Isolation of new mutant alleles for ift172 and lrrc6 that cause kidney cyst formation. (A) Brightfield image of 5-dpf WT sibling and ccn1.9^pd1085 homozygous mutant. Red arrowhead indicates a kidney cyst. (B) Confocal images of transverse sections of 5-dpf WT sibling and ccn1.9^pd1085 mutant stained with phalloidin (red) and DAPI (blue). Arrowheads point to the pronephric ducts and asterisks mark kidney cysts. (C) Linkage analysis for ccn1.9^pd1085 using SNPtrack. (D) The homozygosity interval for ccn1.9^pd1085. (E) Sequencing of genomic DNA of WT and ccn1.9^pd1085 mutant larvae. Mutants bear a G-to-A mutation at an essential splice site in exon 13 of ift172 (underlined). (F) Brightfield image of 5-dpf WT sibling, ift172^{hi2211Tg/pd1085} and ift172^hi2211Tg larvae. (G) Brightfield image of 5-dpf WT sibling and dx33.9^pd1087 mutant larvae. (H) Confocal images of transverse sections of 5-dpf WT sibling and dx33.9^pd1087 mutant larvae stained with phalloidin and DAPI as in B. (I) Linkage analysis for dx33.9^pd1087 using SNPtrack. (J) The homozygosity interval for dx33.9^pd1087. (K) Sequencing of genomic DNA of WT and dx33.9^pd1087 mutant larvae. Mutants are homozygous for a T-to-G nonsense mutation. (L) Rescue of the dx33.9^pd1087 phenotype via injection of WT lrrc6 cRNA.

kif3a^pd1084 mutants present defects in cilia formation and kidney cysts. (A) Brightfield image of 5-dpf WT sibling and dx36.18¹⁰⁸⁴ mutant larvae. Red arrowhead indicates a kidney cyst. (B) Confocal images of transverse sections of 5-dpf WT sibling and dx36.18¹⁰⁸⁴ mutant larvae stained with phalloidin (red) and DAPI (blue). The arrowheads point to the pronephric ducts and the asterisks mark kidney cysts. (C) Confocal image of 3-dpf WT and dx36.18¹⁰⁸⁴ mutant in whole-mount, stained for acetylated tubulin to mark cilia. (D) Linkage analysis for dx36.18¹⁰⁸⁴ using SNPtrack. (E) The homozygosity interval for dx36.18¹⁰⁸⁴. (F) Linkage analysis of the dx36.18¹⁰⁸⁴ locus. (G) Rescue of the dx36.18^pd1084 phenotype with WT human KIF3A cRNA. Rescue was confirmed by genotyping (not shown). (H) Sequencing of genomic DNA of WT and kif3a^pd1084 mutant larvae showing a six nucleotide insertion in kif3a that adds two extra codons between exons 6 and 7 (underlined). (I) Sequencing of cDNA confirms the insertion of codons coding for MQ in kif3a^pd1084 mutants. TMM, threonine, methionine, methionine; CAN, cysteine, alanine, asparagine. (J) Alignment of Kif3a protein sequences from zebrafish, human, mouse, rat and frog.

A truncation at the end of the motor domain of Dync2h1 leads to a cystic kidney phenotype. (A) Brightfield image of 5-dpf WT sibling and aa65.6^pd1086 mutant larvae. Red arrowhead indicates a kidney cyst. (B) Confocal images of transverse sections of 5-dpf WT sibling and aa65.6^pd1086 mutant larvae stained with phalloidin (red) and DAPI (blue). The arrowheads point to pronephric ducts and asterisks mark kidney cysts. (C) Confocal image of 3-dpf WT and aa65.6^pd1086 mutant embryos in whole-mount, stained for acetylated tubulin to mark cilia. (D) Linkage analysis for aa65.6^pd1086 using SNPtrack. (E) The homozygosity interval for aa65.6^pd1086. (F) Linkage analysis using single embryos. (G) Sequencing of genomic DNA of WT and aa65.6^pd1086 mutant larvae. (H) Injection of a morpholino directed against a splice site within the motor domain of dync2h1 phenocopies the aa65.6^pd1086 mutation. (I) Confocal images of transverse sections 3-dpf WT and dync2h1 morphants stained with phalloidin and DAPI, showing distended pronephric ducts (arrowheads). (J) Schematic of the Dync2h1 protein illustrating that the mutation removes a portion of the motor domain.

dync2h1 morpholino validation and supplemental characterization of aa65.6^pd1086 mutant. (A) RT-PCR from RNA of control and dync2h1 splice-site morpholino-injected EK embryos at the one cell stage and harvested at 3 dpf. (B) Ventral view of cartilage in the jaw of 5 dpf alcian-blue stained larvae. (C) View of chromosome 15 in Ensembl showing the four transcripts that constitute the full length dync2h1 in zebrafish and the corresponding protein domains.