FIGURE SUMMARY
Title

Ancient Pbx-Hox Signatures Define Hundreds of Vertebrate Developmental Enhancers

Authors
Parker, H.J., Piccinelli, P., Sauka-Spengler, T., Bronner, M., and Elgar, G.
Source
Full text @ BMC Genomics

Meis2 CNEs from zebrafish and lamprey drive equivalent expression patterns in zebrafish and lamprey embryos. A, multiple alignment of orthologous genomic regions containing the gene c15orf41 (blue peak), downstream of meis2, revealing CNEs (red peaks). Human, zebrafish and lamprey sequences are aligned with the fugu sequence as a baseline. Zebrafish CNE 329X is translocated in the current zebrafish genome assembly so does not appear in this alignment. B-M, orthologous elements from lamprey (B-G) and zebrafish (H-M) drive similar GFP expression patterns in the nervous system of zebrafish embryos at 54hpf: element 3285 in the cranial ganglia (arrows) and primary neurons of the hindbrain and spinal cord (arrowhead) (B, H); 3288 in neurons of the hindbrain posterior to rhombomere (r) 4 (C, I), as determined by comparison with r3r5 RFP expression (D, J); 3299 in the anterior hindbrain - r2-4 for the lamprey homolog (E, F) and r3-4 plus the corresponding neural crest for the zebrafish homolog (K, L); 329X in the hindbrain and neurons of the midbrain (G, M). N-O , embryonic day 14-15 lamprey embryos transgenic for lamprey elements 3285 (N) and 3299 (O) show GFP expression in the cranial ganglia (arrowheads) and anterior hindbrain respectively, consistent with their expression in zebrafish (3285: B, 3299: E). P-Q, dorsal views of the head of lamprey (P) and zebrafish (Q) embryos transgenic for lamprey element 3299. cg: cranial ganglia; hb: hindbrain; mb: midbrain; nc: neural crest; sc: spinal cord.

CNE 3299 harbours essential conserved Pbx-Hox and Meis binding-sites. A, multiple sequence alignment of a region of CNE 3299 from human, zebrafish and lamprey highlighting conserved Pbx-Hox (blue box) and Meis (green box) binding-site motifs. The specific sites mutated in elements sub1 and sub2 are indicated below the alignment. B-C, compared to wild-type 3299 expression (B), mutating the first Pbx-Hox and Meis motif cluster (sub1) results in the loss of reporter expression in the neural crest (arrow) and broader expression in the hindbrain (arrowhead) (C). nc: neural crest.

Pbx-Hox motifs correlate with segment-specific hindbrain and pharyngeal arch reporter expression. A-R, zebrafish elements from the lamprey (A-J, M, O, Q) and jawed vertebrate (K, L, N, P, R) CNE sets drive GFP expression in the hindbrain and pharyngeal arches. Elements: Evi1_40224 (A, B), Tshz3_43509 (C, D), NR2F2_27254 (E, F), Pax2_217 (G, dorsal view: H), ZNF503_32799 (I, J), Nkx6-1_4281 (K, L), Tshz3_24804 (M), Pax9_2099 (N), TshZ3_24805-6 (O), FoxP1_886 (P), Tshz3_24807 (Q), BCL11A_2554 (R). Expression in the hindbrain is often restricted to certain rhombomeres, as shown by comparison with r3r5 RFP expression (B, D, F, H, J, L). Tshz3_24807 drives expression in the trunk musculature (Q). Elements show temporal variation in reporter expression, expressing most strongly at 24-30hpf (C, D), 48-54hpf (A, B, E, F, I, J, Q) or 72-78hpf (G, H, K, L, M, N, O, P, R). hb: hindbrain; pa: pharyngeal arches; m: muscle.

Acknowledgments
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