Biology subjects

Shodja, D. N.

Publications and source records attributed to Shodja, D. N..

5 recordsLinked to original sources

bioRxiv2026

ABCG transporter knockouts alter integument and eye pigmentation with gene-specific effects on viability in butterflies and moths

Insects possess remarkable diversity in pigmentation across life stages, generated from a limited number of pigment precursors. ABCG transporters play central roles in pigmentation by mediating the intracellular transport of these precursors, yet their functions outside a few model systems remain poorly characterized. Here, we investigate the roles of the ABCG transporter genes white (w), scarlet (st), and oily kinshiryu (ok) across five lepidopteran species representing both butterflies and moths. CRISPR-Cas9 knockouts reveal conserved, tissue-specific functions of ABCG transporters throughout development, affecting larval and pupal integuments as well as adult eyes, but not scale coloration. Notably, our data indicate that both ommochrome and uric acid deposition underlie the coloration and opacity of Lepidoptera larvae and pupae, with the relative contributions of these pathways differing across species and stages. We also reveal that the vivid orange coloration of Gulf fritillary caterpillars arises from the interplay of ommochromes and urate granules, providing a clear example of how these pathways combine to produce diverse integument pigmentation. Loss of white was deleterious in four species examined, whereas scarlet knockouts produced viable individuals with easily detectable pigmentation phenotypes, identifying scarlet mutant backgrounds as a practical genetic marker for functional studies. Together, these findings show that conserved ABCG transporter complexes are differentially deployed across tissues and life stages, providing a mechanistic basis for the evolutionary diversification of pigmentation in Lepidoptera and enabling expanded functional genomics and transgenesis in emerging model species. Research HighlightsCRISPR-Cas9 disruption of ABCG transporters across Lepidoptera reveals conserved, tissue-specific roles in pigmentation. Interactions between ommochrome and uric acid deposition generate stage-specific coloration in larval and pupal integument.

genetics↗

bioRxiv2025

A Notch signal required for a morphological novelty in Drosophila has antecedent functions in genital disc eversion

The origin of morphological novelties has long fascinated biologists. Signaling pathways play important roles in the formation of novelties, however, the history of how they become integrated into new developmental programs remains unclear. Here, we investigated the evolution of the posterior lobe, a novel structure in the male genitalia of Drosophila melanogaster. We demonstrated that a Notch signaling center is required for the formation of this novelty, and identified enhancers of the ligand Delta, which allowed us to track the evolutionary history of this signaling center. Surprisingly, we found that the posterior lobe signaling center emerged from a pre-existing role in genital disc eversion. We provide a likely mechanism by which Delta contributes to genital eversion through a network of apical extracellular matrix, which also became integrated into the posterior lobe program. This work demonstrates that novelties may be formed in the context of already complex developmental processes, by appending new roles to pre-existing signals.

developmental biology↗

bioRxiv2025

Minos-mediated transgenesis in the pantry moth Plodia interpunctella

Transposon-mediated transgenesis has been widely used to study gene function in Lepidoptera, with piggyBac being the most commonly employed system. However, because the piggyBac transposase originates from a lepidopteran genome, it raises concerns about endogenous activation, remobilization, and silencing of transgenes, thus questioning its suitability as an optimal tool in Lepidoptera. As an alternative, we evaluated the dipteran-derived Minos transposase for stable germline transformation in the pantry moth, Plodia interpunctella. We injected syncytial embryos with transposase mRNA, along with donor plasmids encoding 3xP3::EGFP and 3xP3::mCherry markers of eye and glial tissues. Across multiple experiments, we found that G0 injectees could transmit Minos transgenes through the germline even in the absence of visible marker expression in the soma, and that large mating pools of G0 founders consistently produced transgenic offspring at efficiencies exceeding 10%. Using these methods, we generated transgenic lines with a dual expression plasmid, using 3xP3::mCherry for driving red fluorescence in eyes and glial tissues, as well as the Fibroin-L promoter expressing the recently developed mBaoJin fluorescent protein in the silk glands. This demonstrated the feasibility of screening two pairs of promoter activity in tissues of interest. Collectively, these results--along with previous findings in the silkworm Bombyx mori--demonstrate that Minos achieves robust germline integration of transgenes in Lepidoptera, offering a valuable pathway to the genetic modification of species where the remobilization or suppression of piggyBac elements might be rampant.

genetics↗

bioRxiv2024

Single-nucleus transcriptomics of wing sexual dimorphism and scale cell specialization in sulphur butterflies

The evolution of sexual secondary characteristics necessitates regulatory factors that confer sexual identity to differentiating tissues and cells. In Colias eurytheme butterflies, males exhibit two specialized wing scale types -- UV-iridescent (UVI) and lanceolate scales -- absent in females and likely integral to male courtship behavior. This study investigates the regulatory mechanisms and single-nucleus transcriptomics underlying these two sexually dimorphic cell types during wing development. We show that Doublesex (Dsx) expression is itself dimorphic and required to repress the UVI cell state in females, while unexpectedly, UVI activation in males is independent from Dsx. In the melanic marginal band, Dsx is required in each sex to enforce the presence of lanceolate scales in males, and their absence in females. Single-nucleus RNAseq reveals that UV-iridescent and lanceolate scale cell precursors each show distinctive gene expression profiles at 40% of pupal development, with marker genes that include regulators of transcription, cell signaling, cytoskeletal patterning, and chitin secretion. Both male-specific cell types share a low expression of the Bric-a-brac (Bab) transcription factor, a key repressor of the UVI fate. Bab ChIP-seq profiling suggests that Bab binds the cis-regulatory regions of gene markers associated to UVI fate, including potential effector genes involved in the regulation of cytoskeletal processes and chitin secretion, and loci showing signatures of recent selective sweeps in an UVI-polymorphic population. These findings open new avenues for exploring wing patterning and scale development, shedding light on the mechanisms driving the specification of sex-specific cell states and the differentiation of specialized cell ultrastructures.

developmental biology↗

bioRxiv2022

Paf1 complex subunit Rtf1 stimulates H2B ubiquitylation by interacting with the highly conserved N-terminal helix of Rad6

Histone modifications coupled to transcription elongation play important roles in regulating the accuracy and efficiency of gene expression. The mono-ubiquitylation of a conserved lysine in H2B (K123 in Saccharomyces cerevisiae; K120 in humans) occurs co-transcriptionally and is required for initiating a histone modification cascade on active genes. H2BK123 ubiquitylation (H2BK123ub) requires the RNA polymerase II (RNAPII)-associated Paf1 transcription elongation complex (Paf1C). Through its Histone Modification Domain (HMD), the Rtf1 subunit of Paf1C directly interacts with the ubiquitin conjugase Rad6, leading to the stimulation of H2BK123ub in vivo and in vitro. To understand the molecular mechanisms that target Rad6 to its histone substrate, we identified the site of interaction for the HMD on Rad6. Using in vitro crosslinking followed by mass spectrometry, we localized the primary contact surface for the HMD to the highly conserved N-terminal helix of Rad6. Using a combination of genetic and biochemical experiments, we identified separation-of-function mutations in S. cerevisiae RAD6 that greatly impair H2BK123 ubiquitylation but not other Rad6 functions. Finally, by employing RNA-sequencing as a sensitive approach for comparing mutant phenotypes, we show that mutating either side of the proposed Rad6-HMD interface yields strikingly similar transcriptome profiles that extensively overlap with those of a mutant that lacks the site of ubiquitylation in H2B. Our results fit a model in which a specific interface between a transcription elongation factor and a ubiquitin conjugase guides substrate selection toward a highly conserved chromatin target during active gene expression. Significance StatementTranscription by RNAPII is tightly coordinated with mechanisms that control chromatin structure. Disruption of this interplay leads to deleterious effects on gene expression and genome architecture. Proteins that associate with RNAPII during transcription elongation play an important role in coupling histone modifications to active transcription. Paf1C, a conserved member of the RNAPII active elongation complex, is required for the ubiquitylation of histone H2B, a modification with effects on nucleosome stability and the methylation and acetylation state of chromatin. Here, we provide new insights into how a conserved domain in Paf1C, which we previously showed to be necessary and sufficient for Paf1C-mediated stimulation of H2B ubiquitylation, interacts with the ubiquitin conjugase for H2B thereby guiding its specificity.

molecular biology↗