Biology subjects

Graze, R. M.

Publications and source records attributed to Graze, R. M..

4 recordsLinked to original sources

bioRxiv2026

A framework for identifying transcript orthologs: the evolution of sex bias in alternative transcript structure in Drosophila

BackgroundRecent advances in long read technologies provide an unprecedented opportunity to study transcript evolution. However, comparative evolutionary studies, even in Drosophila, are limited by inconsistent and incomplete annotation, and the lack of annotated transcript homology. ResultsIn this study of five species spanning 28 million years (D. melanogaster, D. simulans, D. yakuba, D. santomea and D. serrata), we infer transcript homology using reciprocal liftover, and orthology using network analyses, with data validation from long read RNA-seq of male and female head tissue. We build the first genus level annotation, with 15,996 genes and 56,370 transcripts. Expressed transcripts are conserved, 73% of transcript orthologs are detected in all species. Even the improved annotation underestimates the number of genes with alternative transcripts, with 75% of genes expressing multiple structurally diverse transcripts. In a replicated quantitative evaluation of [~]10,000 genes, both male and female-biased transcripts are expressed in 410 (D. melanogaster), 608 (D. simulans), and 493 (D. serrata) genes and in 118 orthologous genes in the D. melanogaster - D. simulans species pair, indicating greater potential for resolution of sexual conflict by alternative transcription than previously appreciated. We identified 605 transcript orthologs conserved for sex bias in the D. melanogaster-D. simulans species pair and of these, 22 male and 19 female-biased transcripts were conserved in sex bias with the outgroup D. serrata, including transcripts of genes involved in brain development, Sxl target Glutamine synthetase 2 and ciboulot. ConclusionsConserved alternative transcripts suggest that transcriptional diversity is a pervasive driver of the evolution of functional diversity.

genomics↗

bioRxiv2025

Multiparent Recombinant Inbred lines crossed to a tester provide novel insights into sources of cis and trans regulation of gene expression

We propose crossing multi-parent recombinant-inbred-lines (RILs) to a common tester and measuring allele specific gene expression in the offspring. Testing whether allelic imbalance between two RIL x Tester crosses is equal, is a test of cis or trans depending on the RIL alleles compared. The study design also enables to separate two sources of trans variation, genetic and environmental, detected via interactions with cis effects. Examining these components of regulatory variation, we demonstrate this approach in a long-read RNA-seq experiment in female abdominal tissue at two time points in Drosophila melanogaster. Among the 40% of all loci that show evidence of genetic variation in cis, trans effects due to the environment are detectable in 31% of loci and trans effects due to genetic background are detectable in 19% of loci with little overlap in sources of trans variation. The loci identified in this study are associated with loci previously reported to exhibit genetic variation in gene expression in a range of tissues and large population samples, suggesting that there is consistent variation for genetic regulation of gene expression. We show that eleven loci in a QTL for thermotolerance, previously shown to differ in expression based on temperature, have evidence for regulation of gene expression regardless of the environment, including Cpr67B, a cuticular protein suggesting a potential functional role for standing variation in gene expression. This study provides a blueprint for efficiently identifying regulatory variation in gene expression, as the tester design maximizes cis variation and enables the efficient assessment of all pairs of RIL alleles relative to the tester, a much smaller study compared to the pairwise direct assessment.

genetics↗

bioRxiv2024

Sex Dimorphism in Expression of Immune Response Genes in Drosophila

Sex dimorphism in immunity is commonly observed in a wide variety of taxa and is thought to arise from fundamental life history differences between females and males. In Drosophila melanogaster, infection with different pathogens typically results in different modes of immune sex dimorphism, with male-or female-bias, likely due to specific disease-causing mechanisms of pathogens and host-pathogen interactions. Studies showed that some pathways, such as IMD and Toll, can explain these sex-dimorphic immune responses in Drosophila. However, it is unclear if sex differences in the immune response observed in D. melanogaster are conserved, even in closely related species. One window into identifying conserved and evolving sex differences in the immune response is to examine the sex-differential expression of immunity-related genes. Here, we aim to understand whether two closely related species, D. melanogaster and D. simulans, show conserved sex dimorphism in innate immunity, focusing on associated changes in gene expression in response to infection with a gram-negative bacterium, Providencia rettgeri. Survival, bacterial load, and bacterial load upon death (BLUD) were investigated to assess overall sex differences. D. melanogaster females and males differed significantly in survival, whereas D. simulans did not. Enrichment analyses revealed that both sexes and species upregulate genes involved in similar immune-related biological processes, but downregulated groups differed. We identified conserved sex differential gene expression of genes in the bacterial infection response pathways IMD, Toll, Jak/STAT, their regulators, and other immune-related gene classes (e.g., BOMs), as well as sex and species differences. In D. melanogaster, the effector antimicrobial peptides (AMPs) regulated by IMD were more highly upregulated relative to D. simulans in both sexes. Moreover, D. melanogaster females uniquely initiated high levels of gene expression that were involved in negative feedback mechanisms that controlled the overstimulation of IMD. Genes in the Toll pathway were also sex-differentially expressed with a higher level of upregulation in D. melanogaster. Remarkably, comparing expression across species, we find that D. simulans likely employs both the conventional peptidoglycan recognition-driven PRR-SPE-Spz pathway and the microbial protease recognition-based Psh-dependent activation of Toll; in contrast, D. melanogaster appears to solely rely on the PRR-SPE-Spz pathway in this context. In summary, our findings indicate that sex differences are conserved in both species for the majority of upregulated genes, while downregulation patterns and specific gene subsets show notable differences between sexes or species.

genetics↗

bioRxiv2024

Regulation of sex differences in innate immunity by sex-determining gene transformer in Drosophila melanogaster

AbstractSex dimorphism is one of the key features of dioecious organisms, which shapes almost all the aspects of life history traits from early development to cessation of life. However, the specific regulatory differences between males and females that underlie sex dimorphism are underexplored for most quantitative traits, including immune sex dimorphism. Complex patterns of variation, for example, with respect to numbers and types of contributing alleles, dynamic changes in gene expression, and context dependency, have created challenges in understanding the mechanistic basis of sex differences in immunity. To investigate the regulatory basis of sex dimorphism in immunity, we focused on the sex determination hierarchy master switch, transformer (tra), in Drosophila melanogaster. Two different perturbations of sex determination were examined, pseudomales (tra-mutant) and pseudofemales (tra-overexpression). Changes in gene expression patterns in response to the infection of Providencia rettgeri, an extracellular gram-negative bacterium, were examined for each of these perturbations and for controls with wild-type sex determination phenotypes. To the best of our knowledge, this is the first study to report the immune response to bacterial infection in any insects with mutant or overexpressed tra genotypes. Survival and bacterial load were first characterized to assess the overall impact of tra on sex differences in immunity. To examine the regulatory role of the tra gene, sex differentially regulated genes were identified in comparisons of wound control to bacterial infected flies for males, females, and tra-mutant or tra-overexpression animals. The survival assay showed that in the absence of the female-specific isoform of tra (TraF), tra-mutant XX animals showed significantly lower survival than wild-type females, and their survival rate aligned with males. The overexpression of TraF in the XY animals resulted in a surprising outcome, much higher survival of these animals relative to both males and females. The DEG analysis of genes with a significant interaction between sex and infection status identified 235 and 417 genes regulated upstream and downstream of tra in the sex hierarchy pathway, respectively. Interestingly, the GO enrichment analysis found 49 bacterial infection response-related biological processes enriched among genes regulated downstream of tra, including the Toll signaling pathway, and no enrichment for immune response-related categories among genes regulated upstream of tra. Further analysis of the genes and regulators of the Toll signaling pathway identified a significant regulatory role of tra or its downstream targets in signal detection, transduction, cellular response, and regulators of the pathway. Moreover, several genes regulated downstream of tra can regulate IMD pathways via the transcription factor NF-kB-Relish and some of its regulators, such as Diap2/IAP2 and Charon. Overall, the findings highlighted a strong potential role of tra to establish immune sex dimorphism in Drosophila.

genomics↗