Expression of NR genes in the CNS
(A–D) Expression in retina, optic tectum, and hindbrain of RARα-A, Reverbα, Reverbβ, and Reverbγ-B, respectively. RORα-B is expressed in one nucleus in ventral diencephalon and in hindbrain rhombomeres (E), RORα-A in retina, optic tectum, epiphysis, and hypophysis (F), RORβ-A in retina, ventral-posterior part of the optic tectum, and in some neuromasts of the posterior lateral line (G), PXR in small diencephalic and telencephalic nuclei as well as in adenohypophysis (H), PNR in epiphysis, ventral part of retina, and some neurons of posterior diencephalon (I), TLL in diencephalon and mesencephalon with more labeling in ventral diencephalon, anterior tegmentum, and optic tectum (J). COUPTFα-A is expressed in the ventral part of the diencephalon, in forebrain ventricular zone, in tegmentum, and hindbrain (K), COUPTFβ displays a similar expression with additional expression in the dorsal half of the diencephalon (L). EAR2-B expression is restricted to dorsoventral stripes in tegmentum, inentricular zone, in tegmentum, and hindbrain (K), COUPTFβ displays a similar expression with additional expression in the dorsal h hindbrain of rhombencephalon, and in spinal cord (M), COUPTFα-B displays an expression in ventral diencephalon, telencephalon ventricular zone, anterior tegmentum, pretectum, and hindbrain (N). ERβ-A is expressed in a small nucleus in the anterior ventral part of the diencephalon (O), while ERRα is expressed in all brain subdivisions except for the forebrain ventricular zone, tegmentum, and dorsal rhombencephalon (P). ERRβ displays a complex expression with a nucleus in ventral telencephalon, nuclei in diencephalon and tegmentum, and an expression in hindbrain (Q), ERRγ has a very similar expression except for the ventral telencephalic nucleus (R). NURR1 is expressed in part of the telencephalon, in a nucleus in anterior diencephalon, in posterior diencephalon and anterior tegmentum, and in the ventral anterior part of rhombencephalon (S). NOR1 is expressed weakly in ventral telencephalon, tegmentum, and hindbrain and strongly in the habenula (T), SF1-A, LRH1, and SF1-B are expressed strongly in the ventral diencephalon (U–W). RXRα-B is expressed at a low basal level in all brain territories with a much stronger intensity in the ventral part of the optic tectum (X). Embryos are in lateral view, anterior to the left, and are 36 hpf except for (A-D, O, W, and X), where they are at 48 hpf. More extensive anatomical descriptions of these expression patterns are presented in Figure S3 and anatomical details are available at ZFIN (http://zfin.org).

Expression of NR Genes in Retina at 72 hpf
(A) Schematic of a zebrafish eye at 72 hpf showing the characteristic multilayered structure. GCL, ganglion cell layer; INL, inner nuclear layer; ONL, outer nuclear layer; ON, optic nerve; PZ, proliferative zone.
(B–F; left panels) Schematic showing in blue the various types of expression patterns found for NR genes in retinas at 72 hpf after whole-mount in situ hybridization and section. (B) Genes expressed in the ONL. (C) Genes expressed in the INL. (D) Genes expressed in the dorsal part of the retina. (E) Genes showing expression in the ventral part of the retina. (F) Genes showing expression in the proliferative zone of the retina.

Overlapping Domains of Expression between PGC1 and ERRs
(A–O) Expression of PGC1 in slow muscle fibers, posterior pronephric ducts, mucous cells, epiphysis, and part of the telencephalon and diencephalon (A–C) overlaps extensively with the expression of ERRs. ERRα is coexpressed with PGC1 in slow muscle fibers, posterior pronephric ducts, telencephalon, and mucous cells (D–F). ERRβ is coexpressed with PGC1 in epiphysis and posterior pronephric ducts (G–I), ERRγ in epiphysis, part of the tegmentum, and posterior pronephric ducts and ERRδ in mucous cells. Embryos are at 24 hpf in lateral view anterior on the left except for (C, F, I, L, and O), which are shown at the 14-somite stage. Posterior part of the embryo is presented in dorsal view, anterior to the left. More extensive anatomical descriptions of these expression patterns are presented in Figure S3 and anatomical details are available at ZFIN (http://zfin.org)

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