Supplemental gene list to accompany Figure 1j, Figure 2d. DeTCT 3' end sequencing carried out on various neural crest mutants at different time points

3' end sequencing of multiple neural crest mutants; tfap2a, tfap2c, sox10, mitfa and yap1 at differing time points. Lists represent relevant pairwise comparisons

Supplemental gene lists to accompany Figure 1i, Figure 2e. FACS of neural crest cells at 22 hpf

FACS followed by RNA-Seq of sox10:mg cells in zebrafish at 22 hpf

Supplemental gene lists to accompany Figure 5b-g. MCL Clustering of tfap2a;tfap2c knockout associated genes.

Gene list to accompany Figure 5b-g. MCL clustering of tfap2a and tfap2c knockout associated genes. the log2 fold changes and adj p-value are derived from tfpa2a/c knockouts compared to wild-type siblings

Supplemental gene list to accompany Figure 2f. 15 individual subset gene lists and full ZFA enrichment.

15 gene lists which are derived from the 15 different subsets found in Figure 2f. An UpSet comparison of tfap2a;tfap2c knockouts at 4 somites, 15 somites, 24 hpf and a neural crest gene enriched set from 22 hpf FACSed and RNA-Seq sequenced cells. Full ZFA enrichment shown in the magenta box

Supplemental gene lists to accompany Figure 4c & h. 14 subset gene lists derived from Figure 4c.

14 Subset gene lists to accompany Figure 4c

Raw data of sex ratios

Sex ratio (as percentage Male) of zebrafish lines compared to the age in days of the mother and father

Raw data of Fertilisation Rates

Data on fertilisation and phenotype rates of clutches laid by wild-type and heterozygous tert<i>^sa6541</i> intercrosses

The number of HSPCs is rescued in a <i>tp53</i> mutant background.

<p>(A) The CHT of 96 hpf larvae from a <i>nol9</i>^{<i>+/sa1022</i>}<i>;tp53</i>^{<i>+/zdf1</i>} x <i>nol9</i>^{<i>+/sa1022</i>}<i>;tp53</i>^{<i>+/zdf1</i>} cross stained by WISH against <i>c-myb</i>. Signal extracted from the corresponding WISH photograph is shown. Numbers represent larvae with the displayed phenotype out of the total number of larvae examined. (B) Quantification of <i>c-myb in situ</i> signal for 96 hpf larvae from a <i>nol9</i>^{<i>+/sa1022</i>}<i>;tp53</i>^{<i>+/zdf1</i>} x <i>nol9</i>^{<i>+/sa1022</i>}<i>;tp53</i>^{<i>+/zdf1</i>} cross, depending on their genotype. Data are represented as the mean number of pixels +/- SEM. <i>nol9</i>^<i>+/+</i><i>;tp53</i>^<i>+/+</i> n = 9; <i>nol9</i>^<i>-/-</i><i>;tp53</i>^<i>+/+</i> n = 11; <i>nol9</i>^<i>-/-</i><i>;tp53</i>^{<i>+/zdf1</i>} n = 19; <i>nol9</i>^<i>-/-</i><i>; tp53</i>^{<i>zdf1/zdf1</i>} n = 10. Two-tailed Student’s <i>t</i>-Test, *, p<0.05; **, p<0.01. (C) Representative pictures of the CHT of 96 hpf larvae from a <i>nol9</i>^{<i>+/sa1022</i>}<i>;tp53</i>^{<i>+/zdf1</i>} x <i>nol9</i>^{<i>+/sa1022</i>}<i>;tp53</i>^{<i>+/zdf1</i>} cross stained by WISH against <i>hbae1</i>. Signal extracted from the corresponding WISH photograph is shown. (D) Quantification of <i>hbae1</i> WISH signal for larvae from a <i>nol9</i>^{<i>+/sa1022</i>}<i>;tp53</i>^{<i>+/zdf1</i>} x <i>nol9</i>^{<i>+/sa1022</i>}<i>;tp53</i>^{<i>+/zdf1</i>} cross, depending on their genotype. Data are represented as the mean number of pixels +/- SEM. <i>nol9</i>^<i>+/+</i><i>;tp53</i>^<i>+/+</i> n = 16; <i>nol9</i>^<i>-/-</i><i>;tp53</i>^<i>+/+</i> n = 14; <i>nol9</i>^<i>-/-</i><i>;tp53</i>^<i>+/-</i> n = 23; <i>nol9</i>^<i>-/-</i><i>;tp53</i>^<i>-/-</i> n = 16. Two-tailed Student’s <i>t</i>-Test, *, p<0.05; **, p<0.01. Within the figure, <i>nol9</i>^{<i>sa1022</i>} allele has been denoted as <i>nol9</i>^<i>-</i> and <i>tp53</i>^<i>zdf1</i> as <i>tp53</i>^<i>-</i>.</p

<i>nol9</i>^{<i>sa1022/sa1022</i>} embryos display tissue-specific upregulation of <i>tp53</i>.

<p>Representative images of embryos stained by whole-mount <i>in situ</i> hybridization against <i>tp53</i>. (A) At 48 hpf, similar levels of <i>tp53</i> signal (arrow) was detected in the CHT of <i>nol9</i>^{<i>sa1022/sa1022</i>} embryos and their wild-type siblings. (B) At 72 hpf, <i>nol9</i>^{<i>sa1022/sa1022</i>} mutant embryos were characterized by more <i>tp53</i> signal in the CHT than their wt siblings. Mann-Whitney U test, p<0.05. (A-B) All embryos are oriented with anterior to the left and dorsal to the top. (C) Schematic representation of digestive organs in a wild-type 72 hpf zebrafish larva. I–intestine, L- liver, P- pancreas. (D) At 72 hpf, <i>nol9</i>^{<i>sa1022/sa1022</i>} mutant embryos display strong <i>tp53</i> signal in the liver (arrowhead) and intestine (arrow), compared to weak signal in the intestine of wild-type siblings. (C-D) Dorsal view anterior up.</p

Loss-of-function <i>nol9</i> mutation leads to a defect in ITS2 pre-rRNA processing.

<p>(A) Expression pattern of <i>nol9</i> by WISH at sphere stage (4 hpf), 12 hpf, 48 hpf, 72 hpf, 96 hpf and 120 hpf. Black arrows indicate branchial arches, white arrow indicates pancreas and arrowhead indicates <i>nol9</i>-expressing cells in the CHT. (B) Representative Northern blot analysis of RNA isolated from 5 dpf <i>nol9</i>^{<i>sa102/sa10222</i>} mutants and control (<i>nol9</i>^<i>+/+</i> and <i>nol9</i>^{<i>+/sa1022</i>}) siblings using 5’ETS, ITS1 and ITS2 probes to detect rRNA processing intermediates. Corresponding rRNA intermediates (a, b, c, d) are indicated in B) and C). (C) Schematic representation of the rRNA intermediates detected in the Northern blot analysis. The sites of hybridization of the 5’ETS, ITS1 and ITS2 probes are indicated in red. (D) Methylene blue staining of the membrane was used to control for equal loading of RNA. wt–<i>nol9</i>^<i>+/+</i>/<i>nol9</i>^{<i>+/sa1022</i>}, mut–<i>nol9</i>^{<i>sa1022/sa1022</i>}.</p