Germline-restricted chromosomes (GRCs) constitute a unique class of chromosomes confined to germ cells. Arising in multiple evolutionarily distant lineages, GRCs have been identified in three insect families (non-biting midges, gall midges, and fungus gnats), each within the order Diptera. Genomic characterisation in fungus gnats has revealed GRCs to be large, gene-rich chromosomes, which, together with their persistence over millennia, implies they play important biological roles within this clade. However, transcription from these chromosomes has yet to be demonstrated, leaving key questions about their function and activity unresolved. Here, we present the first direct analysis of GRC transcription in Diptera, combining immunofluorescence staining with bulk RNA-seq data in the fungus gnat Bradysia coprophila (Sciaridae). We find that transcription from GRCs is highly limited during key developmental stages. In larval and adult gonads, elongating polymerase II appears to be active at all chromosomes except the GRCs in most cells. Furthermore, using stringent filtering criteria, we identify only 10 confidently expressed GRC-linked genes, mostly of unknown function. In addition, we report the surprising presence of a ∼290 kb region of bacterial-derived sequence on GRC2, likely acquired through horizontal transfer from germline-associated endosymbionts. Overall, these findings identify GRCs in fungus gnats as unique chromosomes, largely transcriptionally quiescent during key stages of B. coprophila development, yet capable of maintaining both endogenous and potentially horizontally acquired genes over evolutionary timescales. This raises fundamental questions about the mechanisms that maintain gene content in these chromosomes and their contribution, if any, to germline biology.

Extrachromosomal DNA (ecDNA) contributes to cancer genome instability by enabling high-copy oncogene amplification and genetic intratumoral heterogeneity. Micronuclei (MNs) are common in chromosomally unstable cancers, yet their role in ecDNA-driven tumors remains unclear. Here we investigate how ecDNA damage, mitotic segregation and MN formation are linked. We find that ecDNAs are a major source of MNs following their damage, particularly under replication stress. Replication stress promotes mitotic ecDNA clustering, asymmetric inheritance, mis-segregation into MNs and reduced transcriptional output. Single-MN sequencing reveals that multiple distinct ecDNA species coalesce within individual MNs. Cells inheriting ecDNA[+] MNs display impaired proliferative capacity and are more likely to undergo cell death. In patients with MYCN-amplified neuroblastoma, higher frequencies of ecDNA[+] MNs at diagnosis are associated with improved overall survival. Together, these findings identify ecDNA mis-segregation as a mechanism that limits tumor fitness, highlighting mitotic ecDNA retention as a potential therapeutic vulnerability.

Pregnancy is a distinct physiological context in which the mother hosts and nurtures the development of a genetically distinct fetus. Healthy pregnancy outcomes rely on successful placental development, during which specialized placental cells with fetal genotype, known as trophoblasts, drive the establishment of the maternal-fetal interface, a balanced tissue ecosystem that supports fetal development while safeguarding maternal well-being. Advances in single-cell, single-nuclei and spatial genomics technologies, along with data science, are now providing an unprecedented view of trophoblast regulation, which drives their differentiation into diverse cell subtypes that dynamically transform the maternal niche. More specifically, these cells modulate the immune system and remodel the vasculature to facilitate communication with maternal cells, leading to the successful formation of the maternal-fetal interface. These advances, when combined with in vitro modelling, hold promise for inferring causality in mechanisms that govern genome regulation, cellular behaviour and ultimately pregnancy homeostasis and maladaptive responses.

Epistasis, the genetic interaction between loci, has long been recognized as a fundamental feature of the genetic architecture, but its importance remains controversial. This controversy stems partly from the apparent disconnect between abundant physiological epistasis observed in laboratory settings and the rarity of detectable epistatic interactions in genome-wide association studies (GWAS). Here, I introduce the concept of epistatic redundancy, whereby a focal locus interacts with multiple alternative loci rather than a single partner. Using population genetic simulations, I demonstrate that epistatic redundancy substantially amplifies the influence of epistasis compared to models assuming only pairwise interactions, particularly under U-shaped allele frequency distributions, which are characteristic of natural populations. This framework reconciles theoretical predictions with empirical observations and suggests that current epistasis detection approaches, which focus on pairwise interactions, systematically underestimate the contribution of epistasis. I discuss alternative approaches to detect epistatic redundancy in both association studies and evolving populations.

Neuronal circuits sustain stable function by self-regulating their gene expression and neurosecretion. Patterns for autocrine feedback by neuropeptides are widespread across nervous systems, but how they contribute to neuronal homeostasis is less well understood. Here, we identify an autocrine homeostatic mechanism in a C. elegans peptidergic hub neuron. FLP-1 neuropeptide release activates the inhibitory receptor DMSR-7 on the AVK hub neurons to self-regulate flp-1 transcription, dense-core vesicle accumulation, and peptide secretion. We show that a parallel PDF-1/PDFR-1 pathway drives flp-1 expression, establishing a "push-and-pull" peptidergic feedback on the AVK neurons. AVK's peptidergic output also depends on the number of FLP-1 peptides encoded in its precursor, revealing a dosage mechanism in behavioral regulation. Moreover, flp-1 expression coordinates transcript levels of additional neuropeptides in AVK. These findings uncover FLP-1 as a self-regulating homeostatic controller within a peptidergic hub neuron and fit a model where precursor-encoded redundancy supports stable yet adaptable circuit states.

The DNA damage response (DDR) pathway has emerged as the central signaling network that preserves genome stability by using sensors to monitor the genome for aberrant structures and establishing signaling centers that promote organismal homeostasis. This review revisits the formative years of DDR research, focusing on the genetic dissection of the pathway in Saccharomyces cerevisiae and its evolution into a broadly conserved eukaryotic signaling system. Early studies of ribonucleotide reductase regulation, replication stress-induced transcription, and cell cycle control identified key regulators, including MEC1, DDC2, TEL1, MRC1, RAD53, DUN1, and RAD9, providing the first evidence that DNA damage signaling is propagated through a protein kinase cascade. This cascade is initiated when RPA binds to ssDNA generated by replication blocks and double-strand DNA breaks, thereby activating the apical MEC1/ATR kinase. These discoveries integrate the contemporaneous cell cycle checkpoint literature into a more comprehensive framework in which the DDR coordinates replication fork stability, replication origin firing, nucleotide metabolism, DNA repair, genome maintenance, and cell cycle control to maintain genomic stability. Parallel studies in Schizosaccharomyces pombe, Xenopus, and mammalian systems revealed the remarkable evolutionary conservation of the pathway and linked DDR dysfunction to a wide spectrum of human diseases, including cancer. In retrospect, the emergence of the DDR field highlights the extraordinary power of classical genetics combined with molecular biology to uncover a complex signaling network that now occupies a central position in chromosome biology, cancer research, aging, immunity, and therapeutic responses.

The predictive potential of functional annotation requires that regulatory data be interpreted in the contexts of genes, expression, variants and traits. FAANGMine (https://faangmine.elsiklab.missouri.edu/) is a data warehouse that brings them into a single framework, facilitating the exploration of regulatory elements, variants, QTL, genes and gene annotations in farm animal species. It was designed to highlight reference functional annotation datasets generated by members of the Functional Annotation of Animal Genomes (FAANG) Consortium. FAANGMine was developed using the InterMine biological data warehousing system, enhanced to support the integration of tissue-specific functional annotation data, including chromatin states, chromatin accessibility, chromatin architecture, histone modifications and CTCF binding sites. A rich set of associated metadata supports flexible and focused queries. The functional annotation data are integrated with gene annotation data from a variety of sources as well as pre-computed RNA-seq-based gene expression levels. External data sources include RefSeq, Ensembl, KEGG, Reactome, OrthoDB, Online Mendelian Inheritance in Man, UniProt, Gene Ontology, AnimalQTLdb, InterPro and PubMed. Data retrieval with FAANGMine is achieved with web-based search tools or an application programming interface. In addition to the FAANGMine data-mining application, the FAANGMine website includes JBrowse genome browsers for visualization of regulatory elements in the context of genes, expression, QTL and single nucleotide variants.

Circadian rhythms, ∼24-hour biological cycles, enable organisms to anticipate rhythmic environmental cycles so they can assign proper day and night functions that align with those cycles. Circadian rhythms are defined by their ability to be reset by external cues, their capacity to continue to oscillate in the absence of those cues, and their capacity to maintain clock speed across a range of ambient temperatures, a property known as temperature compensation. In the Neurospora clock, the White Collar Complex (WCC) drives expression of FRQ which nucleates a complex including FRH and CK1a that phosphorylates and thereby represses WCC activity. Work to date has suggested that kinases may be involved in temperature compensation and that in Neurospora the primary target of these is FRQ. Here we investigate the genetic relationship between two clock kinases, Casein Kinase I (encoded by ck-1a) and Casein Kinase II (encoded by cka), in their regulation of temperature compensation using novel alleles, ck-1aD135G and Δcka. A qualitative model supported by biochemical analyses shows that Casein kinase I activity on FRQ decreases with increasing temperature and this decrease is countered by increasing activity of Casein Kinase II. Quantitative proteomics on FRQ across temperatures shows that the FRQ phosphorylation landscape is dependent on temperature and is altered in temperature compensation mutants. In this phosphorylation-driven model for temperature compensation, key temperature compensation-specific domains on FRQ are phosphorylated by Casein Kinase I and Casein Kinase II to regulate period length in response to temperature.

Oocytes grow through biosynthesis of cellular components as well as endocytosis to take up nutrients from the extracellular space. They also develop cortical granules that are exocytosed after fertilization to alter the extracellular environment. We have previously shown that defects in cortical granule formation and exocytosis cause an osmotically sensitive embryo phenotype and embryonic lethality. To identify regulators of cortical granule formation and exocytosis, we characterized a Caenorhabditis elegans emb-20(g27) mutant displaying similar phenotypes at a restrictive temperature (25 °C). The fluorescently labeled cortical granule marker, GFP::CAV-1, mainly localized to cortical granules and the plasma membrane in control oocytes at 15 °C and 25 °C and in emb-20(g27) oocytes at 15 °C. In contrast, GFP::CAV-1 largely accumulated in fine punctate structures in emb-20(g27) mutant oocytes at 25 °C. The emb-20(g27) mutants also exhibited impaired endocytic yolk uptake by oocytes. We revealed that the emb-20(g27) mutant harbors a missense mutation in the fdps-1 gene, which encodes a farnesyl diphosphate synthase in the mevalonate pathway, causing a Glu282-to-Lys substitution. Farnesyl diphosphate is an essential precursor for generating geranylgeranyl groups for the prenylation of RAB small GTPases. We found that the endoplasmic reticulum-to-Golgi transport regulator, RAB-1, and endocytic regulators, such as RAB-5, RAB-7, and RAB-11, lost their organelle localization and became diffusely distributed throughout the cytoplasm and nucleus in emb-20(g27) mutant oocytes at 25 °C, and their prenylation states were drastically affected. These results suggest that EMB-20/FDPS-1 is essential for maintaining appropriate RAB GTPase function to preserve active membrane trafficking in developing oocytes.