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PMID:21289087

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Citation

Lai, CK, Gupta, N, Wen, X, Rangell, L, Chih, B, Peterson, AS, Bazan, JF, Li, L and Scales, SJ (2011) Functional characterization of putative cilia genes by high-content analysis. Mol. Biol. Cell 22:1104-19

Abstract

Cilia are microtubule-based protrusions from the cell surface that are involved in a number of essential signaling pathways, yet little is known about many of the proteins that regulate their structure and function. A number of putative cilia genes have been identified by proteomics and comparative sequence analyses, but functional data are lacking for the vast majority. We therefore monitored the effects in three cell lines of small interfering RNA (siRNA) knockdown of 40 of these genes by high-content analysis. We assayed cilia number, length, and transport of two different cargoes (membranous serotonin receptor 6-green fluorescent protein [HTR6-GFP] and the endogenous Hedgehog [Hh] pathway transcription factor Gli3) by immunofluorescence microscopy; and cilia function using a Gli-luciferase Hh signaling assay. Hh signaling was most sensitive to perturbations, with or without visible structural cilia defects. Validated hits include Ssa2 and mC21orf2 with ciliation defects; Ift46 with short cilia; Ptpdc1 and Iqub with elongated cilia; and Arl3, Nme7, and Ssna1 with distinct ciliary transport but not length defects. Our data confirm various ciliary roles for several ciliome proteins and show it is possible to uncouple ciliary cargo transport from cilia formation in vertebrates.

Links

PubMed PMC3069013 Online version:10.1091/mbc.E10-07-0596

Keywords

3T3 Cells; Animals; Biological Transport/genetics; Cell Line; Cilia/physiology; Cilia/ultrastructure; Gene Expression; Gene Knockdown Techniques; Kruppel-Like Transcription Factors/genetics; Kruppel-Like Transcription Factors/metabolism; Mice; Nerve Tissue Proteins/genetics; Nerve Tissue Proteins/metabolism; Phenotype; RNA, Small Interfering/genetics; RNA, Small Interfering/metabolism; Recombinant Fusion Proteins/genetics; Recombinant Fusion Proteins/metabolism; Signal Transduction/genetics

Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

MOUSE:RO60

acts_upstream_of_or_within

GO:0007224: smoothened signaling pathway

ECO:0000315: mutant phenotype evidence used in manual assertion

P

  • occurs_in:(CL:0000062)

Seeded From UniProt

complete

MOUSE:RO60

acts_upstream_of_or_within

GO:0060271: cilium assembly

ECO:0000315: mutant phenotype evidence used in manual assertion

P

  • occurs_in:(CL:1000546)

Seeded From UniProt

complete

MOUSE:IFT88

acts_upstream_of_or_within

GO:0060271: cilium assembly

ECO:0000315: mutant phenotype evidence used in manual assertion

P

  • occurs_in:(CL:1000546)

Seeded From UniProt

complete

MOUSE:GLI3

located_in

GO:0005929: cilium

ECO:0000314: direct assay evidence used in manual assertion

C

Seeded From UniProt

complete

MOUSE:PTPC1

acts_upstream_of_or_within

GO:0007224: smoothened signaling pathway

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

MOUSE:PTPC1

acts_upstream_of_or_within

GO:0060271: cilium assembly

ECO:0000315: mutant phenotype evidence used in manual assertion

P

  • occurs_in:(CL:1000546)

Seeded From UniProt

complete

MOUSE:CF410

acts_upstream_of_or_within

GO:0007224: smoothened signaling pathway

ECO:0000315: mutant phenotype evidence used in manual assertion

P

  • occurs_in:(CL:0000062)

Seeded From UniProt

complete

MOUSE:CF410

acts_upstream_of_or_within

GO:0060271: cilium assembly

ECO:0000315: mutant phenotype evidence used in manual assertion

P

  • occurs_in:(CL:1000546)

Seeded From UniProt

complete

MOUSE:IQUB

acts_upstream_of_or_within

GO:0007224: smoothened signaling pathway

ECO:0000315: mutant phenotype evidence used in manual assertion

P

  • occurs_in:(CL:0000062)

Seeded From UniProt

complete

MOUSE:IQUB

acts_upstream_of_or_within

GO:0060271: cilium assembly

ECO:0000315: mutant phenotype evidence used in manual assertion

P

  • occurs_in:(CL:1000546)

Seeded From UniProt

complete

MOUSE:IFT46

acts_upstream_of_or_within

GO:0007224: smoothened signaling pathway

ECO:0000315: mutant phenotype evidence used in manual assertion

P

  • occurs_in:(CL:0000062)

Seeded From UniProt

complete

MOUSE:IFT46

acts_upstream_of_or_within

GO:0060271: cilium assembly

ECO:0000315: mutant phenotype evidence used in manual assertion

P

  • occurs_in:(CL:0000062)

Seeded From UniProt

complete

MOUSE:SSNA1

located_in

GO:0005813: centrosome

ECO:0000314: direct assay evidence used in manual assertion

C

Seeded From UniProt

complete

MOUSE:SSNA1

located_in

GO:0036064: ciliary basal body

ECO:0000314: direct assay evidence used in manual assertion

C

Seeded From UniProt

complete

MOUSE:SSNA1

acts_upstream_of_or_within

GO:0060830: ciliary receptor clustering involved in smoothened signaling pathway

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

MOUSE:SSNA1

acts_upstream_of_or_within

GO:0042073: intraciliary transport

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

MOUSE:NDK7

located_in

GO:0005813: centrosome

ECO:0000314: direct assay evidence used in manual assertion

C

Seeded From UniProt

complete

MOUSE:NDK7

located_in

GO:0036064: ciliary basal body

ECO:0000314: direct assay evidence used in manual assertion

C

Seeded From UniProt

complete

MOUSE:NDK7

acts_upstream_of_or_within

GO:0060830: ciliary receptor clustering involved in smoothened signaling pathway

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

MOUSE:NDK7

acts_upstream_of_or_within

GO:0042073: intraciliary transport

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

MOUSE:ARL3

acts_upstream_of_or_within

GO:0007224: smoothened signaling pathway

ECO:0000315: mutant phenotype evidence used in manual assertion

P

  • occurs_in:(CL:0000062)

Seeded From UniProt

complete

MOUSE:ARL3

acts_upstream_of_or_within

GO:0042073: intraciliary transport

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

MOUSE:GLI3

part_of

GO:0005929: cilium

ECO:0000314: direct assay evidence used in manual assertion

C

Seeded From UniProt

complete

MOUSE:IFT88

acts_upstream_of_or_within

GO:0060271: cilium assembly

ECO:0000315: mutant phenotype evidence used in manual assertion

P

occurs_in:(CL:1000546)

Seeded From UniProt

complete


See also

References

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