates.
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Affiliation(s)
- Kerstin Feistel
- University of Hohenheim, Institute of Zoology, Stuttgart, Germany
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92
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Eberl DF, Boekhoff-Falk G. Development of Johnston's organ in Drosophila. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2007; 51:679-87. [PMID: 17891726 PMCID: PMC3417114 DOI: 10.1387/ijdb.072364de] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Hearing is a specialized mechanosensory modality that is refined during evolution to meet the particular requirements of different organisms. In the fruitfly, Drosophila, hearing is mediated by Johnston's organ, a large chordotonal organ in the antenna that is exquisitely sensitive to the near-field acoustic signal of courtship songs generated by male wing vibration. We summarize recent progress in understanding the molecular genetic determinants of Johnston's organ development and discuss surprising differences from other chordotonal organs that likely facilitate hearing. We outline novel discoveries of active processes that generate motion of the antenna for acute sensitivity to the stimulus. Finally, we discuss further research directions that would probe remaining questions in understanding Johnston's organ development, function and evolution.
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Affiliation(s)
- Daniel F Eberl
- Department of Biology, University of Iowa, Iowa City, IA 52242-1324, USA.
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93
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Martinez MJ, Smith AD, Li B, Zhang MQ, Harrod KS. Computational prediction of novel components of lung transcriptional networks. Bioinformatics 2006; 23:21-9. [PMID: 17050569 DOI: 10.1093/bioinformatics/btl531] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
MOTIVATION Little is known regarding the transcriptional mechanisms involved in forming and maintaining epithelial cell lineages of the mammalian respiratory tract. RESULTS Herein, a motif discovery approach was used to identify novel transcriptional regulators in the lung using genes previously found to be regulated by Foxa2 or Wnt signaling pathways. A human-mouse comparison of both novel and known motifs was also performed. Some of the factors and families identified here were previously shown to be involved epithelial cell differentiation (ETS family, HES-1 and MEIS-1), and ciliogenesis (RFX family), but have never been characterized in lung epithelia. Other unidentified over-represented motifs suggest the existence of novel mammalian lung transcription factors. Of the fraction of motifs examined we describe 25 transcription factor family predictions for lung. Fifteen novel factors were shown here to be expressed in mouse lung, and/or human bronchial or distal lung epithelial tissues or lung epithelial cell lineages. AVAILABILITY DME: http://rulai.cshl.edu/dme. MATCOMPARE: http://rulai.cshl.edu/MatCompare. MOTIFCLASS is available from the authors.
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Affiliation(s)
- M Juanita Martinez
- Lovelace Respiratory Research Institute, 2425 Ridgecrest Dr SE, Albuquerque, NM 87108, USA
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94
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Basto R, Lau J, Vinogradova T, Gardiol A, Woods CG, Khodjakov A, Raff JW. Flies without centrioles. Cell 2006; 125:1375-86. [PMID: 16814722 DOI: 10.1016/j.cell.2006.05.025] [Citation(s) in RCA: 529] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Revised: 03/16/2006] [Accepted: 05/03/2006] [Indexed: 01/03/2023]
Abstract
Centrioles and centrosomes have an important role in animal cell organization, but it is uncertain to what extent they are essential for animal development. The Drosophila protein DSas-4 is related to the human microcephaly protein CenpJ and the C. elegans centriolar protein Sas-4. We show that DSas-4 is essential for centriole replication in flies. DSas-4 mutants start to lose centrioles during embryonic development, and, by third-instar larval stages, no centrioles or centrosomes are detectable. Mitotic spindle assembly is slow in mutant cells, and approximately 30% of the asymmetric divisions of larval neuroblasts are abnormal. Nevertheless, mutant flies develop with near normal timing into morphologically normal adults. These flies, however, have no cilia or flagella and die shortly after birth because their sensory neurons lack cilia. Thus, centrioles are essential for the formation of centrosomes, cilia, and flagella, but, remarkably, they are not essential for most aspects of Drosophila development.
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Affiliation(s)
- Renata Basto
- The Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK
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95
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Zhang D, Stumpo DJ, Graves JP, DeGraff LM, Grissom SF, Collins JB, Li L, Zeldin DC, Blackshear PJ. Identification of potential target genes for RFX4_v3, a transcription factor critical for brain development. J Neurochem 2006; 98:860-75. [PMID: 16893423 DOI: 10.1111/j.1471-4159.2006.03930.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Regulatory factor X4 variant transcript 3 (Rfx4_v3) gene disruption in mice demonstrated that interruption of a single allele (heterozygous, +/-) prevented formation of the subcommissural organ, resulting in congenital hydrocephalus, while interruption of two alleles (homozygous, -/-) caused fatal failure of dorsal midline brain structure formation. To identify potential target genes for RFX4_v3, we used microarray analysis to identify differentially expressed genes in Rfx4_v3-deficient mouse brains at embryonic day 10.5, before gross structural changes were apparent. Of 109 differentially expressed transcripts, 24 were chosen for validation and 22 were confirmed by real-time PCR. Many validated genes encoded critical proteins involved in brain morphogenesis, such as the signaling components in the Wnt, bone morphogenetic protein (BMP) and retinoic acid (RA) pathways. Cx3cl1, a CX3C-type chemokine gene that is highly expressed in brain, was down-regulated in the Rfx4_v3-null mice. Both human and mouse Cx3cl1 proximal promoters contained highly conserved X-boxes, known cis-acting elements for RFX protein binding. Using the Cx3cl1 promoter as an example of a target gene, we demonstrated direct binding of RFX4_v3 to the Cx3cl1 promoter, and trans-acting activity of RFX4_v3 protein to stimulate gene expression. These data suggest that RFX4_v3 may act upstream of critical signaling pathways in the process of brain development.
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Affiliation(s)
- Donghui Zhang
- Laboratory of Neurobiology, National Institute of Environmental Health Sciences, National Institutes of Health Research Triangle Park, North Carolina 27709, USA
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96
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Spéder P, Adám G, Noselli S. Type ID unconventional myosin controls left-right asymmetry in Drosophila. Nature 2006; 440:803-7. [PMID: 16598259 DOI: 10.1038/nature04623] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Accepted: 02/01/2006] [Indexed: 01/06/2023]
Abstract
Breaking left-right symmetry in Bilateria embryos is a major event in body plan organization that leads to polarized adult morphology, directional organ looping, and heart and brain function. However, the molecular nature of the determinant(s) responsible for the invariant orientation of the left-right axis (situs choice) remains largely unknown. Mutations producing a complete reversal of left-right asymmetry (situs inversus) are instrumental for identifying mechanisms controlling handedness, yet only one such mutation has been found in mice (inversin) and snails. Here we identify the conserved type ID unconventional myosin 31DF gene (Myo31DF) as a unique situs inversus locus in Drosophila. Myo31DF mutations reverse the dextral looping of genitalia, a prominent left-right marker in adult flies. Genetic mosaic analysis pinpoints the A8 segment of the genital disc as a left-right organizer and reveals an anterior-posterior compartmentalization of Myo31DF function that directs dextral development and represses a sinistral default state. As expected of a determinant, Myo31DF has a trigger-like function and is expressed symmetrically in the organizer, and its symmetrical overexpression does not impair left-right asymmetry. Thus Myo31DF is a dextral gene with actin-based motor activity controlling situs choice. Like mouse inversin, Myo31DF interacts and colocalizes with beta-catenin, suggesting that situs inversus genes can direct left-right development through the adherens junction.
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Affiliation(s)
- Pauline Spéder
- Institute of Signalling, Developmental Biology & Cancer, UMR6543-CNRS, University of Nice Sophia-Antipolis, Parc Valrose, 06108 Nice Cedex 2, France
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97
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Tsuda H, Jafar-Nejad H, Patel AJ, Sun Y, Chen HK, Rose MF, Venken KJT, Botas J, Orr HT, Bellen HJ, Zoghbi HY. The AXH Domain of Ataxin-1 Mediates Neurodegeneration through Its Interaction with Gfi-1/Senseless Proteins. Cell 2005; 122:633-44. [PMID: 16122429 DOI: 10.1016/j.cell.2005.06.012] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Revised: 04/27/2005] [Accepted: 06/09/2005] [Indexed: 11/16/2022]
Abstract
Spinocerebellar ataxia type 1 (SCA1) is a neurodegenerative disease caused by an expanded glutamine tract in human Ataxin-1 (hAtx-1). The expansion stabilizes hAtx-1, leading to its accumulation. To understand how stabilized hAtx-1 induces selective neuronal degeneration, we studied Drosophila Atx-1 (dAtx-1), which has a conserved AXH domain but lacks a polyglutamine tract. Overexpression of hAtx-1 in fruit flies produces phenotypes similar to those of dAtx-1 but different from the polyglutamine peptide alone. We show that the Drosophila and mammalian transcription factors Senseless/Gfi-1 interact with Atx-1's AXH domain. In flies, overexpression of Atx-1 inhibits sensory-organ development by decreasing Senseless protein. Similarly, overexpression of wild-type and glutamine-expanded hAtx-1 reduces Gfi-1 levels in Purkinje cells. Deletion of the AXH domain abolishes the effects of glutamine-expanded hAtx-1 on Senseless/Gfi-1. Interestingly, loss of Gfi-1 mimics SCA1 phenotypes in Purkinje cells. These results indicate that the Atx-1/Gfi-1 interaction contributes to the selective Purkinje cell degeneration in SCA1.
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Affiliation(s)
- Hiroshi Tsuda
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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98
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Efimenko E, Bubb K, Mak HY, Holzman T, Leroux MR, Ruvkun G, Thomas JH, Swoboda P. Analysis of xbx genes in C. elegans. Development 2005; 132:1923-34. [PMID: 15790967 DOI: 10.1242/dev.01775] [Citation(s) in RCA: 163] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cilia and flagella are widespread eukaryotic subcellular components that are conserved from green algae to mammals. In different organisms they function in cell motility, movement of extracellular fluids and sensory reception. While the function and structural description of cilia and flagella are well established, there are many questions that remain unanswered. In particular, very little is known about the developmental mechanisms by which cilia are generated and shaped and how their components are assembled into functional machineries. To find genes involved in cilia development we used as a search tool a promoter motif, the X-box, which participates in the regulation of certain ciliary genes in the nematode Caenorhabditis elegans. By using a genome search approach for X-box promoter motif-containing genes (xbx genes) we identified a list of about 750 xbx genes (candidates). This list comprises some already known ciliary genes as well as new genes, many of which we hypothesize to be important for cilium structure and function. We derived a C. elegans X-box consensus sequence by in vivo expression analysis. We found that xbx gene expression patterns were dependent on particular X-box nucleotide compositions and the distance from the respective gene start. We propose a model where DAF-19, the RFX-type transcription factor binding to the X-box, is responsible for the development of a ciliary module in C. elegans, which includes genes for cilium structure, transport machinery, receptors and other factors.
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Affiliation(s)
- Evgeni Efimenko
- Karolinska Institute, Department of Biosciences and Södertörn University College, Section of Natural Sciences, S-14189 Huddinge, Sweden
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99
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Mitchell DR. Speculations on the evolution of 9+2 organelles and the role of central pair microtubules. Biol Cell 2005; 96:691-6. [PMID: 15567523 PMCID: PMC3321483 DOI: 10.1016/j.biolcel.2004.07.004] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2004] [Accepted: 07/29/2004] [Indexed: 11/19/2022]
Abstract
Motility generated by 9+2 organelles, variably called cilia or flagella, evolved before divergence from the last common ancestor of extant eukaryotes. In order to understand better how motility in these organelles is regulated, evolutionary steps that led to the present 9+2 morphology are considered. In addition, recent advances in our knowledge of flagellar assembly, together with heightened appreciation of the widespread role of cilia in sensory processes, suggest that these organelles may have served multiple roles in early eukaryotic cells. In addition to their function as undulating motility organelles, we speculate that protocilia were the primary determinants of cell polarity and directed motility in early eukaryotes, and that they provided the first defined membrane domain for localization of receptors that allowed cells to respond tactically to environmental cues. Initially, motility associated with these protocilia may have been gliding motility rather than the more complex bend propagation. Once these protocilia became functional motile organelles for beating, we believe that addition of an asymmetric central apparatus, capable of transducing signals to dynein motors and altering beat parameters, provided refined directional control in response to tactic signals. This paper presents hypothesized steps in this evolutionary process, and examples to support these hypotheses.
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Affiliation(s)
- David R Mitchell
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 E. Adams St., Syracuse, NY 13210, USA.
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Barr MM. Caenorhabditis elegans as a model to study renal development and disease: sexy cilia. J Am Soc Nephrol 2005; 16:305-12. [PMID: 15647338 DOI: 10.1681/asn.2004080645] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The nematode Caenorhabditis elegans has no kidney per se, yet "the worm" has proved to be an excellent model to study renal-related issues, including tubulogenesis of the excretory canal, membrane transport and ion channel function, and human genetic diseases including autosomal dominant polycystic kidney disease (ADPKD). The goal of this review is to explain how C. elegans has provided insight into cilia development, cilia function, and human cystic kidney diseases.
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Affiliation(s)
- Maureen M Barr
- School of Pharmacy, University of Wisconsin at Madison, 777 Highland Avenue, Madison, WI 53705, USA.
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