Genetics最新文献

To understand the relative importance of cis and trans effects on regulation, we crossed multi-parent recombinant-inbred lines (RILs) to a common tester and measured allele-specific gene expression in the offspring. Testing the difference of allelic imbalance between two RIL × Tester crosses is a test of cis or trans, depending on the RIL alleles compared. The study design also enables to separation of two sources of trans variation, genetic and environmental, detected via interactions with cis effects. We demonstrate the effectiveness of 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 environment are detectable in 31% of loci and trans effects due to genetic background in 19%, with little overlap in sources of trans variation. The genes identified in this study are associated with genes previously reported to exhibit genetic variation in gene expression. Eleven genes 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 the cuticular protein Cpr67B, suggesting a functional role for standing variation in gene expression. This study provides a blueprint for 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.

First-line cancer treatment frequently fails due to initially rare therapeutic resistance. An important clinical question is then how to schedule subsequent treatments to maximize the probability of tumor eradication. Here, we provide a theoretical solution to this problem by using mathematical analysis and extensive stochastic simulations within the framework of evolutionary rescue theory to determine how best to exploit the vulnerability of small tumors to stochastic extinction. Whereas standard clinical practice is to wait for evidence of relapse, we confirm a recent hypothesis that the optimal time to switch to a second treatment is when the tumor is close to its minimum size before relapse, when it is likely undetectable. This optimum can lie slightly before or slightly after the nadir, depending on tumor parameters. Given that this exact time point may be difficult to determine in practice, we study windows of high extinction probability that lie around the optimal switching point, showing that switching after the relapse has begun is typically better than switching too early. We further reveal how treatment efficacy and tumor demographic and evolutionary parameters influence the predicted clinical outcome, and we determine how best to schedule drugs of unequal efficacy. Our work establishes a foundation for further experimental and clinical investigation of this evolutionarily-informed multi-strike treatment strategy.

Research is an energy- and resource-demanding activity. However, despite emerging sustainability initiatives, a paucity of data and uptake of green initiatives continue to hamper effective and accountable emissions mitigation. Worldwide, >250,000 doctoral students graduate annually across all academic disciplines. Empowering students to engage in carbon accounting can raise awareness of sustainability in research and provide a substantial and robust resource of carbon data alongside a powerful community-driven impetus for decarbonization. Here, we demonstrate how students and other researchers can consistently measure the carbon footprint of their work, using 1 PhD student's research in a Drosophila neuroscience lab as our case study. We present a life cycle assessment of the equivalent carbon dioxide emissions generated by the student's research activities. Moreover, we explain how students can create a "carbon appendix' to their research, as a common framework for disseminating carbon data and revealed strategies for improving research sustainability. We argue that the process of creating a carbon appendix can empower researchers to scrutinize sustainability practices, empower them to implement effective green initiatives, and identify data-driven solutions to meet and exceed funders' sustainability targets.

Posttranscriptional regulation is particularly prominent during the maternal-to-zygotic transition (MZT), a developmental phase during which a large proportion of maternally provided mRNAs is repressed and cleared from metazoan embryos. RNA-binding proteins (RBPs) are key components of the posttranscriptional regulatory machinery. We show that the ORB2 RBP, the Drosophila ortholog of the human cytoplasmic polyadenylation element binding protein (hCPEB) 2-4 protein subfamily, binds to hundreds of maternally provided, rare-codon-enriched mRNAs in early embryos and that ORB2 targets are translationally repressed and unstable during the MZT. We identify a U-rich motif enriched in ORB2 targets' 3'UTRs and show that this motif confers ORB2 binding and repression to a luciferase reporter mRNA in S2 tissue culture cells. When tethered to a luciferase reporter, ORB2 and hCPEB2 (but not ORB and hCPEB1) repress translation and the C-terminal Zinc-binding ("ZZ") domain of ORB2 is necessary and sufficient for repression. ORB2 interacts with a suite of posttranscriptional regulators in early embryos; a subset of these interactions is lost upon deletion of the ZZ domain, notably with the Cup repressive complex. ORB2 targets significantly overlap with those previously identified for the repressive RBP, Smaug (SMG). Analysis of the early embryo's translatome in the presence or absence of the endogenous ZZ domain shows that mRNAs bound by ORB2 but not by SMG move onto polysomes upon ZZ domain deletion, whereas cobound transcripts do not, consistent with coregulation of the latter set of transcripts by both RBPs. Our results assign a function to the ZZ domain and position ORB2 in the posttranscriptional network that regulates maternal transcripts during the Drosophila MZT.

Unsaturated fatty acids (UFAs) are critical components of membrane lipids, but their specific roles in germline development and reproductive health remain poorly defined. Here, we investigated the consequences of UFA depletion in the Caenorhabditis elegans germline using an auxin-inducible degron (AID) system to conditionally degrade FAT-7, the major Δ9 stearoyl-CoA desaturase, in a fat-5; fat-6 double mutant background. This strategy bypassed the lethality associated with complete loss of Δ9 desaturase activity, enabling analysis of UFA deficiency in adult animals. UFA depletion led to a dramatic reduction in brood size, elevated embryonic and larval lethality, and a severe loss of germline nuclei. We found that UFAs are essential for mitotic proliferation, DNA replication, and chromosome organization in the germline. Moreover, reduced UFA levels impaired meiotic progression, accompanied by loss of membrane integrity in the syncytial germline. Notably, UFA deficiency altered the spatial distribution and increased the signal intensity of nuclear pore complex (NPC) proteins, suggesting alterations to the nuclear envelope (NE). Together, our findings demonstrate that UFAs are indispensable for germline maintenance, affecting cell cycle progression, chromosome organization, and membrane architecture. These results underscore a fundamental link between acyl chain composition and reproductive success, highlighting the critical role of lipid homeostasis in the germline.

Apical extracellular matrices (aECMs) are associated with many epithelia and often form a protective layer against biotic and abiotic threats in the environment. Despite their importance, we lack a deep understanding of their structure and dynamics in development and disease. Caenorhabditis elegans molting offers a powerful entry point to understanding developmentally programmed aECM remodeling. Here, we show that the poorly characterized putative protease inhibitor gene mlt-11 is directly regulated by the NHR-23 transcription factor. We identify key cis-regulatory elements required for robust mlt-11 expression. An internal MLT-11::mNeonGreen translational fusion transiently localized to the aECM in the cuticle and embryo. MLT-11::mNeonGreen also lined openings to the exterior (vulva, rectum, and mouth). mlt-11 is necessary to pattern all layers of the adult cuticle, and reduction of MLT-11 levels disrupted the barrier function of the cuticle. Deletion of conserved Kunitz protease inhibitor domains or intervening sequences produced a range of defects including either left or right roller phenotypes and small separations of the cuticle along the length of the animal (microblisters). MLT-11 is processed into at least 2 fragments, and internal and C-terminal mNeonGreen knock-ins display distinct localization patterns. Predicted mlt-11 null mutations caused fully penetrant embryonic lethality and elongation defects. Together, this work suggests that MLT-11 localizes similarly to precuticle components, and conserved sequences play distinct roles in promoting proper assembly of the aECM.

Organisms rely on coordinated networks of DNA repair pathways to protect genomes against toxic double-strand breaks (DSBs), particularly in germ cells. All repair mechanisms must successfully negotiate the local chromatin environment in order to access DNA. For example, nucleosomes can be repositioned by the highly conserved nucleosome remodeling and deacetylase (NuRD) complex. In Caenorhabditis elegans, NuRD functions in the germline to repair DSBs-the loss of NuRD's ATPase subunit, LET-418/CHD4, prevents DSB resolution and therefore reduces fertility. In this study, we challenge germlines with exogenous DNA damage to better understand NuRD's role in repairing DSBs. We find that let-418 mutants are sensitive to cisplatin and hydroxyurea: exposure to either mutagen impedes DSB repair, generates aneuploid oocytes, and reduces fertility and embryonic survival. These defects resemble those seen when the Fanconi anemia (FA) DNA repair pathway is compromised, and we find that LET-418's activity is epistatic to that of the FA component FCD-2/FANCD2. We propose a model in which NuRD is recruited to the site of DNA lesions to remodel chromatin and allow access for FA pathway components. Together, these results implicate NuRD in the repair of both endogenous DSBs and exogenous DNA lesions to preserve genome integrity in developing germ cells.

Understanding the molecular basis of adaptation and the genetic architecture of complex traits are longstanding goals in biology. One problem impeding this understanding is the complexity of continental populations, with their complicated demographic histories, gene flow and secondary contact. In contrast, island populations represent simpler systems where uncovering the genetic basis of complex traits and tracing how traits built up is much more tractable. In Arabidopsis thaliana, the Cape Verde Islands populations represent a case of long-range colonization and adaptation to a divergent selective regime. Here, we describe the development and testing of a new multiparent intercross doubled haploid population of A. thaliana from the Cape Verde Islands. This population balances the representation of natural diversity and overcomes the shortcomings of existing resources, such as biparental recombinant inbred lines and genome-wide association populations. Specifically, it captures variation that segregates within the archipelago but is fixed on individual islands. We mapped the genetic basis of flowering time, rosette size, and photosystem II efficiency (ΦPSII) in this inter-island intercross population, representing traits that we hypothesized may be evolving under strong selection during the colonization of the archipelago. We identified functional loci underlying these traits, including FRI K232X and FLC R3X for flowering time, and IRT1 G130X for ΦPSII and rosette size. Our multiparent intercross population complements existing mapping resources and provides a robust framework for investigating the genetic basis of complex traits in A. thaliana. This work emphasizes the value of island systems and complementary approaches for advancing our understanding of genetic adaptation.

The circadian clock in Drosophila generates the 24 hour (h) rhythmicity in its behaviour. MicroRNAs are essential post-transcriptional regulators that can influence circadian rhythms by modulating clock mRNA expression or by aiding in the rhythmic oscillation of gene transcripts and their protein products. Previous studies identified around 27 miRNAs robustly expressed in Drosophila clock neurons. We conducted a genetic screen of 21 of these relatively underexplored miRNAs to investigate their effects on circadian clock properties. Each miRNA was downregulated in circadian clock neurons using specific sponge lines, and the impact on free running period and rhythm robustness was analyzed through locomotor activity-rest assessments. We observed that downregulation of two miRNAs shortened the free running period, while two miRNAs reduced rhythm robustness. Our findings reveal that miR-275 modulates locomotor activity-rest rhythm, circadian rhythmicity, and the transcript levels of the circadian neuropeptide PIGMENT DISPERSING FACTOR (PDF). Overexpression of Pdf in miR-275 overexpressed flies partially rescued the altered circadian rhythm parameters under 12h light: 12h dark cycles and constant darkness. Overall, this study identifies miR-275 as a critical regulator of circadian locomotor activity-rest rhythm.

The Genome Database for Vaccinium (GDV, https://www.vaccinium.org/) is a knowledgebase serving the global Vaccinium research community. GDV centralizes genetics, genomics, and breeding data for blueberry, cranberry, bilberry, and lingonberry. Launched in 2011, GDV transforms research data into an integrated resource through data curation, standardization, and value-added analyses that enable cross-study comparisons and knowledge synthesis. GDV houses diverse data types including germplasm records, genetic markers, linkage maps, QTL/GWAS results, traits, genome assemblies, gene annotations, and expression profiles. The database team perform comprehensive analyses including homology searches against protein databases, InterPro domain identification, and synteny analyses between Vaccinium genomes to identify orthologous relationships. These analyses facilitate knowledge transfer within and between species, enabling researchers to leverage findings across the Vaccinium genus. Users access data through intuitive search interfaces and specialized tools for genetic map visualization, genome browsing, metabolic pathway exploration, and sequence similarity searches. The integrated Breeding Information Management System (BIMS) enables breeders to manage private breeding programs as well as accessing public breeding data. Currently containing 46 genome assemblies, over 287,000 genetic markers, 4,328 QTL, and 3.3 million gene models, GDV continues expanding through collaborations with the VacCAP project and international research groups. The database evolves based on community needs and emerging data types, ensuring its continued relevance for advancing Vaccinium research and crop improvement efforts worldwide.