Fig 1.
Phylogeny and genomic organisation of qki genes.
(A) Phylogenetic relationships of chordate qki genes inferred from Bayesian analysis of human QKI5 nucleotide sequence and corresponding transcripts from selected species. In the case of multiple genes in one species, each copy is identified by its Ensembl gene name. Nodes are labeled with posterior probability values. The two main branches are denoted by grey boxes. (B) Exon-intron structure of predicted qki transcript variants in zebrafish and mammals. Exons are shown as boxes and introns as lines. The human exon terminology is used for all species, numbering the exons 1–6, 7a, 7b, 7c and 8. The exons are not drawn to scale, the correct sizes are presented in S1 Fig. The colors of the 3’ exons and introns match the transcript variants that include them. The names of the transcript variant are indicated in the boxes to the right, and the colors are according to their similarity with the human transcript variants. The white boxes indicate transcripts containing an extended version of exon 6.
Fig 2.
Syntenic conservation of qki genes.
(A) Shared synteny between the genomic region containing QKI in human chromosome 6 and zebrafish chromosomes 13 and 17. Colored boxes represent genes. Genes in common between human chromosome 6 and zebrafish chromosome 17 are marked in yellow and genes shared between human chromosome 6 and zebrafish chromosome 13 are colored blue. QKI is framed with a thick line. Gene names are the same in zebrafish and human unless marked otherwise. The chromosomes are not shown to scale. (B) Shared synteny between spotted gar (Lepisosteus oculatus) linkage group (LG) 16, zebrafish (Danio rerio) chromosomes 13 and 12, and Tetraodon (Tetraodon lineatus) chromosomes 17 and 2. Black boxes indicate qki homologs and colors represent conservation between species as described in the legend.
Fig 3.
Sequence alignment and conservation between zebrafish and human QKI proteins.
Amino acid sequence alignment including all isoforms found in human and zebrafish. The position of each exon is indicated with black lines above the alignment. The human exon terminology is used for both species. The KH domain is marked with a red line below the alignment. Black background indicates identical amino acids and grey indicates conservative changes.
Fig 4.
Quantitative temporal expression of qki transcripts during development.
Relative mRNA expression of qkia, qki2, and qkib is plotted across indicated developmental time points. Each point represents the average measurement of three biological replicates. Bars correspond to standard deviation of the mean. hpf: hours post-fertilization, dpf: days post-fertilization.
Fig 5.
Spatiotemporal expression of qki genes during development.
Representative images of whole mount in situ hybridization using probes detecting qkia (A), qki2 (B) and qkib (C) expression. Developmental stages are expressed as the number of cells, somites (som), or hours post-fertilization (hpf). Lateral (left panels) and dorsal (right panels) views are shown, anterior to the left. Arrows in B at the 5 somite stage indicate the hindbrain primordium, while arrows at 72 hpf indicate the presumptive lateral line Schwann cells and in C, developing trunk neural tube. ad: adaxial cells, lpm: lateral paraxial mesoderm, som: somites, fb: forebrain, di: diencephalon, vdi: ventral diencephalon, ddi: dorsal diencephalon, dhb: dorsolateral hindbrain, mb: midbrain, mhb: midbrain/hindbrain boundary, hb: hindbrain, vz: ventricular zone, myo: myotome, pf: pectoral fin, cm: cranial muscles, h: heart.
Fig 6.
qki2 and qkib are expressed in neural progenitor cells.
Representative images of combined in situ hybridization and immunofluorescence detecting qki2 (A) and qkib probes (B), both shown in red. Sox2 antibody is shown in green and DAPI in blue. Images shown are within the forebrain, hindbrain and spinal cord and overlays are denoted in the figure header. Scale bars are 50μm for forebrain and hindbrain images, and 20μm for spinal cord images. Asterisks indicate staining artefacts.
Fig 7.
qki2 and qkib are absent from differentiated neurons in developing zebrafish.
Representative images of combined in situ hybridization and immunofluorescence detecting qki2 (A) and qkib probes (B), both shown in red. HuC/D antibody is shown in green. Images shown are within the forebrain, hindbrain and spinal cord.