1
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Coyle MC, Tajima AM, Leon F, Choksi SP, Yang A, Espinoza S, Hughes TR, Reiter JF, Booth DS, King N. An RFX transcription factor regulates ciliogenesis in the closest living relatives of animals. Curr Biol 2023; 33:3747-3758.e9. [PMID: 37552984 PMCID: PMC10530576 DOI: 10.1016/j.cub.2023.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 05/30/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
Cilia allowed our protistan ancestors to sense and explore their environment, avoid predation, and capture bacterial prey.1,2,3 Regulated ciliogenesis was likely critical for early animal evolution,2,4,5,6 and in modern animals, deploying cilia in the right cells at the right time is crucial for development and physiology. Two transcription factors, RFX and FoxJ1, coordinate ciliogenesis in animals7,8,9 but are absent from the genomes of many other ciliated eukaryotes, raising the question of how the regulation of ciliogenesis in animals evolved.10,11 By comparing the genomes of animals with those of their closest living relatives, the choanoflagellates, we found that the genome of their last common ancestor encoded at least three RFX paralogs and a FoxJ1 homolog. Disruption of the RFX homolog cRFXa in the model choanoflagellate Salpingoeca rosetta resulted in delayed cell proliferation and aberrant ciliogenesis, marked by the collapse and resorption of nascent cilia. In cRFXa mutants, ciliogenesis genes and foxJ1 were significantly downregulated. Moreover, the promoters of S. rosetta ciliary genes are enriched for DNA motifs matching those bound by the cRFXa protein in vitro. These findings suggest that an ancestral cRFXa homolog coordinated ciliogenesis in the progenitors of animals and choanoflagellates and that the selective deployment of the RFX regulatory module may have been necessary to differentiate ciliated from non-ciliated cell types during early animal evolution.
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Affiliation(s)
- Maxwell C Coyle
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Adia M Tajima
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Fredrick Leon
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Semil P Choksi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ally Yang
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada
| | - Sarah Espinoza
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - David S Booth
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Nicole King
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
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2
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Brocal-Ruiz R, Esteve-Serrano A, Mora-Martínez C, Franco-Rivadeneira ML, Swoboda P, Tena JJ, Vilar M, Flames N. Forkhead transcription factor FKH-8 cooperates with RFX in the direct regulation of sensory cilia in Caenorhabditis elegans. eLife 2023; 12:e89702. [PMID: 37449480 PMCID: PMC10393296 DOI: 10.7554/elife.89702] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Cilia, either motile or non-motile (a.k.a primary or sensory), are complex evolutionarily conserved eukaryotic structures composed of hundreds of proteins required for their assembly, structure and function that are collectively known as the ciliome. Ciliome gene mutations underlie a group of pleiotropic genetic diseases known as ciliopathies. Proper cilium function requires the tight coregulation of ciliome gene transcription, which is only fragmentarily understood. RFX transcription factors (TF) have an evolutionarily conserved role in the direct activation of ciliome genes both in motile and non-motile cilia cell-types. In vertebrates, FoxJ1 and FoxN4 Forkhead (FKH) TFs work with RFX in the direct activation of ciliome genes, exclusively in motile cilia cell-types. No additional TFs have been described to act together with RFX in primary cilia cell-types in any organism. Here we describe FKH-8, a FKH TF, as a direct regulator of the sensory ciliome genes in Caenorhabditis elegans. FKH-8 is expressed in all ciliated neurons in C. elegans, binds the regulatory regions of ciliome genes, regulates ciliome gene expression, cilium morphology and a wide range of behaviors mediated by sensory ciliated neurons. FKH-8 and DAF-19 (C. elegans RFX) physically interact and synergistically regulate ciliome gene expression. C. elegans FKH-8 function can be replaced by mouse FOXJ1 and FOXN4 but not by other members of other mouse FKH subfamilies. In conclusion, RFX and FKH TF families act jointly as direct regulators of ciliome genes also in sensory ciliated cell types suggesting that this regulatory logic could be an ancient trait predating functional cilia sub-specialization.
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Affiliation(s)
- Rebeca Brocal-Ruiz
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Ainara Esteve-Serrano
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Carlos Mora-Martínez
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | | | - Peter Swoboda
- Department of Biosciences and Nutrition. Karolinska Institute. Campus FlemingsbergStockholmSweden
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de OlavideSevilleSpain
| | - Marçal Vilar
- Molecular Basis of Neurodegeneration Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
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3
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Liu YX, Sun WY, Xue B, Zhang RK, Li WJ, Xie X, Fan ZC. ARL3 mediates BBSome ciliary turnover by promoting its outward movement across the transition zone. J Cell Biol 2022; 221:213491. [PMID: 36129685 PMCID: PMC9499826 DOI: 10.1083/jcb.202111076] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/13/2022] [Accepted: 07/11/2022] [Indexed: 01/16/2023] Open
Abstract
Ciliary receptors and their certain downstream signaling components undergo intraflagellar transport (IFT) as BBSome cargoes to maintain their ciliary dynamics for sensing and transducing extracellular stimuli inside the cell. Cargo-laden BBSomes pass the transition zone (TZ) for ciliary retrieval, but how this passage is controlled remains elusive. Here, we show that phospholipase D (PLD)-laden BBSomes shed from retrograde IFT trains at the proximal ciliary region right above the TZ to act as Arf-like 3 (ARL3) GTPase-specific effectors in Chlamydomonas cilia. Under physiological condition, ARL3GDP binds to the membrane for diffusing into cilia. Following nucleotide exchange, ARL3GTP detaches from the ciliary membrane, binds to retrograde IFT train-shed and PLD-laden BBSomes at the proximal ciliary region right above the TZ, and recruits them to pass the TZ for ciliary retrieval likely via diffusion. ARL3 mediates the ciliary dynamics of certain signaling molecules through facilitating BBSome ciliary retrieval, providing a mechanistic understanding behind why ARL3-related Joubert syndrome shares overlapping phenotypes with Bardet-Biedl syndrome.
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Affiliation(s)
- Yan-Xia Liu
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Wei-Yue Sun
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Bin Xue
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Rui-Kai Zhang
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Wen-Juan Li
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xixian Xie
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhen-Chuan Fan
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Correspondence to Zhen-Chuan Fan:
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4
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Ahn S, Yang H, Son S, Lee HS, Park D, Yim H, Choi HJ, Swoboda P, Lee J. The C. elegans regulatory factor X (RFX) DAF-19M module: A shift from general ciliogenesis to cell-specific ciliary and behavioral specialization. Cell Rep 2022; 39:110661. [PMID: 35417689 DOI: 10.1016/j.celrep.2022.110661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/14/2022] [Accepted: 03/18/2022] [Indexed: 12/28/2022] Open
Abstract
Cilia are important for the interaction with environments and the proper function of tissues. While the basic structure of cilia is well conserved, ciliated cells have various functions. To understand the distinctive identities of ciliated cells, the identification of cell-specific proteins and its regulation is essential. Here, we report the mechanism that confers a specific identity on IL2 neurons in Caenorhabditis elegans, neurons important for the dauer larva-specific nictation behavior. We show that DAF-19M, an isoform of the sole C. elegans RFX transcription factor DAF-19, heads a regulatory subroutine, regulating target genes through an X-box motif variant under the control of terminal selector proteins UNC-86 and CFI-1 in IL2 neurons. Considering the conservation of DAF-19M module in IL2 neurons for nictation and in male-specific neurons for mating behavior, we propose the existence of an evolutionarily adaptable, hard-wired genetic module for distinct behaviors that share the feature "recognizing the environment."
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Affiliation(s)
- Soungyub Ahn
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Heeseung Yang
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Sangwon Son
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hyun Sik Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dongjun Park
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hyunsoo Yim
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.
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5
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Vasquez SSV, van Dam J, Wheway G. An updated SYSCILIA gold standard (SCGSv2) of known ciliary genes, revealing the vast progress that has been made in the cilia research field. Mol Biol Cell 2021; 32:br13. [PMID: 34613793 PMCID: PMC8694072 DOI: 10.1091/mbc.e21-05-0226] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cilia are microtubule-based organelles with important functions in motility and sensation. They contribute to a broad spectrum of developmental disorders called ciliopathies and have recently been linked to common conditions such as cancers and congenital heart disease. There has been increasing interest in the biology of cilia and their contribution to disease over the past two decades. In 2013 we published a "Gold Standard" list of genes confirmed to be associated with cilia. This was published as part of the SYSCILIA consortium for systems biology study dissecting the contribution of cilia to human health and disease, and was named the Syscilia Gold Standard (SCGS). Since this publication, interest in cilia and understanding of their functions have continued to grow, and we now present an updated SCGS version 2. This includes an additional 383 genes, more than doubling the size of SCGSv1. We use this dataset to conduct a review of advances in understanding of cilia biology 2013- 2021 and offer perspectives on the future of cilia research. We hope that this continues to be a useful resource for the cilia community.
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Affiliation(s)
| | - John van Dam
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, 3584 CH Utrecht, Netherlands
| | - Gabrielle Wheway
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, United Kingdom
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6
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Maurya AK, Sengupta P. xbx-4, a homolog of the Joubert syndrome gene FAM149B1, acts via the CCRK and RCK kinase cascade to regulate cilia morphology. Curr Biol 2021; 31:5642-5649.e5. [PMID: 34731674 DOI: 10.1016/j.cub.2021.10.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/23/2021] [Accepted: 10/12/2021] [Indexed: 12/14/2022]
Abstract
Primary cilia are microtubule (MT)-based organelles that mediate sensory functions in multiple cell types. Disruption of cilia structure or function leads to a diverse collection of diseases termed ciliopathies.1-3 The highly conserved CCRK and RCK kinases (ICK/MOK/MAK) negatively regulate cilia length and structure in Chlamydomonas, C. elegans, and mammalian cells.4-10 How the activity of this kinase cascade is tuned to precisely regulate cilia architecture is unclear. Mutations in the Domain of Unknown Function 3719 (DUF3719)-containing protein FAM149B1 have recently been shown to elongate cilia via unknown mechanisms and result in the ciliopathy Joubert syndrome.11 Here we identify XBX-4, a DUF3719-containing protein related to human FAM149B1, as a regulator of the DYF-18 CCRK and DYF-5 MAK kinase pathway in C. elegans. As in dyf-18 and dyf-5 mutants,10 sensory neuron cilia are elongated in xbx-4 mutants and exhibit stabilized axonemal MTs. XBX-4 promotes DYF-18 CCRK function to regulate localization and function of DYF-5 MAK. We find that Joubert syndrome-associated mutations in the XBX-4 DUF3719 domain also elongate cilia in C. elegans. Our results identify a new metazoan-specific regulator of this highly conserved kinase pathway and suggest that FAM149B1 may similarly act via the CCRK/RCK kinase pathway to regulate ciliary homeostasis in humans.
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Affiliation(s)
- Ashish K Maurya
- Department of Biology, MS008, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
| | - Piali Sengupta
- Department of Biology, MS008, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
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7
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Taylor SR, Santpere G, Weinreb A, Barrett A, Reilly MB, Xu C, Varol E, Oikonomou P, Glenwinkel L, McWhirter R, Poff A, Basavaraju M, Rafi I, Yemini E, Cook SJ, Abrams A, Vidal B, Cros C, Tavazoie S, Sestan N, Hammarlund M, Hobert O, Miller DM. Molecular topography of an entire nervous system. Cell 2021; 184:4329-4347.e23. [PMID: 34237253 DOI: 10.1016/j.cell.2021.06.023] [Citation(s) in RCA: 247] [Impact Index Per Article: 82.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/09/2021] [Accepted: 06/14/2021] [Indexed: 02/08/2023]
Abstract
We have produced gene expression profiles of all 302 neurons of the C. elegans nervous system that match the single-cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses distinct codes of ∼23 neuropeptide genes and ∼36 neuropeptide receptors, delineating a complex and expansive "wireless" signaling network. To demonstrate the utility of this comprehensive gene expression catalog, we used computational approaches to (1) identify cis-regulatory elements for neuron-specific gene expression and (2) reveal adhesion proteins with potential roles in process placement and synaptic specificity. Our expression data are available at https://cengen.org and can be interrogated at the web application CengenApp. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity, and function throughout the C. elegans nervous system.
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Affiliation(s)
- Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Gabriel Santpere
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), DCEXS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Alexis Weinreb
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Alec Barrett
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Molly B Reilly
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Chuan Xu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Erdem Varol
- Department of Statistics, Columbia University, New York, NY, USA
| | - Panos Oikonomou
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Lori Glenwinkel
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Rebecca McWhirter
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Abigail Poff
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Manasa Basavaraju
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Ibnul Rafi
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Steven J Cook
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Alexander Abrams
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Berta Vidal
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Cyril Cros
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Saeed Tavazoie
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Marc Hammarlund
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Program in Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA.
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8
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Cevik S, Kaplan OI. The Joubert syndrome protein CEP41 is excluded from the distal segment of cilia in C. elegans. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000406. [PMID: 34113804 PMCID: PMC8185565 DOI: 10.17912/micropub.biology.000406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/21/2021] [Accepted: 06/02/2021] [Indexed: 11/16/2022]
Abstract
Rare diseases are a fundamental issue in today's world, affecting more than 300 million individuals worldwide. According to data from Orphanet and OMIM, about 50-60 new conditions are added to the list of over 6,000 clinically distinct diseases each year, rendering disease diagnosis and treatment even more challenging. Ciliopathies comprise a heterogeneous category of rare diseases made up of over 35 distinct diseases, including Joubert syndrome (JBTS; OMIM 213300), that are caused by functional and structural defects in cilia. JBTS is an autosomal recessive condition characterized by a range of symptoms, including cerebellar vermis hypoplasia and poor muscle tone. There are now a total of 38 genes that cause JBTS, almost all of which encode protein products that are found in cilia and cilia-associated compartments, such as the basal body and transition zone. CEP41 is a JBTS-associated protein that is found in cilia and the basal body of mammals, but its localization in other ciliary organisms remains elusive. C. elegans is an excellent model organism for studying the molecular mechanisms of rare diseases like JBTS. We, therefore, decided to use C. elegans to identify the localization of CEP41. Our microscopy analysis revealed that CEPH-41(CEntrosomal Protein Homolog 41) not only localizes to cilia but is excluded from the distal segment of the amphid and phasmid cilia in C. elegans. Furthermore, we discovered a putative X-box motif located in the promoter of ceph-41 and the expression of ceph-41 is regulated by DAF-19, a sole Regulatory Factor X (RFX) transcription factor.
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Affiliation(s)
- Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Oktay I. Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
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9
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Garbrecht J, Laos T, Holzer E, Dillinger M, Dammermann A. An acentriolar centrosome at the C. elegans ciliary base. Curr Biol 2021; 31:2418-2428.e8. [PMID: 33798427 DOI: 10.1016/j.cub.2021.03.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/13/2021] [Accepted: 03/05/2021] [Indexed: 01/26/2023]
Abstract
In animal cells, the functions of the microtubule cytoskeleton are coordinated by centriole-based centrosomes via γ-tubulin complexes embedded in the pericentriolar material or PCM.1 PCM assembly has been best studied in the context of mitosis, where centriolar SPD-2 recruits PLK-1, which in turn phosphorylates key scaffolding components like SPD-5 and CNN to promote expansion of the PCM polymer.2-4 To what extent these mechanisms apply to centrosomes in interphase or in differentiated cells remains unclear.5 Here, we examine a novel type of centrosome found at the ciliary base of C. elegans sensory neurons, which we show plays important roles in neuronal morphogenesis, cellular trafficking, and ciliogenesis. These centrosomes display similar dynamic behavior to canonical, mitotic centrosomes, with a stable PCM scaffold and dynamically localized client proteins. Unusually, however, they are not organized by centrioles, which degenerate early in terminal differentiation.6 Yet, PCM not only persists but continues to grow with key scaffolding proteins including SPD-5 expressed under control of the RFX transcription factor DAF-19. This assembly occurs in the absence of the mitotic regulators SPD-2, AIR-1 and PLK-1, but requires tethering by PCMD-1, a protein which also plays a role in the initial, interphase recruitment of PCM in early embryos.7 These results argue for distinct mechanisms for mitotic and non-mitotic PCM assembly, with only the former requiring PLK-1 phosphorylation to drive rapid expansion of the scaffold polymer.
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Affiliation(s)
- Joachim Garbrecht
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, A-1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna
| | - Triin Laos
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, A-1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna
| | - Elisabeth Holzer
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Margarita Dillinger
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Alexander Dammermann
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, A-1030 Vienna, Austria.
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10
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De-Castro ARG, Quintas-Gonçalves J, Silva-Ribeiro T, Rodrigues DRM, De-Castro MJG, Abreu CM, Dantas TJ. The IFT20 homolog in Caenorhabditis elegans is required for ciliogenesis and cilia-mediated behavior. MICROPUBLICATION BIOLOGY 2021; 2021. [PMID: 33997658 PMCID: PMC8114103 DOI: 10.17912/micropub.biology.000396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Cilia are microtubule-based organelles that carry out a wide range of critical functions throughout the development of higher animals. Regardless of their type, all cilia rely on a motor-driven, bidirectional transport system known as intraflagellar transport (IFT). Of the many components of the IFT machinery, IFT20 is one of the smallest subunits. Nevertheless, IFT20 has been shown to play critical roles in the assembly of several types of mammalian cilia. Here we show that the IFT20 homolog in Caenorhabditis elegans, IFT-20, is also important for correct cilium assembly in sensory neurons. Strikingly, however, we find that IFT-20-deficient animals are able to assemble short, vestigial cilia. In spite of this, we show that practically all IFT-20-deficient animals fail to respond to environmental cues that are normally detected by cilia to modulate their behavior. Altogether, our results indicate that IFT-20 is critical for both the correct assembly and function of cilia in C. elegans.
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Affiliation(s)
- Ana R G De-Castro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Joana Quintas-Gonçalves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Tiago Silva-Ribeiro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Diogo R M Rodrigues
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Maria J G De-Castro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Carla M Abreu
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Tiago J Dantas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
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11
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Issac J, Raveendran PS, Das AV. RFX1: a promising therapeutic arsenal against cancer. Cancer Cell Int 2021; 21:253. [PMID: 33964962 PMCID: PMC8106159 DOI: 10.1186/s12935-021-01952-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 04/26/2021] [Indexed: 02/08/2023] Open
Abstract
Regulatory factor X1 (RFX1) is an evolutionary conserved transcriptional factor that influences a wide range of cellular processes such as cell cycle, cell proliferation, differentiation, and apoptosis, by regulating a number of target genes that are involved in such processes. On a closer look, these target genes also play a key role in tumorigenesis and associated events. Such observations paved the way for further studies evaluating the role of RFX1 in cancer. These studies were indispensable due to the failure of conventional chemotherapeutic drugs to target key cellular hallmarks such as cancer stemness, cellular plasticity, enhanced drug efflux, de-regulated DNA repair machinery, and altered pathways evading apoptosis. In this review, we compile significant evidence for the tumor-suppressive activities of RFX1 while also analyzing its oncogenic potential in some cancers. RFX1 induction decreased cellular proliferation, modulated the immune system, induced apoptosis, reduced chemoresistance, and sensitized cancer stem cells for chemotherapy. Thus, our review discusses the pleiotropic function of RFX1 in multitudinous gene regulations, decisive protein–protein interactions, and also its role in regulating key cell signaling events in cancer. Elucidation of these regulatory mechanisms can be further utilized for RFX1 targeted therapy.
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Affiliation(s)
- Joby Issac
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud.P.O, Thiruvananthapuram, 695014, Kerala, India
| | - Pooja S Raveendran
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud.P.O, Thiruvananthapuram, 695014, Kerala, India
| | - Ani V Das
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud.P.O, Thiruvananthapuram, 695014, Kerala, India.
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12
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Magescas J, Eskinazi S, Tran MV, Feldman JL. Centriole-less pericentriolar material serves as a microtubule organizing center at the base of C. elegans sensory cilia. Curr Biol 2021; 31:2410-2417.e6. [PMID: 33798428 DOI: 10.1016/j.cub.2021.03.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/18/2021] [Accepted: 03/05/2021] [Indexed: 01/20/2023]
Abstract
During mitosis in animal cells, the centrosome acts as a microtubule organizing center (MTOC) to assemble the mitotic spindle. MTOC function at the centrosome is driven by proteins within the pericentriolar material (PCM), however the molecular complexity of the PCM makes it difficult to differentiate the proteins required for MTOC activity from other centrosomal functions. We used the natural spatial separation of PCM proteins during mitotic exit to identify a minimal module of proteins required for centrosomal MTOC function in C. elegans. Using tissue-specific degradation, we show that SPD-5, the functional homolog of CDK5RAP2, is essential for embryonic mitosis, while SPD-2/CEP192 and PCMD-1, which are essential in the one-cell embryo, are dispensable. Surprisingly, although the centriole is known to be degraded in the ciliated sensory neurons in C. elegans,1-3 we find evidence for "centriole-less PCM" at the base of cilia and use this structure as a minimal testbed to dissect centrosomal MTOC function. Super-resolution imaging revealed that this PCM inserts inside the lumen of the ciliary axoneme and directly nucleates the assembly of dendritic microtubules toward the cell body. Tissue-specific degradation in ciliated sensory neurons revealed a role for SPD-5 and the conserved microtubule nucleator γ-TuRC, but not SPD-2 or PCMD-1, in MTOC function at centriole-less PCM. This MTOC function was in the absence of regulation by mitotic kinases, highlighting the intrinsic ability of these proteins to drive microtubule growth and organization and further supporting a model that SPD-5 is the primary driver of MTOC function at the PCM.
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Affiliation(s)
- Jérémy Magescas
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, 94305, CA, USA.
| | - Sani Eskinazi
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, 94305, CA, USA
| | - Michael V Tran
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, 94305, CA, USA
| | - Jessica L Feldman
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, 94305, CA, USA.
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13
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Disruption of RFX family transcription factors causes autism, attention-deficit/hyperactivity disorder, intellectual disability, and dysregulated behavior. Genet Med 2021; 23:1028-1040. [PMID: 33658631 DOI: 10.1038/s41436-021-01114-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/30/2022] Open
Abstract
PURPOSE We describe a novel neurobehavioral phenotype of autism spectrum disorder (ASD), intellectual disability, and/or attention-deficit/hyperactivity disorder (ADHD) associated with de novo or inherited deleterious variants in members of the RFX family of genes. RFX genes are evolutionarily conserved transcription factors that act as master regulators of central nervous system development and ciliogenesis. METHODS We assembled a cohort of 38 individuals (from 33 unrelated families) with de novo variants in RFX3, RFX4, and RFX7. We describe their common clinical phenotypes and present bioinformatic analyses of expression patterns and downstream targets of these genes as they relate to other neurodevelopmental risk genes. RESULTS These individuals share neurobehavioral features including ASD, intellectual disability, and/or ADHD; other frequent features include hypersensitivity to sensory stimuli and sleep problems. RFX3, RFX4, and RFX7 are strongly expressed in developing and adult human brain, and X-box binding motifs as well as RFX ChIP-seq peaks are enriched in the cis-regulatory regions of known ASD risk genes. CONCLUSION These results establish a likely role of deleterious variation in RFX3, RFX4, and RFX7 in cases of monogenic intellectual disability, ADHD and ASD, and position these genes as potentially critical transcriptional regulators of neurobiological pathways associated with neurodevelopmental disease pathogenesis.
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14
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Lemeille S, Paschaki M, Baas D, Morlé L, Duteyrat JL, Ait-Lounis A, Barras E, Soulavie F, Jerber J, Thomas J, Zhang Y, Holtzman MJ, Kistler WS, Reith W, Durand B. Interplay of RFX transcription factors 1, 2 and 3 in motile ciliogenesis. Nucleic Acids Res 2020; 48:9019-9036. [PMID: 32725242 PMCID: PMC7498320 DOI: 10.1093/nar/gkaa625] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022] Open
Abstract
Cilia assembly is under strict transcriptional control during animal development. In vertebrates, a hierarchy of transcription factors (TFs) are involved in controlling the specification, differentiation and function of multiciliated epithelia. RFX TFs play key functions in the control of ciliogenesis in animals. Whereas only one RFX factor regulates ciliogenesis in C. elegans, several distinct RFX factors have been implicated in this process in vertebrates. However, a clear understanding of the specific and redundant functions of different RFX factors in ciliated cells remains lacking. Using RNA-seq and ChIP-seq approaches we identified genes regulated directly and indirectly by RFX1, RFX2 and RFX3 in mouse ependymal cells. We show that these three TFs have both redundant and specific functions in ependymal cells. Whereas RFX1, RFX2 and RFX3 occupy many shared genomic loci, only RFX2 and RFX3 play a prominent and redundant function in the control of motile ciliogenesis in mice. Our results provide a valuable list of candidate ciliary genes. They also reveal stunning differences between compensatory processes operating in vivo and ex vivo.
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Affiliation(s)
- Sylvain Lemeille
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Marie Paschaki
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Dominique Baas
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Laurette Morlé
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Jean-Luc Duteyrat
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Aouatef Ait-Lounis
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Emmanuèle Barras
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Fabien Soulavie
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Julie Jerber
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Joëlle Thomas
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Yong Zhang
- Department of Medicine and Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Michael J Holtzman
- Department of Medicine and Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri
| | - W Stephen Kistler
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
| | - Walter Reith
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Bénédicte Durand
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
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15
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Hong CJ, Yeon J, Yeo BK, Woo H, An HK, Heo W, Kim K, Yu SW. Fas-apoptotic inhibitory molecule 2 localizes to the lysosome and facilitates autophagosome-lysosome fusion through the LC3 interaction region motif-dependent interaction with LC3. FASEB J 2020; 34:161-179. [PMID: 31914609 DOI: 10.1096/fj.201901626r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/20/2019] [Accepted: 10/08/2019] [Indexed: 01/08/2023]
Abstract
Fas-apoptotic inhibitory molecule 2 (FAIM2) is a member of the transmembrane BAX inhibitor motif-containing (TMBIM) family. TMBIM family is comprised of six anti-apoptotic proteins that suppress cell death by regulating endoplasmic reticulum Ca2+ homeostasis. Recent studies have implicated two TMBIM proteins, GRINA and BAX Inhibitor-1, in mediating cytoprotection via autophagy. However, whether FAIM2 plays a role in autophagy has been unknown. Here we show that FAIM2 localizes to the lysosomes at basal state and facilitates autophagy through interaction with microtubule-associated protein 1 light chain 3 proteins in human neuroblastoma SH-SY5Y cells. FAIM2 overexpression increased autophagy flux, while autophagy flux was impaired in shRNA-mediated knockdown (shFAIM2) cells, and the impairment was more evident in the presence of rapamycin. In shFAIM2 cells, autophagosome maturation through fusion with lysosomes was impaired, leading to accumulation of autophagosomes. A functional LC3-interacting region motif within FAIM2 was essential for the interaction with LC3 and rescue of autophagy flux in shFAIM2 cells while LC3-binding property of FAIM2 was dispensable for the anti-apoptotic function in response to Fas receptor-mediated apoptosis. Suppression of autophagosome maturation was also observed in a null mutant of Caenorhabditis elegans lacking xbx-6, the ortholog of FAIM2. Our study suggests that FAIM2 is a novel regulator of autophagy mediating autophagosome maturation through the interaction with LC3.
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Affiliation(s)
- Caroline Jeeyeon Hong
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Jihye Yeon
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Bo Kyoung Yeo
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Hanwoong Woo
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Hyun-Kyu An
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Woojung Heo
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Kyuhyung Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Seong-Woon Yu
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
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16
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CiliaCarta: An integrated and validated compendium of ciliary genes. PLoS One 2019; 14:e0216705. [PMID: 31095607 PMCID: PMC6522010 DOI: 10.1371/journal.pone.0216705] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/26/2019] [Indexed: 12/25/2022] Open
Abstract
The cilium is an essential organelle at the surface of mammalian cells whose dysfunction causes a wide range of genetic diseases collectively called ciliopathies. The current rate at which new ciliopathy genes are identified suggests that many ciliary components remain undiscovered. We generated and rigorously analyzed genomic, proteomic, transcriptomic and evolutionary data and systematically integrated these using Bayesian statistics into a predictive score for ciliary function. This resulted in 285 candidate ciliary genes. We generated independent experimental evidence of ciliary associations for 24 out of 36 analyzed candidate proteins using multiple cell and animal model systems (mouse, zebrafish and nematode) and techniques. For example, we show that OSCP1, which has previously been implicated in two distinct non-ciliary processes, causes ciliogenic and ciliopathy-associated tissue phenotypes when depleted in zebrafish. The candidate list forms the basis of CiliaCarta, a comprehensive ciliary compendium covering 956 genes. The resource can be used to objectively prioritize candidate genes in whole exome or genome sequencing of ciliopathy patients and can be accessed at http://bioinformatics.bio.uu.nl/john/syscilia/ciliacarta/.
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17
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Moreno E, Lenuzzi M, Rödelsperger C, Prabh N, Witte H, Roeseler W, Riebesell M, Sommer RJ. DAF‐19/RFX controls ciliogenesis and influences oxygen‐induced social behaviors in
Pristionchus pacificus. Evol Dev 2018; 20:233-243. [DOI: 10.1111/ede.12271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Eduardo Moreno
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Maša Lenuzzi
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Christian Rödelsperger
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Neel Prabh
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Hanh Witte
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Waltraud Roeseler
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Metta Riebesell
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Ralf J. Sommer
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
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18
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The complexity of the cilium: spatiotemporal diversity of an ancient organelle. Curr Opin Cell Biol 2018; 55:139-149. [PMID: 30138887 DOI: 10.1016/j.ceb.2018.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 02/06/2023]
Abstract
Cilia are microtubule-based appendages present on almost all vertebrate cell types where they mediate a myriad of cellular processes critical for development and homeostasis. In humans, impaired ciliary function is associated with an ever-expanding repertoire of phenotypically-overlapping yet highly variable genetic disorders, the ciliopathies. Extensive work to elucidate the structure, function, and composition of the cilium is offering hints that the `static' representation of the cilium is a gross oversimplification of a highly dynamic organelle whose functions are choreographed dynamically across cell types, developmental, and homeostatic contexts. Understanding this diversity will require discerning ciliary versus non-ciliary roles for classically-defined `ciliary' proteins; defining ciliary protein-protein interaction networks within and beyond the cilium; and resolving the spatiotemporal diversity of ciliary structure and function. Here, focusing on one evolutionarily conserved ciliary module, the intraflagellar transport system, we explore these ideas and propose potential future studies that will improve our knowledge gaps of the oversimplified cilium and, by extension, inform the reasons that underscore the striking range of clinical pathologies associated with ciliary dysfunction.
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19
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Yi P, Xie C, Ou G. The kinases male germ cell-associated kinase and cell cycle-related kinase regulate kinesin-2 motility inCaenorhabditis elegansneuronal cilia. Traffic 2018; 19:522-535. [DOI: 10.1111/tra.12572] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Peishan Yi
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences and MOE Key Laboratory for Protein Science; Tsinghua University; Beijing China
| | - Chao Xie
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences and MOE Key Laboratory for Protein Science; Tsinghua University; Beijing China
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences and MOE Key Laboratory for Protein Science; Tsinghua University; Beijing China
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20
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Muthaiyan Shanmugam M, Bhan P, Huang HY, Hsieh J, Hua TE, Wu GH, Punjabi H, Lee Aplícano VD, Chen CW, Wagner OI. Cilium Length and Intraflagellar Transport Regulation by Kinases PKG-1 and GCK-2 in Caenorhabditis elegans Sensory Neurons. Mol Cell Biol 2018; 38:e00612-17. [PMID: 29378827 PMCID: PMC5854826 DOI: 10.1128/mcb.00612-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 12/21/2017] [Accepted: 01/18/2018] [Indexed: 12/31/2022] Open
Abstract
To understand how ciliopathies such as polycystic kidney disease or Bardet-Biedl syndrome develop, we need to understand the basic molecular mechanisms underlying cilium development. Cilium growth depends on the presence of functional intraflagellar transport (IFT) machinery, and we hypothesized that various kinases and phosphatases might be involved in this regulatory process. A candidate screen revealed two kinases, PKG-1 (a cGMP-dependent protein kinase) and GCK-2 (a mitogen-activated protein kinase kinase kinase kinase 3 [MAP4K3] kinase involved in mTOR signaling), significantly affecting dye filling, chemotaxis, cilium morphology, and IFT component distribution. PKG-1 and GCK-2 show similar expression patterns in Caenorhabditis elegans cilia and colocalize with investigated IFT machinery components. In pkg-1 mutants, a high level of accumulation of kinesin-2 OSM-3 in distal segments was observed in conjunction with an overall reduction of anterograde and retrograde IFT particle A transport, likely as a function of reduced tubulin acetylation. In contrast, in gck-2 mutants, both kinesin-2 motility and IFT particle A motility were significantly elevated in the middle segments, in conjunction with increased tubulin acetylation, possibly the cause of longer cilium growth. Observed effects in mutants can be also seen in manipulating upstream and downstream effectors of the respective cGMP and mTOR pathways. Importantly, transmission electron microscopy (TEM) analysis revealed no structural changes in cilia of pkg-1 and gck-2 mutants.
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Affiliation(s)
- Muniesh Muthaiyan Shanmugam
- National Tsing Hua University, Institute of Molecular and Cellular Biology, Department of Life Science, Hsinchu, Taiwan, Republic of China
| | - Prerana Bhan
- National Tsing Hua University, Institute of Molecular and Cellular Biology, Department of Life Science, Hsinchu, Taiwan, Republic of China
| | - Hsin-Yi Huang
- National Tsing Hua University, Institute of Molecular and Cellular Biology, Department of Life Science, Hsinchu, Taiwan, Republic of China
| | - Jung Hsieh
- National Tsing Hua University, Institute of Molecular and Cellular Biology, Department of Life Science, Hsinchu, Taiwan, Republic of China
| | - Tzu-En Hua
- Electron Microscopy Core Facility, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Gong-Her Wu
- National Tsing Hua University, Institute of Molecular and Cellular Biology, Department of Life Science, Hsinchu, Taiwan, Republic of China
| | - Helly Punjabi
- National Tsing Hua University, Institute of Molecular and Cellular Biology, Department of Life Science, Hsinchu, Taiwan, Republic of China
| | - Víctor Daniel Lee Aplícano
- National Tsing Hua University, Institute of Molecular and Cellular Biology, Department of Life Science, Hsinchu, Taiwan, Republic of China
| | - Chih-Wei Chen
- National Tsing Hua University, Institute of Molecular and Cellular Biology, Department of Life Science, Hsinchu, Taiwan, Republic of China
| | - Oliver Ingvar Wagner
- National Tsing Hua University, Institute of Molecular and Cellular Biology, Department of Life Science, Hsinchu, Taiwan, Republic of China
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21
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Sugiaman-Trapman D, Vitezic M, Jouhilahti EM, Mathelier A, Lauter G, Misra S, Daub CO, Kere J, Swoboda P. Characterization of the human RFX transcription factor family by regulatory and target gene analysis. BMC Genomics 2018; 19:181. [PMID: 29510665 PMCID: PMC5838959 DOI: 10.1186/s12864-018-4564-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Evolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. Here, we provide a comprehensive analysis of all the eight human RFX genes (RFX1-8), their spatial and temporal expression profiles, potential upstream regulators and target genes. RESULTS We extracted all known human RFX1-8 gene expression profiles from the FANTOM5 database derived from transcription start site (TSS) activity as captured by Cap Analysis of Gene Expression (CAGE) technology. RFX genes are broadly (RFX1-3, RFX5, RFX7) and specifically (RFX4, RFX6) expressed in different cell types, with high expression in four organ systems: immune system, gastrointestinal tract, reproductive system and nervous system. Tissue type specific expression profiles link defined RFX family members with the target gene batteries they regulate. We experimentally confirmed novel TSS locations and characterized the previously undescribed RFX8 to be lowly expressed. RFX tissue and cell type specificity arises mainly from differences in TSS architecture. RFX transcript isoforms lacking a DNA binding domain (DBD) open up new possibilities for combinatorial target gene regulation. Our results favor a new grouping of the RFX family based on protein domain composition. We uncovered and experimentally confirmed the TFs SP2 and ESR1 as upstream regulators of specific RFX genes. Using TF binding profiles from the JASPAR database, we determined relevant patterns of X-box motif positioning with respect to gene TSS locations of human RFX target genes. CONCLUSIONS The wealth of data we provide will serve as the basis for precisely determining the roles RFX TFs play in human development and disease.
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Affiliation(s)
| | - Morana Vitezic
- Department of Biology, Bioinformatics Centre, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark
| | - Eeva-Mari Jouhilahti
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, University of Oslo, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Sougat Misra
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- School of Basic and Medical Biosciences, King's College London, London, UK
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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22
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De Stasio EA, Mueller KP, Bauer RJ, Hurlburt AJ, Bice SA, Scholtz SL, Phirke P, Sugiaman-Trapman D, Stinson LA, Olson HB, Vogel SL, Ek-Vazquez Z, Esemen Y, Korzynski J, Wolfe K, Arbuckle BN, Zhang H, Lombard-Knapp G, Piasecki BP, Swoboda P. An Expanded Role for the RFX Transcription Factor DAF-19, with Dual Functions in Ciliated and Nonciliated Neurons. Genetics 2018; 208:1083-1097. [PMID: 29301909 PMCID: PMC5844324 DOI: 10.1534/genetics.117.300571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/02/2017] [Indexed: 02/06/2023] Open
Abstract
Regulatory Factor X (RFX) transcription factors (TFs) are best known for activating genes required for ciliogenesis in both vertebrates and invertebrates. In humans, eight RFX TFs have a variety of tissue-specific functions, while in the worm Caenorhabditis elegans, the sole RFX gene, daf-19, encodes a set of nested isoforms. Null alleles of daf-19 confer pleiotropic effects including altered development with a dauer constitutive phenotype, complete absence of cilia and ciliary proteins, and defects in synaptic protein maintenance. We sought to identify RFX/daf-19 target genes associated with neuronal functions other than ciliogenesis using comparative transcriptome analyses at different life stages of the worm. Subsequent characterization of gene expression patterns revealed one set of genes activated in the presence of DAF-19 in ciliated sensory neurons, whose activation requires the daf-19c isoform, also required for ciliogenesis. A second set of genes is downregulated in the presence of DAF-19, primarily in nonsensory neurons. The human orthologs of some of these neuronal genes are associated with human diseases. We report the novel finding that daf-19a is directly or indirectly responsible for downregulation of these neuronal genes in C. elegans by characterizing a new mutation affecting the daf-19a isoform (tm5562) and not associated with ciliogenesis, but which confers synaptic and behavioral defects. Thus, we have identified a new regulatory role for RFX TFs in the nervous system. The new daf-19 candidate target genes we have identified by transcriptomics will serve to uncover the molecular underpinnings of the pleiotropic effects that daf-19 exerts on nervous system function.
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Affiliation(s)
| | | | - Rosemary J Bauer
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | | | - Sophie A Bice
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Sophie L Scholtz
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Prasad Phirke
- Department of Biosciences and Nutrition, Karolinska Institute, 141 83 Huddinge, Sweden
| | | | - Loraina A Stinson
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Haili B Olson
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Savannah L Vogel
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | | | - Yagmur Esemen
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Jessica Korzynski
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Kelsey Wolfe
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Bonnie N Arbuckle
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - He Zhang
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | | | - Brian P Piasecki
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, 141 83 Huddinge, Sweden
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23
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Sigg MA, Menchen T, Lee C, Johnson J, Jungnickel MK, Choksi SP, Garcia G, Busengdal H, Dougherty GW, Pennekamp P, Werner C, Rentzsch F, Florman HM, Krogan N, Wallingford JB, Omran H, Reiter JF. Evolutionary Proteomics Uncovers Ancient Associations of Cilia with Signaling Pathways. Dev Cell 2018; 43:744-762.e11. [PMID: 29257953 DOI: 10.1016/j.devcel.2017.11.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 09/18/2017] [Accepted: 11/17/2017] [Indexed: 12/19/2022]
Abstract
Cilia are organelles specialized for movement and signaling. To infer when during evolution signaling pathways became associated with cilia, we characterized the proteomes of cilia from sea urchins, sea anemones, and choanoflagellates. We identified 437 high-confidence ciliary candidate proteins conserved in mammals and discovered that Hedgehog and G-protein-coupled receptor pathways were linked to cilia before the origin of bilateria and transient receptor potential (TRP) channels before the origin of animals. We demonstrated that candidates not previously implicated in ciliary biology localized to cilia and further investigated ENKUR, a TRP channel-interacting protein identified in the cilia of all three organisms. ENKUR localizes to motile cilia and is required for patterning the left-right axis in vertebrates. Moreover, mutation of ENKUR causes situs inversus in humans. Thus, proteomic profiling of cilia from diverse eukaryotes defines a conserved ciliary proteome, reveals ancient connections to signaling, and uncovers a ciliary protein that underlies development and human disease.
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Affiliation(s)
- Monika Abedin Sigg
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Tabea Menchen
- Department of General Pediatrics, University Children's Hospital Muenster, Muenster 48149, Germany
| | - Chanjae Lee
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffery Johnson
- Gladstone Institute of Cardiovascular Disease and Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA
| | - Melissa K Jungnickel
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Semil P Choksi
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Galo Garcia
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Henriette Busengdal
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5008, Norway
| | - Gerard W Dougherty
- Department of General Pediatrics, University Children's Hospital Muenster, Muenster 48149, Germany
| | - Petra Pennekamp
- Department of General Pediatrics, University Children's Hospital Muenster, Muenster 48149, Germany
| | - Claudius Werner
- Department of General Pediatrics, University Children's Hospital Muenster, Muenster 48149, Germany
| | - Fabian Rentzsch
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5008, Norway
| | - Harvey M Florman
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Nevan Krogan
- Gladstone Institute of Cardiovascular Disease and Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Heymut Omran
- Department of General Pediatrics, University Children's Hospital Muenster, Muenster 48149, Germany
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
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24
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Antagonistic regulation of trafficking to Caenorhabditis elegans sensory cilia by a Retinal Degeneration 3 homolog and retromer. Proc Natl Acad Sci U S A 2017; 115:E438-E447. [PMID: 29282322 DOI: 10.1073/pnas.1712302115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Sensory neurons often possess cilia with elaborate membrane structures that are adapted to the sensory modality of the host cell. Mechanisms that target sensory transduction proteins to these specialized membrane domains remain poorly understood. Here, we show that a homolog of the human retinal dystrophy gene Retinal Degeneration 3 (RD3) is a Golgi-associated protein required for efficient trafficking of a sensory receptor, the receptor-type guanylate cyclase GCY-9, to cilia in chemosensory neurons of the nematode Caenorhabditis elegans The trafficking defect caused by mutation of the nematode RD3 homolog is suppressed in vivo by mutation of key components of the retromer complex, which mediates recycling of cargo from endosomes to the Golgi. Our data show that there exists a critical balance in sensory neurons between the rates of anterograde and retrograde trafficking of cargo destined for the sensory cilium and this balance requires molecular specialization at an early stage of the secretory pathway.
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25
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Kim B, Suo B, Emmons SW. Gene Function Prediction Based on Developmental Transcriptomes of the Two Sexes in C. elegans. Cell Rep 2017; 17:917-928. [PMID: 27732864 PMCID: PMC5656000 DOI: 10.1016/j.celrep.2016.09.051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/03/2016] [Accepted: 09/16/2016] [Indexed: 11/29/2022] Open
Abstract
We compare whole-animal RNA-seq transcriptomes for C. elegans males and hermaphrodites from the late L3 larval stage to young adulthood. During this interval, male sexual structures develop, including extensive neurogenesis and synaptogenesis that nearly doubles the size of the nervous system. Previous genome-wide expression studies in C. elegans have usually focused on only one sex—the hermaphrodite—and there are a relatively large number of genes that remain without meaningful annotation. In the present study, differential expression analysis of the RNA-seq data revealed 1,751 genes expressed at a higher level in the male. By differential expression and co-expression analyses, we identified transcription factors required for differentiation of male genital structures, semen proteins, and candidates for components of synapse function. Comparison with other prediction tools suggests that our dataset can expand gene predictions. The results validate the dataset as a rich resource for future gene discovery in C. elegans.
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Affiliation(s)
- Byunghyuk Kim
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Bangxia Suo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Scott W Emmons
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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26
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Piasecki BP, Sasani TA, Lessenger AT, Huth N, Farrell S. MAPK-15 is a ciliary protein required for PKD-2 localization and male mating behavior in Caenorhabditis elegans. Cytoskeleton (Hoboken) 2017; 74:390-402. [PMID: 28745435 DOI: 10.1002/cm.21387] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 06/14/2017] [Accepted: 07/05/2017] [Indexed: 12/16/2022]
Abstract
Cilia are conserved cellular structures that facilitate sensory-based processes, including those required for neuronal and kidney functions. Here, we show that the human mitogen activated kinase-15 (MAPK-15) ortholog in Caenorhabditis elegans encodes a ciliary protein. A strain harboring a mutation in the catalytic site of the kinase domain results in ciliary-specific defects in tail neurons of both hermaphrodite and male worms, manifesting in dye uptake, dendrite extension, and male mating behavior defects. Transgenic-fusion constructs for two mapk-15 isoforms (A and C) with full-length kinase domains were generated. Expression of either the A- or C-specific isoform rescues the dye-filling and male-mating defective phenotypes, confirming the ciliary function of mapk-15. Expression of mapk-15 occurs in many ciliated-sensory neurons of the head and tail in hermaphrodite and male worms. Localization of MAPK-15 isoforms A and C occurs in the cell body, dendritic processes, and cilia. A C. elegans ortholog of polycystin-2, a protein that when defective in mammals results in autosomal dominant polycystic kidney disease, is mislocalized in the male ray neurons of mapk-15 mutant worms. Expression of the mapk-15 gene by the pkd-2 promoter partially rescues the male-mating defects observed in mapk-15 mutant animals. Expression of mapk-15 is DAF-19/RFX dependent in some CSNs and DAF-19/RFX independent in others. Collectively, these data suggest that MAPK-15 functions upstream of PKD-2 localization to modulate ciliary sensory functions.
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Affiliation(s)
| | - Thomas A Sasani
- Department of Biology, Lawrence University, Appleton, Wisconsin.,Department of Human Genetics, University of Utah, Salt Lake City, Utah
| | | | - Nicholas Huth
- Department of Biology, Lawrence University, Appleton, Wisconsin
| | - Shane Farrell
- Department of Biology, Lawrence University, Appleton, Wisconsin
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27
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Quigley IK, Kintner C. Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression. PLoS Genet 2017; 13:e1006538. [PMID: 28103240 PMCID: PMC5245798 DOI: 10.1371/journal.pgen.1006538] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 12/14/2016] [Indexed: 11/18/2022] Open
Abstract
Cooperative transcription factor binding at cis-regulatory sites in the genome drives robust eukaryotic gene expression, and many such sites must be coordinated to produce coherent transcriptional programs. The transcriptional program leading to motile cilia formation requires members of the DNA-binding forkhead (Fox) and Rfx transcription factor families and these factors co-localize to cilia gene promoters, but it is not clear how many cilia genes are regulated by these two factors, whether these factors act directly or indirectly, or how these factors act with specificity in the context of a 3-dimensional genome. Here, we use genome-wide approaches to show that cilia genes reside at the boundaries of topological domains and that these areas have low enhancer density. We show that the transcription factors Foxj1 and Rfx2 binding occurs in the promoters of more cilia genes than other known cilia transcription factors and that while Rfx2 binds directly to promoters and enhancers equally, Foxj1 prefers direct binding to enhancers and is stabilized at promoters by Rfx2. Finally, we show that Rfx2 and Foxj1 lie at the anchor endpoints of chromatin loops, suggesting that target genes are activated when Foxj1 bound at distal sites is recruited via a loop created by Rfx2 binding at both sites. We speculate that the primary function of Rfx2 is to stabilize distal enhancers with proximal promoters by operating as a scaffolding factor, bringing key regulatory domains bound by Foxj1 into close physical proximity and enabling coordinated cilia gene expression. The multiciliated cell extends hundreds of motile cilia to produce fluid flow in the airways and other organ systems. The formation of this specialized cell type requires the coordinated expression of hundreds of genes in order to produce all the protein parts motile cilia require. While a relatively small number of transcription factors has been identified that promote gene expression during multiciliate cell differentiation, it is not clear how they work together to coordinate the expression of genes required for multiple motile ciliation. Here, we show that two transcription factors known to drive cilia formation, Foxj1 and Rfx2, play complementary roles wherein Foxj1 activates target genes but tends not to bind near them in the genome, whereas Rfx2 can’t activate target genes by itself but instead acts as a scaffold by localizing Foxj1 to the proper targets. These results suggest not only a mechanism by which complex gene expression is coordinated in multiciliated cells, but also how transcriptional programs in general could be modular and deployed across different cellular contexts with the same basic promoter configuration.
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Affiliation(s)
- Ian K. Quigley
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies La Jolla, California, United States of America
- * E-mail:
| | - Chris Kintner
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies La Jolla, California, United States of America
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28
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Bainbridge C, Rodriguez A, Schuler A, Cisneros M, Vidal-Gadea AG. Magnetic orientation in C. elegans relies on the integrity of the villi of the AFD magnetosensory neurons. ACTA ACUST UNITED AC 2016; 110:76-82. [PMID: 27940210 DOI: 10.1016/j.jphysparis.2016.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/28/2016] [Accepted: 12/01/2016] [Indexed: 01/07/2023]
Abstract
The magnetic field of the earth provides many organisms with sufficient information to successfully navigate through their environments. While evidence suggests the widespread use of this sensory modality across many taxa, it remains an understudied sensory modality. We have recently showed that the nematode C. elegans orients to earth-strength magnetic fields using the first pair of described magnetosensory neurons, AFDs. The AFD cells are a pair of ciliated sensory neurons crowned by fifty villi known to be implicated in temperature sensation. We investigated the potential importance of these subcellular structures for the performance of magnetic orientation. We show that ciliary integrity and villi number are essential for magnetic orientation. Mutants with impairments AFD cilia or villi structure failed to orient to magnetic fields. Similarly, C. elegans larvae possessing immature AFD neurons with fewer villi were also unable to orient to magnetic fields. Larvae of every stage however retained the ability to orient to thermal gradients. To our knowledge, this is the first behavioral separation of magnetic and thermal orientation in C. elegans. We conclude that magnetic orientation relies on the function of both cilia and villi in the AFD neurons. The role of villi in multiple sensory transduction pathways involved in the sensory transduction of vectorial stimuli further supports the likely role of the villi of the AFD neurons as the site for magnetic field transduction. The genetic and behavioral tractability of C. elegans make it a promising system for uncovering potentially conserved molecular mechanisms by which animals across taxa detect and orient to magnetic fields.
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Affiliation(s)
- Chance Bainbridge
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Anjelica Rodriguez
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Andrew Schuler
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Michael Cisneros
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Andrés G Vidal-Gadea
- School of Biological Sciences, Illinois State University, Normal, IL, USA. http://biology.illinoisstate.edu/avidal
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29
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Whole-Organism Developmental Expression Profiling Identifies RAB-28 as a Novel Ciliary GTPase Associated with the BBSome and Intraflagellar Transport. PLoS Genet 2016; 12:e1006469. [PMID: 27930654 PMCID: PMC5145144 DOI: 10.1371/journal.pgen.1006469] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 11/08/2016] [Indexed: 01/18/2023] Open
Abstract
Primary cilia are specialised sensory and developmental signalling devices extending from the surface of most eukaryotic cells. Defects in these organelles cause inherited human disorders (ciliopathies) such as retinitis pigmentosa and Bardet-Biedl syndrome (BBS), frequently affecting many physiological and developmental processes across multiple organs. Cilium formation, maintenance and function depend on intracellular transport systems such as intraflagellar transport (IFT), which is driven by kinesin-2 and IFT-dynein motors and regulated by the Bardet-Biedl syndrome (BBS) cargo-adaptor protein complex, or BBSome. To identify new cilium-associated genes, we employed the nematode C. elegans, where ciliogenesis occurs within a short timespan during late embryogenesis when most sensory neurons differentiate. Using whole-organism RNA-Seq libraries, we discovered a signature expression profile highly enriched for transcripts of known ciliary proteins, including FAM-161 (FAM161A orthologue), CCDC-104 (CCDC104), and RPI-1 (RP1/RP1L1), which we confirm are cilium-localised in worms. From a list of 185 candidate ciliary genes, we uncover orthologues of human MAP9, YAP, CCDC149, and RAB28 as conserved cilium-associated components. Further analyses of C. elegans RAB-28, recently associated with autosomal-recessive cone-rod dystrophy, reveal that this small GTPase is exclusively expressed in ciliated neurons where it dynamically associates with IFT trains. Whereas inactive GDP-bound RAB-28 displays no IFT movement and diffuse localisation, GTP-bound (activated) RAB-28 concentrates at the periciliary membrane in a BBSome-dependent manner and undergoes bidirectional IFT. Functional analyses reveal that whilst cilium structure, sensory function and IFT are seemingly normal in a rab-28 null allele, overexpression of predicted GDP or GTP locked variants of RAB-28 perturbs cilium and sensory pore morphogenesis and function. Collectively, our findings present a new approach for identifying ciliary proteins, and unveil RAB28, a GTPase most closely related to the BBS protein RABL4/IFT27, as an IFT-associated cargo with BBSome-dependent cell autonomous and non-autonomous functions at the ciliary base. Ciliopathies are genetic disorders that arise from loss or mutation of genes that encode proteins which play roles in the biology of cilia, organelles found on most of the cells in the human body. Ciliopathy-associated ailments include–but are not limited to–kidney dysfunction, blindness, skeletal abnormalities, as well as brain disorders. Although a great number of cilium-targeted proteins are known, it is thought that a large proportion remain unidentified. Here, we use a developmental gene expression series to discover novel cilia genes in the nematode Caenorhabditis elegans. We present several cilium-localised proteins resulting from our analysis, including RAB-28, a GTPase previously implicated in the degenerative eye disease known as cone-rod dystrophy. Through live videomicroscopy, we show that RAB-28 undergoes bidirectional transport within the cilium. A RAB-28 inactivating mutation results in loss of transport, while an activating mutation results in stronger localisation at the ciliary base and robust transport, although overexpression results in a variety of cilia-related defects. Both the wild type and activating mutant proteins require the Bardet-Biedl Syndrome-related complex of proteins for their transport, linking RAB-28 to an established ciliary transport machinery.
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30
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Wei Q, Zhang Y, Schouteden C, Zhang Y, Zhang Q, Dong J, Wonesch V, Ling K, Dammermann A, Hu J. The hydrolethalus syndrome protein HYLS-1 regulates formation of the ciliary gate. Nat Commun 2016; 7:12437. [PMID: 27534274 PMCID: PMC4992140 DOI: 10.1038/ncomms12437] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 06/30/2016] [Indexed: 12/18/2022] Open
Abstract
Transition fibres (TFs), together with the transition zone (TZ), are basal ciliary structures thought to be crucial for cilium biogenesis and function by acting as a ciliary gate to regulate selective protein entry and exit. Here we demonstrate that the centriolar and basal body protein HYLS-1, the C. elegans orthologue of hydrolethalus syndrome protein 1, is required for TF formation, TZ organization and ciliary gating. Loss of HYLS-1 compromises the docking and entry of intraflagellar transport (IFT) particles, ciliary gating for both membrane and soluble proteins, and axoneme assembly. Additional depletion of the TF component DYF-19 in hyls-1 mutants further exacerbates TZ anomalies and completely abrogates ciliogenesis. Our data support an important role for HYLS-1 and TFs in establishment of the ciliary gate and underline the importance of selective protein entry for cilia assembly.
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Affiliation(s)
- Qing Wei
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yingyi Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Clementine Schouteden
- Max F. Perutz Laboratories, Vienna Biocenter (VBC), University of Vienna, A-1030 Vienna, Austria
| | - Yuxia Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Qing Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Jinhong Dong
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Veronika Wonesch
- Max F. Perutz Laboratories, Vienna Biocenter (VBC), University of Vienna, A-1030 Vienna, Austria
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Alexander Dammermann
- Max F. Perutz Laboratories, Vienna Biocenter (VBC), University of Vienna, A-1030 Vienna, Austria
| | - Jinghua Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota 55905, USA.,Mayo Translational PKD Center, Mayo Clinic, Rochester, Minnesota 55905, USA
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31
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Tammimies K, Bieder A, Lauter G, Sugiaman-Trapman D, Torchet R, Hokkanen ME, Burghoorn J, Castrén E, Kere J, Tapia-Páez I, Swoboda P. Ciliary dyslexia candidate genes DYX1C1 and DCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs. FASEB J 2016; 30:3578-3587. [PMID: 27451412 PMCID: PMC5024701 DOI: 10.1096/fj.201500124rr] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 07/05/2016] [Indexed: 11/11/2022]
Abstract
DYX1C1, DCDC2, and KIAA0319 are
three of the most replicated dyslexia candidate genes (DCGs). Recently, these DCGs
were implicated in functions at the cilium. Here, we investigate the regulation of
these DCGs by Regulatory Factor X transcription factors (RFX TFs), a gene family
known for transcriptionally regulating ciliary genes. We identify conserved X-box
motifs in the promoter regions of DYX1C1, DCDC2, and
KIAA0319 and demonstrate their functionality, as well as the
ability to recruit RFX TFs using reporter gene and electrophoretic mobility shift
assays. Furthermore, we uncover a complex regulation pattern between
RFX1, RFX2, and RFX3 and their
significant effect on modifying the endogenous expression of DYX1C1
and DCDC2 in a human retinal pigmented epithelial cell line
immortalized with hTERT (hTERT-RPE1). In addition, induction of ciliogenesis
increases the expression of RFX TFs and DCGs. At the protein level, we show that
endogenous DYX1C1 localizes to the base of the cilium, whereas DCDC2 localizes along
the entire axoneme of the cilium, thereby validating earlier localization studies
using overexpression models. Our results corroborate the emerging role of DCGs in
ciliary function and characterize functional noncoding elements, X-box promoter
motifs, in DCG promoter regions, which thus can be targeted for mutation screening in
dyslexia and ciliopathies associated with these genes.—Tammimies, K., Bieder,
A., Lauter, G., Sugiaman-Trapman, D., Torchet, R., Hokkanen, M.-E., Burghoorn, J.,
Castrén, E., Kere, J., Tapia-Páez, I., Swoboda, P. Ciliary dyslexia
candidate genes DYX1C1 and DCDC2 are regulated by
Regulatory Factor (RF) X transcription factors through X-box promoter motifs.
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Affiliation(s)
- Kristiina Tammimies
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Center of Neurodevelopmental Disorders (KIND), Pediatric Neuropsychiatry Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Andrea Bieder
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Rachel Torchet
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Jan Burghoorn
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Eero Castrén
- Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland; and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Isabel Tapia-Páez
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden;
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden;
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Loucks CM, Bialas NJ, Dekkers MPJ, Walker DS, Grundy LJ, Li C, Inglis PN, Kida K, Schafer WR, Blacque OE, Jansen G, Leroux MR. PACRG, a protein linked to ciliary motility, mediates cellular signaling. Mol Biol Cell 2016; 27:2133-44. [PMID: 27193298 PMCID: PMC4927285 DOI: 10.1091/mbc.e15-07-0490] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 05/09/2016] [Indexed: 01/15/2023] Open
Abstract
Cilia are cellular projections that can be motile to generate fluid flow or nonmotile to enable signaling. Both forms are based on shared components, and proteins involved in ciliary motility, like PACRG, may also function in ciliary signaling. Caenorhabditis elegans PACRG acts in a subset of nonmotile cilia to influence a learning behavior and promote longevity. Cilia are microtubule-based organelles that project from nearly all mammalian cell types. Motile cilia generate fluid flow, whereas nonmotile (primary) cilia are required for sensory physiology and modulate various signal transduction pathways. Here we investigate the nonmotile ciliary signaling roles of parkin coregulated gene (PACRG), a protein linked to ciliary motility. PACRG is associated with the protofilament ribbon, a structure believed to dictate the regular arrangement of motility-associated ciliary components. Roles for protofilament ribbon–associated proteins in nonmotile cilia and cellular signaling have not been investigated. We show that PACRG localizes to a small subset of nonmotile cilia in Caenorhabditis elegans, suggesting an evolutionary adaptation for mediating specific sensory/signaling functions. We find that it influences a learning behavior known as gustatory plasticity, in which it is functionally coupled to heterotrimeric G-protein signaling. We also demonstrate that PACRG promotes longevity in C. elegans by acting upstream of the lifespan-promoting FOXO transcription factor DAF-16 and likely upstream of insulin/IGF signaling. Our findings establish previously unrecognized sensory/signaling functions for PACRG and point to a role for this protein in promoting longevity. Furthermore, our work suggests additional ciliary motility-signaling connections, since EFHC1 (EF-hand containing 1), a potential PACRG interaction partner similarly associated with the protofilament ribbon and ciliary motility, also positively regulates lifespan.
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Affiliation(s)
- Catrina M Loucks
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Nathan J Bialas
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | | | - Denise S Walker
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Laura J Grundy
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - P Nick Inglis
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Katarzyna Kida
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - William R Schafer
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gert Jansen
- Department of Cell Biology, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Hanke-Gogokhia C, Wu Z, Gerstner CD, Frederick JM, Zhang H, Baehr W. Arf-like Protein 3 (ARL3) Regulates Protein Trafficking and Ciliogenesis in Mouse Photoreceptors. J Biol Chem 2016; 291:7142-55. [PMID: 26814127 DOI: 10.1074/jbc.m115.710954] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Indexed: 12/22/2022] Open
Abstract
Arf-like protein 3 (ARL3) is a ubiquitous small GTPase expressed in ciliated cells of plants and animals. Germline deletion ofArl3in mice causes multiorgan ciliopathy reminiscent of Bardet-Biedl or Joubert syndromes. As photoreceptors are elegantly compartmentalized and have cilia, we probed the function of ARL3 (ADP-ribosylation factor (Arf)-like 3 protein) by generating rod photoreceptor-specific (prefix(rod)) and retina-specific (prefix(ret))Arl3deletions. In predegenerate(rod)Arl3(-/-)mice, lipidated phototransduction proteins showed trafficking deficiencies, consistent with the role of ARL3 as a cargo displacement factor for lipid-binding proteins. By contrast,(ret)Arl3(-/-)rods and cones expressing Cre recombinase during embryonic development formed neither connecting cilia nor outer segments and degenerated rapidly. Absence of cilia infers participation of ARL3 in ciliogenesis and axoneme formation. Ciliogenesis was rescued, and degeneration was reversed in part by subretinal injection of adeno-associated virus particles expressing ARL3-EGFP. The conditional knock-out phenotypes permitted identification of two ARL3 functions, both in the GTP-bound form as follows: one as a regulator of intraflagellar transport participating in photoreceptor ciliogenesis and the other as a cargo displacement factor transporting lipidated protein to the outer segment. Surprisingly, a farnesylated inositol polyphosphate phosphatase only trafficked from the endoplasmic reticulum to the Golgi, thereby excluding it from a role in photoreceptor cilia physiology.
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Affiliation(s)
- Christin Hanke-Gogokhia
- From the Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, and the Department of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Zhijian Wu
- the NEI, National Institutes of Health, Bethesda, Maryland 20892
| | - Cecilia D Gerstner
- From the Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, and
| | - Jeanne M Frederick
- From the Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, and
| | - Houbin Zhang
- the Sichuan Provincial Key Laboratory for Human Disease Gene Study, Institute of Laboratory Medicine, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, 610072 Sichuan, China, the School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072 Sichuan, China, and
| | - Wolfgang Baehr
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, Utah 84132, From the Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, and the Department of Biology, University of Utah, Salt Lake City, Utah 84112
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Lokaj M, Kösling SK, Koerner C, Lange SM, van Beersum SEC, van Reeuwijk J, Roepman R, Horn N, Ueffing M, Boldt K, Wittinghofer A. The Interaction of CCDC104/BARTL1 with Arl3 and Implications for Ciliary Function. Structure 2015; 23:2122-32. [PMID: 26455799 PMCID: PMC4635315 DOI: 10.1016/j.str.2015.08.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/26/2015] [Accepted: 08/29/2015] [Indexed: 01/23/2023]
Abstract
Cilia are small antenna-like cellular protrusions critical for many developmental signaling pathways. The ciliary protein Arl3 has been shown to act as a specific release factor for myristoylated and farnesylated ciliary cargo molecules by binding to the effectors Unc119 and PDE6δ. Here we describe a newly identified Arl3 binding partner, CCDC104/CFAP36. Biochemical and structural analyses reveal that the protein contains a BART-like domain and is called BARTL1. It recognizes an LLxILxxL motif at the N-terminal amphipathic helix of Arl3, which is crucial for the interaction with the BART-like domain but also for the ciliary localization of Arl3 itself. These results seem to suggest a ciliary role of BARTL1, and possibly link it to the Arl3 transport network. We thus speculate on a regulatory mechanism whereby BARTL1 aids the presentation of active Arl3 to its GTPase-activating protein RP2 or hinders Arl3 membrane binding in the area of the transition zone.
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Affiliation(s)
- Mandy Lokaj
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Stefanie K Kösling
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Carolin Koerner
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Sven M Lange
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Sylvia E C van Beersum
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Jeroen van Reeuwijk
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Ronald Roepman
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Nicola Horn
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tübingen, Nägelestrasse 5, 72074 Tübingen, Germany
| | - Marius Ueffing
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tübingen, Nägelestrasse 5, 72074 Tübingen, Germany
| | - Karsten Boldt
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tübingen, Nägelestrasse 5, 72074 Tübingen, Germany
| | - Alfred Wittinghofer
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany.
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Taylor SP, Dantas TJ, Duran I, Wu S, Lachman RS, Nelson SF, Cohn DH, Vallee RB, Krakow D. Mutations in DYNC2LI1 disrupt cilia function and cause short rib polydactyly syndrome. Nat Commun 2015; 6:7092. [PMID: 26077881 PMCID: PMC4470332 DOI: 10.1038/ncomms8092] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 04/02/2015] [Indexed: 12/16/2022] Open
Abstract
The short rib polydactyly syndromes (SRPSs) are a heterogeneous group of autosomal recessive, perinatal lethal skeletal disorders characterized primarily by short, horizontal ribs, short limbs and polydactyly. Mutations in several genes affecting intraflagellar transport (IFT) cause SRPS but they do not account for all cases. Here we identify an additional SRPS gene and further unravel the functional basis for IFT. We perform whole-exome sequencing and identify mutations in a new disease-producing gene, cytoplasmic dynein-2 light intermediate chain 1, DYNC2LI1, segregating with disease in three families. Using primary fibroblasts, we show that DYNC2LI1 is essential for dynein-2 complex stability and that mutations in DYNC2LI1 result in variable length, including hyperelongated, cilia, Hedgehog pathway impairment and ciliary IFT accumulations. The findings in this study expand our understanding of SRPS locus heterogeneity and demonstrate the importance of DYNC2LI1 in dynein-2 complex stability, cilium function, Hedgehog regulation and skeletogenesis.
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Affiliation(s)
- S Paige Taylor
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Tiago J Dantas
- Department of Pathology and Cell Biology, Columbia University, New York, New York 10032, USA
| | - Ivan Duran
- Department of Orthopaedic Surgery and Orthopaedic Institute for Children, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Sulin Wu
- Department of Orthopaedic Surgery and Orthopaedic Institute for Children, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Ralph S Lachman
- International Skeletal Dysplasia Registry, University of California, Los Angeles, Los Angeles, California 90095, USA
| | | | - Stanley F Nelson
- 1] Department of Human Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA [2] Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Daniel H Cohn
- 1] Department of Orthopaedic Surgery and Orthopaedic Institute for Children, University of California, Los Angeles, Los Angeles, California 90095, USA [2] International Skeletal Dysplasia Registry, University of California, Los Angeles, Los Angeles, California 90095, USA [3] Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Richard B Vallee
- Department of Pathology and Cell Biology, Columbia University, New York, New York 10032, USA
| | - Deborah Krakow
- 1] Department of Human Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA [2] Department of Orthopaedic Surgery and Orthopaedic Institute for Children, University of California, Los Angeles, Los Angeles, California 90095, USA [3] International Skeletal Dysplasia Registry, University of California, Los Angeles, Los Angeles, California 90095, USA
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36
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Kroes HY, Monroe GR, van der Zwaag B, Duran KJ, de Kovel CG, van Roosmalen MJ, Harakalova M, Nijman IJ, Kloosterman WP, Giles RH, Knoers NVAM, van Haaften G. Joubert syndrome: genotyping a Northern European patient cohort. Eur J Hum Genet 2015; 24:214-20. [PMID: 25920555 DOI: 10.1038/ejhg.2015.84] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 02/09/2015] [Accepted: 03/25/2015] [Indexed: 11/09/2022] Open
Abstract
Joubert syndrome (JBS) is a rare neurodevelopmental disorder belonging to the group of ciliary diseases. JBS is genetically heterogeneous, with >20 causative genes identified to date. A molecular diagnosis of JBS is essential for prediction of disease progression and genetic counseling. We developed a targeted next-generation sequencing (NGS) approach for parallel sequencing of 22 known JBS genes plus 599 additional ciliary genes. This method was used to genotype a cohort of 51 well-phenotyped Northern European JBS cases (in some of the cases, Sanger sequencing of individual JBS genes had been performed previously). Altogether, 21 of the 51 cases (41%) harbored biallelic pathogenic mutations in known JBS genes, including 14 mutations not previously described. Mutations in C5orf42 (12%), TMEM67 (10%), and AHI1 (8%) were the most prevalent. C5orf42 mutations result in a purely neurological Joubert phenotype, in one case associated with postaxial polydactyly. Our study represents a population-based cohort of JBS patients not enriched for consanguinity, providing insight into the relative importance of the different JBS genes in a Northern European population. Mutations in C5orf42 are relatively frequent (possibly due to a Dutch founder mutation) and mutations in CEP290 are underrepresented compared with international cohorts. Furthermore, we report a case with heterozygous mutations in CC2D2A and B9D1, a gene associated with the more severe Meckel-Gruber syndrome that was recently published as a potential new JBS gene, and discuss the significance of this finding.
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Affiliation(s)
- Hester Y Kroes
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Glen R Monroe
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bert van der Zwaag
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Karen J Duran
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Carolien G de Kovel
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mark J van Roosmalen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Magdalena Harakalova
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ies J Nijman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wigard P Kloosterman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rachel H Giles
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nine V A M Knoers
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gijs van Haaften
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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37
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Gholkar AA, Senese S, Lo YC, Capri J, Deardorff WJ, Dharmarajan H, Contreras E, Hodara E, Whitelegge JP, Jackson PK, Torres JZ. Tctex1d2 associates with short-rib polydactyly syndrome proteins and is required for ciliogenesis. Cell Cycle 2015; 14:1116-25. [PMID: 25830415 PMCID: PMC4614626 DOI: 10.4161/15384101.2014.985066] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/28/2014] [Accepted: 11/03/2014] [Indexed: 12/26/2022] Open
Abstract
Short-rib polydactyly syndromes (SRPS) arise from mutations in genes involved in retrograde intraflagellar transport (IFT) and basal body homeostasis, which are critical for cilia assembly and function. Recently, mutations in WDR34 or WDR60 (candidate dynein intermediate chains) were identified in SRPS. We have identified and characterized Tctex1d2, which associates with Wdr34, Wdr60 and other dynein complex 1 and 2 subunits. Tctex1d2 and Wdr60 localize to the base of the cilium and their depletion causes defects in ciliogenesis. We propose that Tctex1d2 is a novel dynein light chain important for trafficking to the cilium and potentially retrograde IFT and is a new molecular link to understanding SRPS pathology.
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Affiliation(s)
- Ankur A. Gholkar
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Silvia Senese
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Yu-Chen Lo
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
- Program in Bioengineering; University of California; Los Angeles, CA USA
| | - Joseph Capri
- Pasarow Mass Spectrometry Laboratory; The Jane and Terry Semel Institute for Neuroscience and Human Behavior; David Geffen School of Medicine; University of California; Los Angeles, CA USA
| | - William J Deardorff
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Harish Dharmarajan
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Ely Contreras
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Emmanuelle Hodara
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Julian P Whitelegge
- Pasarow Mass Spectrometry Laboratory; The Jane and Terry Semel Institute for Neuroscience and Human Behavior; David Geffen School of Medicine; University of California; Los Angeles, CA USA
- Molecular Biology Institute; University of California; Los Angeles, CA USA
| | - Peter K Jackson
- Baxter Laboratory for Stem Cell Biology; Department of Microbiology & Immunology; Stanford University School of Medicine; Stanford, CA USA
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
- Molecular Biology Institute; University of California; Los Angeles, CA USA
- Jonsson Comprehensive Cancer Center; University of California; Los Angeles, CA USA
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38
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Arnaiz O, Cohen J, Tassin AM, Koll F. Remodeling Cildb, a popular database for cilia and links for ciliopathies. Cilia 2014; 3:9. [PMID: 25422781 PMCID: PMC4242763 DOI: 10.1186/2046-2530-3-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 10/30/2014] [Indexed: 12/12/2022] Open
Abstract
Background New generation technologies in cell and molecular biology generate large amounts
of data hard to exploit for individual proteins. This is particularly true for
ciliary and centrosomal research. Cildb is a multi–species knowledgebase
gathering high throughput studies, which allows advanced searches to identify
proteins involved in centrosome, basal body or cilia biogenesis, composition and
function. Combined to localization of genetic diseases on human chromosomes given
by OMIM links, candidate ciliopathy proteins can be compiled through Cildb
searches. Methods Othology between recent versions of the whole proteomes was computed using
Inparanoid and ciliary high throughput studies were remapped on these recent
versions. Results Due to constant evolution of the ciliary and centrosomal field, Cildb has been
recently upgraded twice, with new species whole proteomes and new ciliary studies,
and the latter version displays a novel BioMart interface, much more intuitive
than the previous ones. Conclusions This already popular database is designed now for easier use and is up to date in
regard to high throughput ciliary studies.
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Affiliation(s)
- Olivier Arnaiz
- Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, Gif sur Yvette, 91198, France
| | - Jean Cohen
- Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, Gif sur Yvette, 91198, France
| | - Anne-Marie Tassin
- Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, Gif sur Yvette, 91198, France
| | - France Koll
- Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, Gif sur Yvette, 91198, France
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39
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Vieillard J, Jerber J, Durand B. Contrôle transcriptionnel des gènes ciliaires. Med Sci (Paris) 2014; 30:968-75. [DOI: 10.1051/medsci/20143011010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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40
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Ciliary dysfunction impairs beta-cell insulin secretion and promotes development of type 2 diabetes in rodents. Nat Commun 2014; 5:5308. [PMID: 25374274 DOI: 10.1038/ncomms6308] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/18/2014] [Indexed: 11/08/2022] Open
Abstract
Type 2 diabetes mellitus is affecting more than 382 million people worldwide. Although much progress has been made, a comprehensive understanding of the underlying disease mechanism is still lacking. Here we report a role for the β-cell primary cilium in type 2 diabetes susceptibility. We find impaired glucose handling in young Bbs4(-/-) mice before the onset of obesity. Basal body/ciliary perturbation in murine pancreatic islets leads to impaired first phase insulin release ex and in vivo. Insulin receptor is recruited to the cilium of stimulated β-cells and ciliary/basal body integrity is required for activation of downstream targets of insulin signalling. We also observe a reduction in the number of ciliated β-cells along with misregulated ciliary/basal body gene expression in pancreatic islets in a diabetic rat model. We suggest that ciliary function is implicated in insulin secretion and insulin signalling in the β-cell and that ciliary dysfunction could contribute to type 2 diabetes susceptibility.
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41
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Li Y, Calvo SE, Gutman R, Liu JS, Mootha VK. Expansion of biological pathways based on evolutionary inference. Cell 2014; 158:213-25. [PMID: 24995987 DOI: 10.1016/j.cell.2014.05.034] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 02/06/2014] [Accepted: 05/12/2014] [Indexed: 01/24/2023]
Abstract
The availability of diverse genomes makes it possible to predict gene function based on shared evolutionary history. This approach can be challenging, however, for pathways whose components do not exhibit a shared history but rather consist of distinct "evolutionary modules." We introduce a computational algorithm, clustering by inferred models of evolution (CLIME), which inputs a eukaryotic species tree, homology matrix, and pathway (gene set) of interest. CLIME partitions the gene set into disjoint evolutionary modules, simultaneously learning the number of modules and a tree-based evolutionary history that defines each module. CLIME then expands each module by scanning the genome for new components that likely arose under the inferred evolutionary model. Application of CLIME to ∼1,000 annotated human pathways and to the proteomes of yeast, red algae, and malaria reveals unanticipated evolutionary modularity and coevolving components. CLIME is freely available and should become increasingly powerful with the growing wealth of eukaryotic genomes.
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Affiliation(s)
- Yang Li
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Statistics, Harvard University, Cambridge, MA 02138, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02141, USA
| | - Roee Gutman
- Department of Biostatistics, Brown University, Providence, RI 02912, USA
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA 02138, USA.
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02141, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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42
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Choksi SP, Lauter G, Swoboda P, Roy S. Switching on cilia: transcriptional networks regulating ciliogenesis. Development 2014; 141:1427-41. [DOI: 10.1242/dev.074666] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cilia play many essential roles in fluid transport and cellular locomotion, and as sensory hubs for a variety of signal transduction pathways. Despite having a conserved basic morphology, cilia vary extensively in their shapes and sizes, ultrastructural details, numbers per cell, motility patterns and sensory capabilities. Emerging evidence indicates that this diversity, which is intimately linked to the different functions that cilia perform, is in large part programmed at the transcriptional level. Here, we review our understanding of the transcriptional control of ciliary biogenesis, highlighting the activities of FOXJ1 and the RFX family of transcriptional regulators. In addition, we examine how a number of signaling pathways, and lineage and cell fate determinants can induce and modulate ciliogenic programs to bring about the differentiation of distinct cilia types.
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Affiliation(s)
- Semil P. Choksi
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
| | - Gilbert Lauter
- Karolinska Institute, Department of Biosciences and Nutrition, S-141 83 Huddinge, Sweden
| | - Peter Swoboda
- Karolinska Institute, Department of Biosciences and Nutrition, S-141 83 Huddinge, Sweden
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore
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43
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Chung MI, Kwon T, Tu F, Brooks ER, Gupta R, Meyer M, Baker JC, Marcotte EM, Wallingford JB. Coordinated genomic control of ciliogenesis and cell movement by RFX2. eLife 2014; 3:e01439. [PMID: 24424412 PMCID: PMC3889689 DOI: 10.7554/elife.01439] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 11/27/2013] [Indexed: 12/16/2022] Open
Abstract
The mechanisms linking systems-level programs of gene expression to discrete cell biological processes in vivo remain poorly understood. In this study, we have defined such a program for multi-ciliated epithelial cells (MCCs), a cell type critical for proper development and homeostasis of the airway, brain and reproductive tracts. Starting from genomic analysis of the cilia-associated transcription factor Rfx2, we used bioinformatics and in vivo cell biological approaches to gain insights into the molecular basis of cilia assembly and function. Moreover, we discovered a previously un-recognized role for an Rfx factor in cell movement, finding that Rfx2 cell-autonomously controls apical surface expansion in nascent MCCs. Thus, Rfx2 coordinates multiple, distinct gene expression programs in MCCs, regulating genes that control cell movement, ciliogenesis, and cilia function. As such, the work serves as a paradigm for understanding genomic control of cell biological processes that span from early cell morphogenetic events to terminally differentiated cellular functions. DOI: http://dx.doi.org/10.7554/eLife.01439.001.
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Affiliation(s)
- Mei-I Chung
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Taejoon Kwon
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Fan Tu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Eric R Brooks
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Rakhi Gupta
- Department of Genetics, Stanford University, Stanford, United States
| | - Matthew Meyer
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Julie C Baker
- Department of Genetics, Stanford University, Stanford, United States
| | - Edward M Marcotte
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States
| | - John B Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States
- Howard Hughes Medical Institute, University of Texas at Austin, Austin, United States
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44
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Ishikawa H, Ide T, Yagi T, Jiang X, Hirono M, Sasaki H, Yanagisawa H, Wemmer KA, Stainier DY, Qin H, Kamiya R, Marshall WF. TTC26/DYF13 is an intraflagellar transport protein required for transport of motility-related proteins into flagella. eLife 2014; 3:e01566. [PMID: 24596149 PMCID: PMC3936282 DOI: 10.7554/elife.01566] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cilia/flagella are assembled and maintained by the process of intraflagellar transport (IFT), a highly conserved mechanism involving more than 20 IFT proteins. However, the functions of individual IFT proteins are mostly unclear. To help address this issue, we focused on a putative IFT protein TTC26/DYF13. Using live imaging and biochemical approaches we show that TTC26/DYF13 is an IFT complex B protein in mammalian cells and Chlamydomonas reinhardtii. Knockdown of TTC26/DYF13 in zebrafish embryos or mutation of TTC26/DYF13 in C. reinhardtii, produced short cilia with abnormal motility. Surprisingly, IFT particle assembly and speed were normal in dyf13 mutant flagella, unlike in other IFT complex B mutants. Proteomic and biochemical analyses indicated a particular set of proteins involved in motility was specifically depleted in the dyf13 mutant. These results support the concept that different IFT proteins are responsible for different cargo subsets, providing a possible explanation for the complexity of the IFT machinery. DOI: http://dx.doi.org/10.7554/eLife.01566.001.
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Affiliation(s)
- Hiroaki Ishikawa
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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Zebrafish Ciliopathy Screen Plus Human Mutational Analysis Identifies C21orf59 and CCDC65 Defects as Causing Primary Ciliary Dyskinesia. Am J Hum Genet 2013; 93:672-86. [PMID: 24094744 DOI: 10.1016/j.ajhg.2013.08.015] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/24/2013] [Accepted: 08/28/2013] [Indexed: 11/21/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is caused when defects of motile cilia lead to chronic airway infections, male infertility, and situs abnormalities. Multiple causative PCD mutations account for only 65% of cases, suggesting that many genes essential for cilia function remain to be discovered. By using zebrafish morpholino knockdown of PCD candidate genes as an in vivo screening platform, we identified c21orf59, ccdc65, and c15orf26 as critical for cilia motility. c21orf59 and c15orf26 knockdown in zebrafish and planaria blocked outer dynein arm assembly, and ccdc65 knockdown altered cilia beat pattern. Biochemical analysis in Chlamydomonas revealed that the C21orf59 ortholog FBB18 is a flagellar matrix protein that accumulates specifically when cilia motility is impaired. The Chlamydomonas ida6 mutant identifies CCDC65/FAP250 as an essential component of the nexin-dynein regulatory complex. Analysis of 295 individuals with PCD identified recessive truncating mutations of C21orf59 in four families and CCDC65 in two families. Similar to findings in zebrafish and planaria, mutations in C21orf59 caused loss of both outer and inner dynein arm components. Our results characterize two genes associated with PCD-causing mutations and elucidate two distinct mechanisms critical for motile cilia function: dynein arm assembly for C21orf59 and assembly of the nexin-dynein regulatory complex for CCDC65.
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46
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Henriksson J, Piasecki BP, Lend K, Bürglin TR, Swoboda P. Finding ciliary genes: a computational approach. Methods Enzymol 2013; 525:327-50. [PMID: 23522477 DOI: 10.1016/b978-0-12-397944-5.00016-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
In the nematode worm Caenorhabditis elegans and several other animal species, many ciliary genes are regulated by RFX (Regulatory Factor binding to the X-box) transcription factors (TFs), which bind to X-box promoter motifs and thereby directly activate ciliary gene expression. This setup (RFX TF/X-box/ciliary gene) makes it possible to search for novel ciliary gene candidates genome-wide by using the X-box promoter motif as a search parameter. We present a computational approach that (i) identifies and extracts from whole genomes genes and the corresponding promoter sequences and annotations; (ii) searches through promoters for regulatory sequence elements (like promoter motifs) by using training sets of known instances of these elements; (iii) scores (evaluates) and sorts all positive hits in a database; and (iv) outputs a list of candidate genes and promoters with a given regulatory sequence element. Evolutionary conservation across species (orthology) of genes, promoters, or regulatory sequence elements is used as an important strengthening feature during the overall search approach. Our computational approach is set up in a modular fashion: not every part needs to be used for a particular search effort. In principle, our approach has broad applications. It applies to any group of genes that share common (conserved) regulation through common (conserved) regulatory sequence elements.
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Affiliation(s)
- Johan Henriksson
- Department of Biosciences and Nutrition, Center for Biosciences at NOVUM, Karolinska Institute, Huddinge, Sweden.
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Patel-King RS, Gilberti RM, Hom EFY, King SM. WD60/FAP163 is a dynein intermediate chain required for retrograde intraflagellar transport in cilia. Mol Biol Cell 2013; 24:2668-77. [PMID: 23864713 PMCID: PMC3756919 DOI: 10.1091/mbc.e13-05-0266] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Retrograde intraflagellar transport (IFT) is required for assembly of cilia. We identify a Chlamydomonas flagellar protein (flagellar-associated protein 163 [FAP163]) as being closely related to the D1bIC(FAP133) intermediate chain (IC) of the dynein that powers this movement. Biochemical analysis revealed that FAP163 is present in the flagellar matrix and is actively trafficked by IFT. Furthermore, FAP163 copurified with D1bIC(FAP133) and the LC8 dynein light chain, indicating that it is an integral component of the retrograde IFT dynein. To assess the functional role of FAP163, we generated an RNA interference knockdown of the orthologous protein (WD60) in planaria. The Smed-wd60(RNAi) animals had a severe ciliary assembly defect that dramatically compromised whole-organism motility. Most cilia were present as short stubs that had accumulated large quantities of IFT particle-like material between the doublet microtubules and the membrane. The few remaining approximately full-length cilia had a chaotic beat with a frequency reduced from 24 to ∼10 Hz. Thus WD60/FAP163 is a dynein IC that is absolutely required for retrograde IFT and ciliary assembly.
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Affiliation(s)
- Ramila S Patel-King
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, CT 06030, USA
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48
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van Dam TJ, Wheway G, Slaats GG, Huynen MA, Giles RH. The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium. Cilia 2013; 2:7. [PMID: 23725226 PMCID: PMC3674929 DOI: 10.1186/2046-2530-2-7] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 05/28/2013] [Indexed: 12/21/2022] Open
Abstract
The multinational SYSCILIA consortium aims to gain a mechanistic understanding of the cilium. We utilize multiple parallel high-throughput (HTP) initiatives to develop predictive models of relationships between complex genotypes and variable phenotypes of ciliopathies. The models generated are only as good as the wet laboratory data fed into them. It is therefore essential to orchestrate a well-annotated and high-confidence dataset to be able to assess the quality of any HTP dataset. Here, we present the inaugural SYSCILIA gold standard of known ciliary components as a public resource.
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Affiliation(s)
- Teunis Jp van Dam
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands.
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49
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Xie Y, Moussaif M, Choi S, Xu L, Sze JY. RFX transcription factor DAF-19 regulates 5-HT and innate immune responses to pathogenic bacteria in Caenorhabditis elegans. PLoS Genet 2013; 9:e1003324. [PMID: 23505381 PMCID: PMC3591283 DOI: 10.1371/journal.pgen.1003324] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 01/04/2013] [Indexed: 02/06/2023] Open
Abstract
In Caenorhabditis elegans the Toll-interleukin receptor domain adaptor protein TIR-1 via a conserved mitogen-activated protein kinase (MAPK) signaling cascade induces innate immunity and upregulates serotonin (5-HT) biosynthesis gene tph-1 in a pair of ADF chemosensory neurons in response to infection. Here, we identify transcription factors downstream of the TIR-1 signaling pathway. We show that common transcription factors control the innate immunity and 5-HT biosynthesis. We demonstrate that a cysteine to tyrosine substitution in an ARM motif of the HEAT/Arm repeat region of the TIR-1 protein confers TIR-1 hyperactivation, leading to constitutive tph-1 upregulation in the ADF neurons, increased expression of intestinal antimicrobial genes, and enhanced resistance to killing by the human opportunistic pathogen Pseudomonas aeruginosa PA14. A forward genetic screen for suppressors of the hyperactive TIR-1 led to the identification of DAF-19, an ortholog of regulatory factor X (RFX) transcription factors that are required for human adaptive immunity. We show that DAF-19 concerts with ATF-7, a member of the activating transcription factor (ATF)/cAMP response element-binding B (CREB) family of transcription factors, to regulate tph-1 and antimicrobial genes, reminiscent of RFX-CREB interaction in human immune cells. daf-19 mutants display heightened susceptibility to killing by PA14. Remarkably, whereas the TIR-1-MAPK-DAF-19/ATF-7 pathway in the intestinal immunity is regulated by DKF-2/protein kinase D, we found that the regulation of tph-1 expression is independent of DKF-2 but requires UNC-43/Ca2+/calmodulin-dependent protein kinase (CaMK) II. Our results suggest that pathogenic cues trigger a common core-signaling pathway via tissue-specific mechanisms and demonstrate a novel role for RFX factors in neuronal and innate immune responses to infection. Toll-interleukin receptor (TIR)–domain adaptor proteins are keys to activate signaling cascades inducing transcriptional responses to internal and external pathogenic signals in evolutionary disparate organisms. Despite lacking a homolog of the mammalian innate immunity transcriptional regulator nuclear factor-kappaB (NF-κB), the nematode Caenorhabditis elegans responds to infections by activating TIR-1 signaling targets in the innate immune system and in neurons. Through a genetic screen for factors required for TIR-1 signaling to upregulate the serotonin biosynthesis gene tph-1, we identified DAF-19, an ortholog of regulatory factor X (RFX) transcription factors that were initially discovered in human immune cells. We show that DAF-19 concerts with ATF-7, a member of the activating transcription factor (ATF)/cAMP response element-binding B (CREB) family of transcription factors, to upregulate tph-1 in the ADF chemosensory neurons and antimicrobial genes in the intestine in response to bacterial infection, reminiscent of RFX-CREB interaction in human immune cells. daf-19 mutants display heightened susceptibility to killing by the human pathogen Pseudomonas aeruginosa PA14. Our studies suggest that RFX transcriptional regulation, which is essential for human adaptive immunity, has an ancient role in controlling serotonin biosynthesis and innate immunity.
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Affiliation(s)
| | | | | | | | - Ji Ying Sze
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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50
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Hoh RA, Stowe TR, Turk E, Stearns T. Transcriptional program of ciliated epithelial cells reveals new cilium and centrosome components and links to human disease. PLoS One 2012; 7:e52166. [PMID: 23300604 PMCID: PMC3534086 DOI: 10.1371/journal.pone.0052166] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 11/15/2012] [Indexed: 01/11/2023] Open
Abstract
Defects in the centrosome and cilium are associated with a set of human diseases having diverse phenotypes. To further characterize the components that define the function of these organelles we determined the transcriptional profile of multiciliated tracheal epithelial cells. Cultures of mouse tracheal epithelial cells undergoing differentiation in vitro were derived from mice expressing GFP from the ciliated-cell specific FOXJ1 promoter (FOXJ1:GFP). The transcriptional profile of ciliating GFP+ cells from these cultures was defined at an early and a late time point during differentiation and was refined by subtraction of the profile of the non-ciliated GFP- cells. We identified 649 genes upregulated early, when most cells were forming basal bodies, and 73 genes genes upregulated late, when most cells were fully ciliated. Most, but not all, of known centrosome proteins are transcriptionally upregulated early, particularly Plk4, a master regulator of centriole formation. We found that three genes associated with human disease states, Mdm1, Mlf1, and Dyx1c1, are upregulated during ciliogenesis and localize to centrioles and cilia. This transcriptome for mammalian multiciliated epithelial cells identifies new candidate centrosome and cilia proteins, highlights similarities between components of motile and primary cilia, and identifies new links between cilia proteins and human disease.
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Affiliation(s)
- Ramona A. Hoh
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Timothy R. Stowe
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Erin Turk
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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