A microRNA imparts robustness against environmental fluctuation during development

Abstract

The microRNA miR-7 is perfectly conserved from annelids to humans, and yet some of the genes that it regulates in Drosophila are not regulated in mammals. We have explored the role of lineage restricted targets, using Drosophila, in order to better understand the evolutionary significance of microRNA-target relationships. From studies of two well characterized developmental regulatory networks, we find that miR-7 functions in several interlocking feedback and feedforward loops, and propose that its role in these networks is to buffer them against perturbation. To directly demonstrate this function for miR-7, we subjected the networks to temperature fluctuation and found that miR-7 is essential for the maintenance of regulatory stability under conditions of environmental flux. We suggest that some conserved microRNAs like miR-7 may enter into novel genetic relationships to buffer developmental programs against variation and impart robustness to diverse regulatory networks.

Figure 1. Non-conserved expression and targeting of miR-7

(A–C) Localization of miR-7 RNA (purple) and Sens protein (green) in developing antenna (A), leg (B) and wing (C) discs. The miR-7 RNA is detected in the cytoplasm of proprioceptor and olfactory SOP cells, which are marked with Sens-positive nuclei. Comparable sensory organs in vertebrates do not express miR-7. (D) Overlap of predicted miR-7 targets in Drosophila and human is limited to nine orthologous genes.

Figure 2. Regulation of miR-7 expression in photoreceptors

(A) Schematic representation of the transgenic reporter for miR-7 enhancer activity in vivo. The enhancer contains binding sites for Ttk69 (Ttk1–2), Yan and Pnt-P1 (Ebs1–4), and Ato/Da (Prn1–2). The enhancer was placed upstream of a minimal promoter and nuclear GFP coding sequence. (B,B′) Localization of miR-7 RNA (red) and Elav protein (blue) in a developing eye disc. The vertical red stripe in (B′) corresponds to cells in the morphogenetic furrow (arrowhead), which is the zone of R8 photoreceptor determination. To the right of this zone other photoreceptors are then determined, as marked by their expression of Elav. (C,C′) miR-7 enhancer activity in a developing eye disc, as detected by the (miR-7)E>GFP reporter (green). Elav (blue) marks photoreceptor cells. The vertical green stripe in (C′) corresponds to cells in the morphogenetic furrow (arrowhead). Expression is weakly variegated, suggesting additional regulatory elements might be missing. (D–F) miR-7 enhancer activity as detected by the reporter (green) in wildtype (D), yan¹ (E), GMR≫Pnt-P1 (F) eye discs. Enhancer activity is stronger in yan¹ and GMR≫Pnt-P1 precursor cells, which are not marked with Elav (purple). The GMR driver expresses genes (in this case Pnt-P1) in precursor and photoreceptor cells. (G,H) miR-7 RNA detected by colorimetric in situ hybridization in wildtype (G), and GMR≫Ttk69 (H) eye discs. (I,J) miR-7 enhancer activity as reported (green) in wildtype (I) and GMR≫Ttk69 (J) eye discs. (K,L) miR-7 enhancer activity as reported (green) in GMR≫EGFR.Act (EGFR.λtop) (K) and GMR≫EGFR.DN (L) eye discs. These mutants drive constitutively active EGFR and dominant negative EGFR, respectively, in photoreceptors and their precursors. (M–P) Wildtype (M and O), and N^ts3 (N and P) larvae were shifted to the restrictive temperature (31°C) for 19 hrs before analysis. (M,N) miR-7 RNA detected by in situ hybridization. (O,P) miR-7 enhancer activity as detected by the reporter.

Figure 3. miR-7 stabilization of gene regulatory networks

(A) The network controlling photoreceptor determination. Shown are signal transduction components (yellow), transcription factors (blue) and miR-7 (red) in the network. The miRNA participates in two interlocking coherent feedforward loops, labeled 1 and 2. Loop 1 is highlighted in green and loop 2 is in orange. A typical coherent feedforward loop of this type is shown to the right. The interlocked loops together construct a double-negative feedback loop between miR-7 and Yan. (B) The network controlling SOP determination. Components are color-coded as in (A). miR-7 participates in an incoherent feedforward loop highlighted in green. A typical incoherent feedforward loop of this type is shown to the right. The feedforward loop is also interconnected with a double-negative feedback loop between Atonal and E(spl), with miR-7 as an effector of Atonal, and E(spl) directly inhibiting Atonal (orange).

Figure 4. The enhancer drives miR-7 expression in SOP cells

(A–C) miR-7 RNA (purple) in antenna (A), leg (B) and wing (C) discs. (D–F) miR-7 enhancer activity (green) in antenna (D), leg (E) and wing (F) discs that are counterstained for nuclei in blue. (G–I″) miR-7 enhancer activity as reported (cyan) in antenna (G,G′), leg (H,H′) and wing (I,I′) discs. (G,G″,H,H″,I,I″) Discs were counterstained for Ato protein (red). Merged fluorescence due to reporter GFP and Ato colocalization appears white.

Figure 5. Regulation of miR-7 expression in photoreceptors

(A–F) miR-7 enhancer activity (green) in ptc>Ato (A–C), and ptc>Sc (D–F) imaginal discs that are counterstained for nuclei in blue. The ptc driver expresses Ato and Sc in a stripe of cells along the anteroposterior (vertical) midline of the discs. (G and H) miR-7 enhancer activity (green) in wildtype (G), and GMR>Ato (H) eye discs. (I–L) Activity of the mutated miR-7 enhancer with altered Ato-binding sites. (miR-7)E>GFP(-Prn) reporter expression (green) in eye (I), leg (J), wing (K), and antenna (L) discs. The leg, wing, and antenna were counterstained for nuclei in blue. The eye disc was counterstained for Elav protein in red. Note the enhancer is inactive in the morphogenetic furrow (arrowhead) of the eye where R8 photoreceptors are determined.

Figure 6. miR-7 regulates Ato expression and SOP determination

(A–L) SOP cells are marked with Sens protein in green. (A) A wing disc at low magnification shows the pattern of all wing SOPs, with a grey box highlighting the dorsal radius SOP group. (B–L) High magnification view of the dorsal radius group from (B) wildtype, (C) miR-7^Δ1/Df(2R)exu1, (D) dpp≫Ato, (E) dpp≫dsRed-miR-7, (F) dpp≫miR-7-140₁, (G) dpp≫E(spl)m7, (H) dpp≫dsRed-miR-7≫E(spl)m7, (I) dpp≫E(spl)m8, (J) dpp≫dsRed-miR-7≫E(spl)m8, (K) dpp≫E(spl)mδ, (L) dpp≫dsRed-miR-7≫E(spl)mδ wing discs. The dpp driver expresses miR-7 and E(spl) genes in a stripe of cells along the anteroposterior midline of the wing, which is visualized by the dsRed fluorescence from the dsRed-miR-7 chimera gene, observed in panels (E,H,J,L). The arrow in (E) points to an expanded cluster of dorsal radius SOP cells where miR-7 is misexpressed, relative to a cluster of SOP cells in wildtype, as highlighted with the arrow in (B). The miR-7-140₁ transgene, when misexpressed, gives a comparable phenotype but is not marked by dsRed. (M) Percentage of adults with ectopic or missing external sensory bristles (scutellar and sternopleural) observed in various mutants. N indicates total animals scored for wildtype (n=198), dpp≫Ato (n=89), dpp≫dsRed-miR-7 (n=118), dpp≫E(spl)m7 (n=193), dpp≫E(spl)m8 (n=166), dpp≫E(spl)mδ, dpp≫dsRed-miR-7≫E(spl)m7 (n=111), dpp≫dsRed-miR-7≫E(spl)m8 (n=168), and dpp≫dsRed-miR-7≫E(spl)mδ(n=313) (N, O) miR-7 enhancer activity as reported (green) in the wing dorsal radius group counterstained with dsRed (red) from control ptc≫dsRed (N) and ptc≫dsRed-miR-7 (O) animals. (P,Q) Ato protein (green) in wildtype (P) and hairy≫dsRed-miR-7 (Q) eye discs. dsRed (red) indicates where miR-7 is misexpressed. (R,S) R8 photoreceptors marked with Sens (green) and other photoreceptors marked with Elav (blue) in wildtype (R) and hairy≫dsRed-miR-7 (S) eye discs. dsRed (red) indicates area where miR-7 is misexpressed. Photoreceptor clusters normally have a single R8 cell. Circles in (S) highlight some mutant clusters with more than one R8 cell.

Figure 7. miR-7 stabilizes gene expression and SOP determination under temperature fluctuation

(A–B′) Ato protein (purple) in wildtype (A,A′), and miR-7^Δ1/Df(2R)exu1 mutant (B,B′) eye discs from animals grown under uniform temperature conditions. (A,B) show maximal projections of confocal z stacks. (A′,B′) show single focal planes. (C–D′) Ato (purple) and Yan (green) proteins in wildtype (C,C′) and miR-7^Δ1/Df(2R)exu1 mutant (D,D′) eye discs from animals grown under fluctuating temperature conditions. Images are maximal projections of confocal z stacks. (E-E″) Ato (red) and Sens (green) proteins in wildtype antennal discs from animals grown under fluctuating temperature steps. Sens marks the SOPs while Ato marks the PNCs. Sensory organs are progressively more developed in each panel. (E) An arc of coeloconic sensilla SOPs co-expressing Sens and Ato is first evident (purple arrowheads), along with the nascent Johnston’s organ, marked JO. A ring of cells expressing Ato surrounds the initial arista SOPs (arrow). (E′) SOP numbers increase within each organ system, and expression of Ato in these cells is reduced. (E″) There appears new rows of SOPs that are enveloped by cells with upregulated Ato (box). (F-F″) miR-7^Δ1/Df(2R)exu1 mutant antennal discs from animals grown under fluctuating temperature conditions. (F) The nascent Johnston’s organ (JO) appears normal, but the arc of coeloconic sensilla SOPs (purple arrowheads) is depleted at the top of the arc. Cells in the arista domain do not express a ring of Ato and do not form arista SOPs (arrow). (F′) Deficits in SOP cell number and spacing in the arista and coeloconic SOPs are further seen. (F″) In addition to reduced SOP numbers, there is little or no up-regulation of Ato in cells enveloping new SOPs (box).