Biology subjects

Glassford, W. J.

Publications and source records attributed to Glassford, W. J..

5 recordsLinked to original sources

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↗

bioRxiv2024

Predicting the DNA binding specificity of mutated transcription factors using family-level biophysically interpretable machine learning

Sequence-specific interactions of transcription factors (TFs) with genomic DNA underlie many cellular processes. High-throughput in vitro binding assays coupled with machine learning have made it possible to accurately define such molecular recognition in a biophysically interpretable way for hundreds of TFs across many structural families, providing new avenues for predicting how the sequence preference of a TF is impacted by disease-associated mutations in its DNA binding domain. We developed a method based on a reference-free tetrahedral representation of variation in base preference within a given structural family that can be used to accurately predict the effect of mutations in the protein sequence of the TF. Using the basic helix-loop-helix (bHLH) and homeodomain families as test cases, our results demonstrate the feasibility of accurately predicting the shifts ({Delta}{Delta}{Delta}G/RT) in binding free energy associated with TF mutants by leveraging high-quality DNA binding models for sets of homologous wild-type TFs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/577115v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@3a6674org.highwire.dtl.DTLVardef@1c4de4org.highwire.dtl.DTLVardef@3dcd6forg.highwire.dtl.DTLVardef@17a63c5_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

genomics↗

bioRxiv2022

Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors

In eukaryotes, members of large transcription factor families often exhibit similar DNA binding properties in vitro, yet initiate paralog-specific gene regulatory networks in vivo. The serially homologous first (T1) and third (T3) thoracic legs of Drosophila, which result from alternative gene regulatory networks specified by the Hox proteins Scr and Ubx, respectively, offer a unique opportunity to address this paradox in vivo. Genome-wide analyses using epitope-tagged alleles of both Hox loci in the T1 and T3 leg imaginal discs, which are the precursors to the adult appendages and ventral body regions, show that [~]8% of Hox binding is paralog-specific. Binding specificity is mediated by interactions with distinct cofactors in different domains: the known Hox cofactor Exd acts in the proximal domain and is necessary for Scr to bind many of its paralog-specific targets, while in the distal leg domain, we identified the homeodomain protein Distal-less (Dll) as a novel Hox cofactor that enhances Scr binding to a different subset of genomic loci. Reporter genes confirm the in vivo roles of Scr+Dll and suggest that [~]1/3 of paralog-specific Hox binding in enhancers is functional. Together, these findings provide a genome-wide view of how Hox paralogs, and perhaps paralogs of other transcription factor families, orchestrate alternative downstream gene networks and suggest the importance of multiple, context-specific cofactors.

molecular biology↗

bioRxiv2019

An atlas of transcription factors expressed in the Drosophila melanogaster pupal terminalia

During development, transcription factors and signaling molecules govern gene regulatory networks to direct the formation of unique morphologies. As changes in gene regulatory networks are often implicated in morphological evolution, mapping transcription factor landscapes is important, especially in tissues that undergo rapid evolutionary change. The terminalia (genital and anal structures) of Drosophila melanogaster and its close relatives exhibit dramatic changes in morphology between species. While previous studies have found network components important for patterning the larval genital disc, the networks governing adult structures during pupal development have remained uncharted. Here, we performed RNA-seq in whole Drosophila melanogaster terminalia followed by in situ hybridization for 100 highly expressed transcription factors during pupal development. We find that the terminalia is highly patterned during pupal stages and that specific transcription factors mark separate structures and substructures. Our results are housed online in a searchable database (flyterminalia.pitt.edu) where they can serve as a resource for the community. This work lays a foundation for future investigations into the gene regulatory networks governing the development and evolution of Drosophila terminalia.\n\nSummaryWe performed RNA-seq in whole Drosophila melanogaster terminalia (genitalia and analia) followed by in situ hybridization for 100 highly expressed transcription factors during pupal development. We find that the pupal terminalia is highly patterned with specific transcription factors marking separate structures and substructures. Our results are housed online in a searchable database (flyterminalia.pitt.edu) where they can serve as a resource for the community. This work lays a foundation for future investigations into the gene regulatory networks governing the development and evolution of Drosophila terminalia.

genetics↗

bioRxiv2017

Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control

Female Aedes aegypti mosquitoes infect hundreds of millions of people each year with dangerous viral pathogens including dengue, yellow fever, Zika, and chikungunya. Progress in understanding the biology of this insect, and developing tools to fight it, has been slowed by the lack of a high-quality genome assembly. Here we combine diverse genome technologies to produce AaegL5, a dramatically improved and annotated assembly, and demonstrate how it accelerates mosquito science and control. We anchored the physical and cytogenetic maps, resolved the size and composition of the elusive sex-determining \"M locus\", significantly increased the known members of the glutathione-S-transferase genes important for insecticide resistance, and doubled the number of chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites. Using high-resolution QTL and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. We predict that AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly arboviral vector.

genomics↗