Transcriptional interactions between the pannier isoforms and the cofactor U-shaped during neural development in Drosophila

Dissecting roles of pannier splice variants during pupal and adult morphogenesis in Henosepilachna vigintioctopunctata

The GATA transcription factor gene, pannier (pnr), has been extensively studied in Drosophila, revealing its crucial role in dorsal closure, heart development and the regulation of cuticular bristle patterns in adults. However, studies on the functions of pnr in the development of coleopteran insects are still scarce. Herein, we identified the pnr gene in Henosepilachna vigintioctopunctata and discovered two splicing variants named Hvpnr-α and Hvpnr-β respectively. Temporal expression analysis revealed that Hvpnr, Hvpnr-α and Hvpnr-β were expressed at various stages including egg, larval, pupal and adult stages. To investigate the developmental role of Hvpnr in H. vigintioctopunctata, RNA interference (RNAi) assays were conducted on third-instar larvae. Injection of dsHvpnr, dsHvpnr-α and dsHvpnr-β and co-injection of dsHvpnr-α and dsHvpnr-β (dsRNAs mix) all resulted in significant downregulation of the target transcripts. In pupae developed from dsHvpnr-treated larvae, the symmetric black spots on both sides of the mesothorax, metathorax and tergites approached and connected. Pupal morphometric analysis revealed that dsHvpnr, dsHvpnr-α and dsRNAs mix injections significantly narrowed the spacing of dorsal symmetric spots, contracted spiracle distances on tergite sides, diminished pronotum width and markedly reduced inter-compound eye spacing compared to controls. In addition, injections of dsHvpnr and dsRNAs mix significantly reduced the oviposition in female adults. Silencing of Hvpnr led to the disappearance of the scutellum in adults, preventing the elytra from closing and properly attaching to the dorsal side of the abdomen. It is noteworthy that dsHvpnr-α or dsRNA mix induced scutellum formation defects in adults, while knockdown of Hvpnr-β had no impact. Furthermore, in stark contrast to previous studies on ladybird species such as Harmonia axyridis and Coccinella septempunctata, silencing Hvpnr did not affect melanin synthesis in pupae and adults in H. vigintioctopunctata. These findings demonstrate that among the splice variants of Hvpnr, Hvpnr-α plays a dominant regulatory role in the post-embryonic morphogenesis of H. vigintioctopunctata. This study also shows that Hvpnr is not involved in melanin synthesis, indicating significant functional differentiation of pnr during the evolution of ladybirds.

Modulation of Global Gene Expression by Aneuploidy and CNV of Dosage Sensitive Regulatory Genes

Aneuploidy, which disrupts the genetic balance due to partial genome dosage changes, is usually more detrimental than euploidy variation. To investigate the modulation of gene expression in aneuploidy, we analyzed the transcriptome sequencing data of autosomal and sex chromosome trisomy in Drosophila. The results showed that most genes on the varied chromosome (cis) present dosage compensation, while the remainder of the genome (trans) produce widespread inverse dosage effects. Some altered functions and pathways were identified as the common characteristics of aneuploidy, and several possible regulatory genes were screened for an inverse dosage effect. Furthermore, we demonstrated that dosage changes of inverse regulator Inr-a/pcf11 can produce a genome-wide inverse dosage effect. All these findings suggest that the mechanism of genomic imbalance is related to the changes in the stoichiometric relationships of macromolecular complex members that affect the overall function. These studies may deepen the understanding of gene expression regulatory mechanisms.

Variation in Pleiotropic Hub Gene Expression Is Associated with Interspecific Differences in Head Shape and Eye Size in Drosophila

Revealing the mechanisms underlying the breathtaking morphological diversity observed in nature is a major challenge in Biology. It has been established that recurrent mutations in hotspot genes cause the repeated evolution of morphological traits, such as body pigmentation or the gain and loss of structures. To date, however, it remains elusive whether hotspot genes contribute to natural variation in the size and shape of organs. As natural variation in head morphology is pervasive in Drosophila, we studied the molecular and developmental basis of differences in compound eye size and head shape in two closely related Drosophila species. We show differences in the progression of retinal differentiation between species and we applied comparative transcriptomics and chromatin accessibility data to identify the GATA transcription factor Pannier (Pnr) as central factor associated with these differences. Although the genetic manipulation of Pnr affected multiple aspects of dorsal head development, the effect of natural variation is restricted to a subset of the phenotypic space. We present data suggesting that this developmental constraint is caused by the coevolution of expression of pnr and its cofactor u-shaped (ush). We propose that natural variation in expression or function of highly connected developmental regulators with pleiotropic functions is a major driver for morphological evolution and we discuss implications on gene regulatory network evolution. In comparison to previous findings, our data strongly suggest that evolutionary hotspots are not the only contributors to the repeated evolution of eye size and head shape in Drosophila.

Membrane-Anchored Hairless Protein Restrains Notch Signaling Activity

The Notch signaling pathway governs cell-to-cell communication in higher eukaryotes. In Drosophila, after cleavage of the transmembrane receptor Notch, the intracellular domain of Notch (ICN) binds to the transducer Suppressor of Hairless (Su(H)) and shuttles into the nucleus to activate Notch target genes. Similarly, the Notch antagonist Hairless transfers Su(H) into the nucleus to repress Notch target genes. With the aim to prevent Su(H) nuclear translocation, Hairless was fused to a transmembrane domain to anchor the protein at membranes. Indeed, endogenous Su(H) co-localized with membrane-anchored Hairless, demonstrating their binding in the cytoplasm. Moreover, adult phenotypes uncovered a loss of Notch activity, in support of membrane-anchored Hairless sequestering Su(H) in the cytosol. A combined overexpression of membrane-anchored Hairless with Su(H) lead to tissue proliferation, which is in contrast to the observed apoptosis after ectopic co-overexpression of the wild-type genes, indicating a shift to a gain of Notch activity. A mixed response, general de-repression of Notch signaling output, plus inhibition at places of highest Notch activity, perhaps reflects Su(H)’s role as activator and repressor, supported by results obtained with the Hairless-binding deficient Su(H)^LLL mutant, inducing activation only. Overall, the results strengthen the idea of Su(H) and Hairless complex formation within the cytosolic compartment.

Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies

Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic evolution. An exceptional contribution of cis-regulatory divergence has been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and stage-specific expression. We argue that the regulatory context must be considered in comparative expression studies.