title: An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes.
abstract: Defects in primary cilium biogenesis underlie the ciliopathies, a growing group of genetic disorders. We describe a whole-genome siRNA-based reverse genetics screen for defects in biogenesis and/or maintenance of the primary cilium, obtaining a global resource. We identify 112 candidate ciliogenesis and ciliopathy genes, including 44 components of the ubiquitin-proteasome system, 12 G-protein-coupled receptors, and 3 pre-mRNA processing factors (PRPF6, PRPF8 and PRPF31) mutated in autosomal dominant retinitis pigmentosa. The PRPFs localize to the connecting cilium, and PRPF8- and PRPF31-mutated cells have ciliary defects. Combining the screen with exome sequencing data identified recessive mutations in PIBF1, also known as CEP90, and C21orf2, also known as LRRC76, as causes of the ciliopathies Joubert and Jeune syndromes. Biochemical approaches place C21orf2 within key ciliopathy-associated protein modules, offering an explanation for the skeletal and retinal involvement observed in individuals with C21orf2 variants. Our global, unbiased approaches provide insights into ciliogenesis complexity and identify roles for unanticipated pathways in human genetic disease.
authors.affiliation: Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
authors.forename: Gabrielle
authors.initials: G
authors.lastname: Wheway
authors.affiliation: Genetics and Genomic Medicine and Birth Defects Research Centre, Institute of Child Health, University College London, London, WC1N 1EH, UK.|Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.|Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.|Pediatric Genetics Section, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg 79112, Germany.
authors.forename: Miriam
authors.initials: M
authors.lastname: Schmidts
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.|Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
authors.forename: Dorus A
authors.initials: DA
authors.lastname: Mans
authors.affiliation: Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Szymanska
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.|Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
authors.forename: Thanh-Minh T
authors.initials: TT
authors.lastname: Nguyen
authors.affiliation: Department of Medical Genetics and Alberta Children's Hospital Research Institute for Child and Maternal Health, Calgary, T3B 6A8, AB, Canada.
authors.forename: Hilary
authors.initials: H
authors.lastname: Racher
authors.affiliation: Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
authors.forename: Ian G
authors.initials: IG
authors.lastname: Phelps
authors.affiliation: Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Grischa
authors.initials: G
authors.lastname: Toedt
authors.affiliation: School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland.
authors.forename: Julie
authors.initials: J
authors.lastname: Kennedy
authors.affiliation: Department of Cell and Matrix Biology, Institute of Zoology, Johannes Gutenberg University of Mainz, 55122 Mainz, Germany.
authors.forename: Kirsten A
authors.initials: KA
authors.lastname: Wunderlich
authors.affiliation: Department of Cell and Matrix Biology, Institute of Zoology, Johannes Gutenberg University of Mainz, 55122 Mainz, Germany.
authors.forename: Nasrin
authors.initials: N
authors.lastname: Sorusch
authors.affiliation: Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
authors.forename: Zakia A
authors.initials: ZA
authors.lastname: Abdelhamed
authors.affiliation: Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
authors.forename: Subaashini
authors.initials: S
authors.lastname: Natarajan
authors.affiliation: Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
authors.forename: Warren
authors.initials: W
authors.lastname: Herridge
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.|Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
authors.forename: Jeroen
authors.initials: J
authors.lastname: van Reeuwijk
authors.affiliation: Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of Tübingen, 72074 Tübingen, Germany.
authors.forename: Nicola
authors.initials: N
authors.lastname: Horn
authors.affiliation: Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of Tübingen, 72074 Tübingen, Germany.
authors.forename: Karsten
authors.initials: K
authors.lastname: Boldt
authors.affiliation: Section of Genetics, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
authors.forename: David A
authors.initials: DA
authors.lastname: Parry
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.|Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
authors.forename: Stef J F
authors.initials: SJF
authors.lastname: Letteboer
authors.affiliation: Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, Box 268, New York, NY 10065, USA.
authors.forename: Susanne
authors.initials: S
authors.lastname: Roosing
authors.affiliation: BioScreening Technology Group, Biomedical Health Research Centre, St. James's University Hospital, Leeds, LS9 7TF, UK.
authors.forename: Matthew
authors.initials: M
authors.lastname: Adams
authors.affiliation: BioScreening Technology Group, Biomedical Health Research Centre, St. James's University Hospital, Leeds, LS9 7TF, UK.
authors.forename: Sandra M
authors.initials: SM
authors.lastname: Bell
authors.affiliation: BioScreening Technology Group, Biomedical Health Research Centre, St. James's University Hospital, Leeds, LS9 7TF, UK.
authors.forename: Jacquelyn
authors.initials: J
authors.lastname: Bond
authors.affiliation: BioScreening Technology Group, Biomedical Health Research Centre, St. James's University Hospital, Leeds, LS9 7TF, UK.
authors.forename: Julie
authors.initials: J
authors.lastname: Higgins
authors.affiliation: BioScreening Technology Group, Biomedical Health Research Centre, St. James's University Hospital, Leeds, LS9 7TF, UK.
authors.forename: Ewan E
authors.initials: EE
authors.lastname: Morrison
authors.affiliation: BioScreening Technology Group, Biomedical Health Research Centre, St. James's University Hospital, Leeds, LS9 7TF, UK.
authors.forename: Darren C
authors.initials: DC
authors.lastname: Tomlinson
authors.affiliation: Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, 3584 CX, The Netherlands.
authors.forename: Gisela G
authors.initials: GG
authors.lastname: Slaats
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
authors.forename: Teunis J P
authors.initials: TJP
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authors.affiliation: Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, K1H 8L1, ON, Canada.
authors.forename: Lijia
authors.initials: L
authors.lastname: Huang
authors.affiliation: Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany.
authors.forename: Kristin
authors.initials: K
authors.lastname: Kessler
authors.affiliation: Animal Physiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Giessl
authors.affiliation: Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
authors.forename: Clare V
authors.initials: CV
authors.lastname: Logan
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Evan A
authors.initials: EA
authors.lastname: Boyle
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
authors.affiliation: Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.
authors.forename: Shamsa
authors.initials: S
authors.lastname: Anazi
authors.affiliation: Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.
authors.forename: Mohammed
authors.initials: M
authors.lastname: Aldahmesh
authors.affiliation: Department of Ophthalmology, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.|Department of Ophthalmology, College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia.
authors.forename: Selwa
authors.initials: S
authors.lastname: Al Hazzaa
authors.affiliation: Robarts Research Institute, University of Western Ontario, London, N6G 2V4, ON, Canada.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Hegele
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
authors.forename: Carole
authors.initials: C
authors.lastname: Ober
authors.affiliation: Department of Pediatrics and Child Health & Department of Biochemistry and Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg, R3E 3P5, MB, Canada.
authors.forename: Patrick
authors.initials: P
authors.lastname: Frosk
authors.affiliation: Department of Pediatrics and Child Health & Department of Biochemistry and Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg, R3E 3P5, MB, Canada.
authors.forename: Aizeddin A
authors.initials: AA
authors.lastname: Mhanni
authors.affiliation: Department of Pediatrics and Child Health & Department of Biochemistry and Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg, R3E 3P5, MB, Canada.
authors.forename: Bernard N
authors.initials: BN
authors.lastname: Chodirker
authors.affiliation: Department of Pediatrics and Child Health & Department of Biochemistry and Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg, R3E 3P5, MB, Canada.
authors.forename: Albert E
authors.initials: AE
authors.lastname: Chudley
authors.affiliation: Department of Medical Genetics and Alberta Children's Hospital Research Institute for Child and Maternal Health, Calgary, T3B 6A8, AB, Canada.
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authors.initials: R
authors.lastname: Lamont
authors.affiliation: Department of Medical Genetics and Alberta Children's Hospital Research Institute for Child and Maternal Health, Calgary, T3B 6A8, AB, Canada.
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authors.initials: FP
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authors.affiliation: Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, K1H 8L1, ON, Canada.
authors.forename: Chandree L
authors.initials: CL
authors.lastname: Beaulieu
authors.affiliation: Department of Medical Genetics and Alberta Children's Hospital Research Institute for Child and Maternal Health, Calgary, T3B 6A8, AB, Canada.
authors.forename: Paul
authors.initials: P
authors.lastname: Gordon
authors.affiliation: Department of Medical Genetics and Alberta Children's Hospital Research Institute for Child and Maternal Health, Calgary, T3B 6A8, AB, Canada.
authors.forename: Richard T
authors.initials: RT
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authors.affiliation: Department of Pediatrics, University of California San Francisco, San Francisco, CA 92093, USA.
authors.forename: Clem
authors.initials: C
authors.lastname: Donahue
authors.affiliation: Department of Radiology, University of California San Francisco, San Francisco, CA 92093, USA.
authors.forename: A James
authors.initials: AJ
authors.lastname: Barkovich
authors.affiliation: Department of Pathology, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
authors.forename: Louis
authors.initials: L
authors.lastname: Wolf
authors.affiliation: Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
authors.forename: Carmel
authors.initials: C
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authors.affiliation: Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany.
authors.forename: Christian T
authors.initials: CT
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authors.affiliation: Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, K1H 8L1, ON, Canada.
authors.forename: Kym M
authors.initials: KM
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authors.affiliation: Department of Ophthalmology, Leeds Teaching Hospitals NHS Trust, St. James's University Hospital, Leeds, LS9 7TF, UK.
authors.forename: Martin
authors.initials: M
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authors.affiliation: Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
authors.forename: Chris F
authors.initials: CF
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authors.affiliation: Department of Medical Genetics, Belfast City Hospital and Queens University, Belfast, BT12 6BA, UK.
authors.forename: Fiona
authors.initials: F
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authors.affiliation: Department of Pediatrics and Adolescent Medicine, University Hospital Muenster, 48149 Muenster, Germany.
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authors.initials: H
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authors.affiliation: Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
authors.forename: Martijn A
authors.initials: MA
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authors.affiliation: Moorfields Eye Hospital NHS Foundation Trust and NIHR Ophthalmology Biomedical Research Centre, London, EC1V 2PD, UK.|UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, UK.
authors.forename: Panagiotis I
authors.initials: PI
authors.lastname: Sergouniotis
authors.affiliation: Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.|Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.
authors.forename: Fowzan S
authors.initials: FS
authors.lastname: Alkuraya
authors.affiliation: Department of Medical Genetics and Alberta Children's Hospital Research Institute for Child and Maternal Health, Calgary, T3B 6A8, AB, Canada.
authors.forename: Jillian S
authors.initials: JS
authors.lastname: Parboosingh
authors.affiliation: Department of Medical Genetics and Alberta Children's Hospital Research Institute for Child and Maternal Health, Calgary, T3B 6A8, AB, Canada.
authors.forename: A Micheil
authors.initials: AM
authors.lastname: Innes
authors.affiliation: Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, L69 3BX, UK.
authors.forename: Colin E
authors.initials: CE
authors.lastname: Willoughby
authors.affiliation: Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, 3584 CX, The Netherlands.
authors.forename: Rachel H
authors.initials: RH
authors.lastname: Giles
authors.affiliation: Moorfields Eye Hospital NHS Foundation Trust and NIHR Ophthalmology Biomedical Research Centre, London, EC1V 2PD, UK.|UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, UK.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Webster
authors.affiliation: Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of Tübingen, 72074 Tübingen, Germany.|Research Unit of Protein Science, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, 85764 Neuherberg, Germany.
authors.forename: Marius
authors.initials: M
authors.lastname: Ueffing
authors.affiliation: School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland.
authors.forename: Oliver
authors.initials: O
authors.lastname: Blacque
authors.affiliation: Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, Box 268, New York, NY 10065, USA.
authors.forename: Joseph G
authors.initials: JG
authors.lastname: Gleeson
authors.affiliation: Department of Cell and Matrix Biology, Institute of Zoology, Johannes Gutenberg University of Mainz, 55122 Mainz, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Wolfrum
authors.affiliation: Genetics and Genomic Medicine and Birth Defects Research Centre, Institute of Child Health, University College London, London, WC1N 1EH, UK.
authors.forename: Philip L
authors.initials: PL
authors.lastname: Beales
authors.affiliation: Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Toby
authors.initials: T
authors.lastname: Gibson
authors.affiliation: Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.|Divisions of Developmental Medicine and Genetic Medicine, Seattle Children's Research Institute, University of Washington, Seattle, WA 98105, USA.
authors.forename: Dan
authors.initials: D
authors.lastname: Doherty
authors.affiliation: Genetics and Genomic Medicine and Birth Defects Research Centre, Institute of Child Health, University College London, London, WC1N 1EH, UK.
authors.forename: Hannah M
authors.initials: HM
authors.lastname: Mitchison
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.|Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
authors.forename: Ronald
authors.initials: R
authors.lastname: Roepman
authors.affiliation: Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
authors.forename: Colin A
authors.initials: CA
authors.lastname: Johnson
mesh_terms: D000015:Abnormalities, Multiple; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D002526:Cerebellar Diseases / Q000235:genetics; D002531:Cerebellum / Q000002:abnormalities; D002923:Cilia / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D002925:Ciliary Motility Disorders / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D003598:Cytoskeletal Proteins; D030541:Databases, Genetic; D004613:Ellis-Van Creveld Syndrome / Q000235:genetics; D005124:Eye Abnormalities / Q000235:genetics; D005819:Genetic Markers; D020022:Genetic Predisposition to Disease; D005820:Genetic Testing / Q000379:methods*; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D057809:HEK293 Cells; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D052177:Kidney Diseases, Cystic / Q000235:genetics; D008565:Membrane Proteins / Q000172:deficiency / Q000235:genetics; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D009154:Mutation; D010641:Phenotype; D010786:Photoreceptor Cells / Q000378:metabolism / Q000648:ultrastructure; D011257:Pregnancy Proteins / Q000235:genetics / Q000378:metabolism; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D034622:RNA Interference; D015203:Reproducibility of Results; D012160:Retina / Q000002:abnormalities; D013491:Suppressor Factors, Immunologic / Q000235:genetics / Q000378:metabolism; D014162:Transfection; D015027:Zebrafish / Q000235:genetics / Q000378:metabolism
chemical_list: C111475:CFAP410 protein, human; D003598:Cytoskeletal Proteins; D005819:Genetic Markers; D008565:Membrane Proteins; C110058:PIBF1 protein, human; C491677:Pibf1 protein, mouse; D011257:Pregnancy Proteins; D011506:Proteins; D013491:Suppressor Factors, Immunologic; C583064:TMEM67 protein, mouse