Composite of all NR expression patterns over the course of embryogenesis. Embryos are oriented anterior to the left, and dorsal up. Nuclei are red, and RNA is blue.

Graphic summary of NR tissue distributions. Stages of development and individual tissues are indicated as a series of boxes. For each NR, the top four rows indicate various tissues during different stages of embryonic development (Stages 1−5, 6−10, 11−14, and 15−17, respectively) and the bottom row indicates tissues of wandering 3rd instar larva. Each tissue is represented by a unique color as specified in the color key at the top. NOS transcript distributions are also shown for comparison (bottom left).

NR expression patterns during early embryogenesis. (A, B) E78 in stage 2 and 5 embryos respectively, showing no maternal RNA (A), and zygotic transcription during stage 5 (B, K). White arrowheads indicate nascent transcripts in epithelial nuclei, and clear arrowheads in yolk nuclei. (C, D) tll in stage 3 (C) and 5 (D, L) embryos. Arrowheads show basal enrichment. Focus on the plane of the nuclei within the anterior tll stripe shows both nascent (white arrowhead in L) and cytoplasmic (clear arrowhead in L) transcripts. (E, F) HR4 in stage 2 and 5 embryos, respectively. Maternally provided transcripts are completely degraded by stage 5 with no zygotic replenishment. (G, H) E75 in stage 2 and 4 embryos, respectively. Transcripts are rapidly removed from the posterior plasm (pp) and the peripheral cortex. (I, M) HR78 in a stage 5 embryo. The arrowhead in (M) indicates enrichment around the yolk nuclei. (J, N) dHNF4 in stage 2 and 5 embryos showing maternal (J) and zygotic (N) expression. Panels K−N are greater-magnification images of embryos stained for the receptors indicated.

NR expression in the mesoderm and gut. (A−D, J, K) E75 in stage 6−14 embryos. During stages 6 and 7, E75 mRNA is enriched in foci within the yolk (yk), enriched basally in the epithelial layer (asterisks in A and K), perinuclearly around yolk nuclei (arrowhead in A). Arrowhead in K) indicates localization on filopodia-like processes. At germband extension (B), E75 is seen in posterior midgut cells (pmg) and continues to be enriched in yolk foci (yk). After germband retraction (C, D) expression is seen in the developing midgut (mg), interstitial cell precursors (i), tracheal system (ts), salivary glands (sg), and yolk nuclei (yn). (E) During gastrulation, HR39 is enriched in mesoderm (ms), basal epithelia (asterisk) and around yolk nuclei (arrowhead). (F, L−O) Ftz-F1 transcripts are enriched in the mesoderm (ms) and basal epithelia during gastrulation (asterisk in L). Later (F), it is expressed in ventral nerve cord (vnc), midgut (mg), salivary glands (sg in M), yolk nulcei (arrowhead in M), tracheal system (ts in M), and the border between hindgut and midgut (arrowhead in panel N), as well as the proventriculus (pv in panel O). (G, Q) E78 in stage 8 and 13 embryos respectively, showing enrichment in mesoderm (ms) in small cytoplasmic foci (arrowheads in G), and around yolk nuclei (arrowhead in Q). (H, R) HR3 expression in midgut (mg), salivary glands (sg) and posterior spiracles (ps). (I, S, T) HR4 probe in stage 14 and 16 embryos showing expression in midgut (mg), hindgut (hg), yolk nuclei (yn), salivary gland lumen (sg) and somatic muscles (m in panel T). (P) dERR probe at stage 15, showing widespread expression with enrichment in the hindgut (hg) and tracheal system (ts) lumen (asterisk). (U) tll transcripts inside yolk nuclei (arrowhead) of a stage 14 embryo. Panels J−U are greater-magnification images of embryos stained for the receptors indicated.

Other sites of NR expression. (A−C) dHNF4 expression and localization seen in cytoplasmic foci and enriched basally at stage 6 (arrowhead and asterisk in panel A respectively), oenocytes (oe) and Malpighian tubules (mt) during stage15 (B−C). (D−E) svp in stage 12 and 15 showing expression the peripheral nervous system (pns) and oenocytes (oe) and localization in ventral nerve cord (vnc) nuclei. (F−I) tll expression I and localization during stages 6−14. (F) Strong anterior stripe at stage 6 with nascent and cytoplasmic puncta (arrowhead). (G) shows puncta in posterior (clear arrowhead) and pole cell expression with perinuclear localization (white arrowhead). (H, I) Head expression resolves to a subset of brain primordia (white arrowheads). PNS (Peripheral Nervous System) expression (clear arrowheads) is also seen. (J−M) HR51 in stage 14−16 embryos showing expression in ectodermal stripes (ec) and posterior outside part of the spiracles (ps). (L) Tracheal progenitor cell staining, limited predominantly to the dorsal trunk, and later (M) in the pharynx (ph) and the salivary glands (sg). (N−P) E75 at stage 15 is clearly expressed in the developing tracheal system (ts), along with strong luminal surface localization and basal puncta (white arrowhead in O) in salivary gland cells. (Q, R) Tracheal staining is also seen with the HR3 probe as well as amnioserosa (as) nuclei and ectodermal (ec) foci. Panels A, C−H, K, L, and O−R are higher-magnification photos of embryos stained for the receptors indicated.

3rd instar larval expression in the gut, Malpighian tubules and fat body. Intestine (A-D), Malpighian tubules (E−H) fat body (I, J) and lymph glands (K, L). NRs probed are indicated at the lower left of each panel. Arrows in (A) and (C) indicate cytoplasmic foci. “Half–moon” perinuclear expression of E75 is shown in (B) (arrowhead), and sub-nuclear foci for dsf in D) (arrowhead). In the Malpighian tubules, large cytoplasmic foci are common (arrowheads in E, G, H). E75 again forms a “half–moon” perinuclear pattern (asterisks in F). HR83 is seen in relatively few foci (asterisk in G). (I) Typical fat body localization as revealed by svp, as opposed to E75 (J), which once again exhibits perinuclear localization (asterisk). (K, L) Lymph gland primary (1º) and secondary lobes (2º) show ‘foci’ between nuclei (arrowheads in K , L), as well as uniformly diffuse staining at varying levels (L). Pericardial cells are marked by an asterisk.

3rd instar expression in the prothoracic gland, salivary gland, lymph gland and brain. Typical expression patterns are shown for the prothoracic gland (A−E), salivary glands (F−I), ventral nerve cord (J), and brain (K-O). NR identities are indicated at the lower left of each panel. Subcellular distributions in the prothoracic gland vary from perinuclear (A) to cytoplasmic foci in various sizes and distributions (B−D, arrowheads) or diffuse cytoplasmic (asterisk in E). In the salivary glands, tll (F) and E75 (G) are localized in tight “half-moon” perinuclear patterns, whereas E78 (H) exhibits more diffuse perinuclear localization (arrowhead in H). Conversely, svp is distributed relatively uniformly, with some enrichment around nuclei (I; arrowhead). (J) HR38 is subcellularly localized in ventral nerve cord axons (arrowhead). Brain lobe patterns (K-O) are highly variable, including expression in optic lobes (N; ol) and mushroom bodies (O; mb).

3rd instar larval expression in imaginal discs. (A-D) Examples of expression patterns in wing discs. HR39 is enriched dorsally in the wing pouch (A; arrowhead). dsf expression is limited (B; arrowhead ), whereas EcR is expressed throughout most of the disc (C) with enrichment in the hinge (asterisk) and body wall (arrowhead). usp expression is also widespread, but unlike the others is diffuse (D). In the eye disc (E-H, the morphogenetic furrow (f) and differentiating photoreceptors (arrowheads) are common site of expression. (I-K) Examples of leg disc expression patterns. (L) Larval testis with HR83 expressed in somatic cyst cells (arrowhead).

Perinuclear E75 expression overlaps with rough ER. (A) Third instar salivary gland cells are shown stained for E75 transcripts (red) and a marker of rough ER (Sec61alpha-GFP; green). Nuclei are blue. Individual channels for E75 (A′) and Sec61alpha-GFP (A′′) are shown to the right. Arrowheads indicate locations where overlap is clearest. (B) Same experiment done in an Oregon R (wild type) larval salivary gland as a negative control.

Expression of NOS. (A) Early stage embryo showing modest maternal expression with enrichment in the yolk (yk) away from the periphery and pole plasm (pp). (B) During gastrulation zygotic expression leads to basally localized transcripts in the epithelial cell layer (asterisks) and new expression in the yolk (yk) with perinuclear localization (arrowhead). (C) This pattern continues during germband extension (asterisk- basal enrichment, arrowhead- yolk nuclei perinuclear localization). During late embryogenesis (D), NOS is expressed in the salivary glands (sg), tracheal system (different focal plane), posterior spiracles (ps), hindgut (hg), midgut (mg) and part of the somatic muscles (sm). (E, F) Greater-magnification images of stage 5 embryos showing similarity between NOS and Drosophila Estrogen-related receptor (dERR) localization patterns with enrichment around yolk nuclei (yn; arrowheads). (G, H) Greater-magnification stage 16 embryos showing expression of NOS and HR3 at the somatic muscles (sm). (I−P) 3rd instar larval expression patterns showing expression in the prothoracic glands (I), fat body (J), portions of the gastric caeca (K), salivary gland (L) and eye (M, dorsal view; N, lateral view), wing (O) and leg (P) imaginal discs. Arrowheads show features of subcellular localization. F, morphogenic furrow.