G3: Genes|Genomes|Genetics最新文献

RAD52 is a conserved member of the homologous recombination repair (HRR) apparatus from yeast to humans. Mutating conserved amino acids in the internal and external DNA binding domains of the human RAD52 protein (HsRAD52) has discrete effects in vitro. Previous studies have shown that HsRAD52 supports multiple mechanisms of HRR in budding yeast, suggesting the utility of this model system for exploring the correspondence between losses of HsRAD52 function in vitro and their impact in vivo. We report that disrupting the internal and external DNA binding domains of HsRAD52 produced distinct effects on the repair of genomic DNA double-strand breaks (DSB) by conservative and non-conservative HRR in budding yeast, suggesting that these domains contribute to separate mechanisms in vivo. The further elucidation of the effects of perturbations in the structure and biochemical function of HsRAD52 in living systems will provide new insight into its ability to support DSB repair, cancer susceptibility as well as new avenues for targeting HRR-deficient cancers.

The acorn weevil Curculio nanulus (Coleoptera: Curculionidae) is a seed predator that lays its eggs inside developing acorns and hickory nuts in the western United States. The female weevil uses her elongated rostrum to excavate a hole into the seed, creating a protected site for oviposition. Natural history traits among Curculio species-such as host specificity and variation in larval diapause-suggest a dynamic evolutionary relationship with their host plants. These traits are best studied through a comparative genomic framework, but such analyses cannot currently be undertaken due to the lack of whole-genome assemblies for Curculio species. To address this gap, we generated a whole-genome assembly for C. nanulus using PacBio HiFi sequencing. The resulting assembly is ∼1.5 Gbp in length, with high contiguity (contig N50 = 7.7 Mbp) and gene completeness (BUSCO score: 98.97%). To enable comparative analysis, we also assembled the genome of the pecan weevil, Curculio caryae, using publicly available PacBio HiFi reads. For both species, we annotated repetitive elements and protein-coding genes and compared these features with those of other weevil genomes. Our results reveal a marked expansion of repetitive elements within Curculio and its close relatives. These genomic resources provide a foundation for investigating seed predation, co-speciation, and host-parasite evolutionary dynamics in Curculio and related taxa, as well as their impacts on forest ecology.

Triple-negative breast cancer (TNBC) is the deadliest subtype of breast cancer (BC) with few targeted therapies. To identify novel genetic modifiers of TNBC, we created a murine model incorporating high levels of genetic and phenotypic diversity. C3(1)-T-antigen ("C3Tag") mice, which develop spontaneous basal-like TNBC tumors, were systematically crossed with a large set of sequenced BXD recombinant inbred strains to produce isogenic hybrids segregating for C3Tag. The severity of TNBC traits including tumor latency, multiplicity, and survival was highly variable and heritable. We mapped modifiers of TNBC and identified loci on chromosomes 16 and 10 associated with tumor multiplicity and latency, respectively. Candidate genes were prioritized including a lysosomal enzyme involved in cell proliferation, Gns; tumor suppressor Rassf3; and Rab-modifying Tbc1d30. In tumors from BC patients, higher GNS, RASSF3, and TBC1D30 expression associated with poor overall survival. In sum, we developed a clinically relevant, BXD-BC model which provides robust genetic heterogeneity enabling the identification of conserved modifiers and mediators of BC.

Ribosomal DNA (rDNA) encodes the precursor transcripts for ribosomal RNAs (rRNAs), which are processed into the structural and catalytic components of the ribosome, making them indispensable for protein synthesis and cell viability. Uniquely, the transcribed human rDNA locus is exceptionally GC-rich, a feature that promotes the formation of non-canonical DNA structures (NCS) such as R-loops, G-quadruplexes (G4s), and i-motifs (iMs). While previous studies have reported NCS in specific regions of human rDNA, there is no comprehensive map of their distribution across the entire human rDNA sequence. Here, we use validated computational tools to systematically identify predicted NCS sequences (PNCSS) across the human rDNA locus. Our analyses reveal that R-loop-, G4-, and iM-forming sequences are non-randomly distributed in the rDNA. These PNCSS are enriched in non-coding spacer regions, including 5' external transcriber spacer (5'ETS), internal transcriber spacers (ITS1 and ITS2), and the 3'ETS. PNCSS are also enriched in specific subdomains of the 28S coding region, while they are strikingly depleted from the 18S region. These motifs exhibit strong strand asymmetry, frequent co-localization, and evolutionarily conserved enrichment across vertebrate species. Notably, regions enriched for PNCSS are inversely correlated with RNA polymerase I (Pol I) occupancy, suggesting these structures might impede transcription and serve regulatory or quality control functions. Together, our findings define a coherent and conserved non-canonical structure architecture within the human rDNA locus. These PNCSS represent genomic hotspots for structural elements that regulate rDNA biology and represent targetable features for therapeutic intervention.

The molecular basis of mating behavior in the important disease vector mosquito, Aedes aegypti, remains poorly characterized. We investigated the functional role of a pickpocket gene, ppk315, in male mating behavior using both RNAi-mediated knockdown and CRISPR/Cas9 approaches. Behavioral assays revealed that RNAi-treated males (dsPPK315) made fewer mating attempts, were less responsive to female acoustic cues, and were less likely to achieve copulation, though their latency to initiate contact when attempts were made was comparable to controls. Males with a CRISPR/Cas9-induced disruption to ppk315 exhibited reduced success in inseminating multiple females, consistent with previous reports from RNAi knockdown males, ruling out off-target effects as the source of behavioral changes. In contrast to the results of behavioral assays with RNAi, ppk315 mutant males (ppk315-/-) attempted copulation as frequently as wild-type males (ppk315+/+) but were slower to contact females. Despite these impairments in one-on-one interactions, both dsPPK315 and ppk315-/- males displayed normal mating success under competitive swarm-like conditions, potentially due to the socially facilitated activation of mating behavior. Collectively, our findings support a role for ppk315 in the initiation of mating behaviors via sensory detection, with context-dependent consequences for reproductive success.

Ribosomal DNA (rDNA) occurs as tandem arrays of a repeat unit containing the genes encoding 18S, 5.8S, and 28S rRNA separated by spacers. These rRNAs form the catalytic core of ribosomes and thus play a crucial role in protein synthesis. Due to its repetitive nature, rDNA copy number varies within and between eukaryotic species through recombination, which also results in homogenization of repeat sequences within species (concerted evolution). However, the recombination rate within rDNA has not been extensively estimated. Despite concerted evolution and strong selection to maintain the sequence of rRNA genes, some transposons insert into specific sequences in the 28S gene. We used short-read whole-genome sequences to examine the dynamics of change in rDNA copy number and sequence variation in 90 samples from clonally propagated Daphnia obtusa mutation accumulation (MA) lines over ∼95 generations. We also tracked the number of Pokey elements, a DNA transposon that inserts into the 28S gene of species in the subgenus Daphnia. We observed an overall decline in rDNA copy number across MA lines between generations 5 and ∼87, although both increases and decreases were observed over short intervals. The diploid 28S copy number ranged from 144 to 1,274, with a mean of 425.2. Diploid Pokey number varied from 65 to 537 and was significantly positively correlated with 28S copy number. Moreover, the element persisted in all lines even after large reductions in 28S copy number. We found that estimating rates of rDNA copy number change over long intervals resulted in substantial underestimates, as shorter intervals revealed that large copy number changes could occur in as few as 5 generations. We identified 5 rDNA haplotypes based on 58 single nucleotide polymorphisms (SNPs) that were distributed across the 18S and 28S genes, and the 3 non-repetitive intergenic spacer regions. We also identified 6 Pokey haplotypes based on 113 SNPs. The number of these haplotypes was strongly correlated with the number of the 3 most common rDNA haplotypes. By tracking changes in haplotype frequency and copy number within 4 MA lines over short time intervals, we estimated the mean rDNA recombination rate to be 0.094 events/generation. These results reveal that rapid changes can occur in rDNA over short timescales and show that Pokey transposon dynamics are tightly linked to rDNA structure.

Trehalose is the major sugar in insect hemolymph and plays a diverse role. Its level is regulated by the dynamics of biosynthesis and distribution by sugar transporters. The metabolic balance between trehalose synthesis and uptake remains poorly understood, despite its critical role in homeostasis. Here, we examined the role of the putative gut-specific sugar transporter, HaST46, in regulating trehalose levels in Helicoverpa armigera, a model Lepidopteran pest. Analysis of publicly available transcriptomics, proteomics data, and qRT-PCR study suggests that HaST46 showed localization in the posterior midgut and its expression alters in response to dietary contents. The liquid chromatography-mass spectrometry (LC-MS) analysis of HaST46 overexpressing Sf9 cells indicated that trehalose transport is preferred over glucose. HaST46 expression was found to be modulated tissue-specific manner in response to dietary trehalose availability. Furthermore, trehalose synthesis genes were found to be downregulated in the case of a 50 mM trehalose diet. This suggests that a potential increase in exogenous trehalose uptake may attenuate its endogenous synthesis. HaST46 overexpression and silencing lead to altered trehalose levels in the insect, while also having impact on trehalose metabolizing enzymes. Overall, our findings reveal the role of gut predominant sugar transporter, HaST46, in metabolic fine-tuning between exogenous trehalose uptake and endogenous synthesis.

Transfer RNAs (tRNAs) ensure accurate decoding of the genetic code. However, mutations in tRNAs can lead to misincorporation of an amino acid that differs from the genetic message in a process known as mistranslation. As mistranslating tRNAs modify how the genetic message is decoded, they have potential as therapeutic tools for diseases caused by nonsense and missense mutations. Despite this, they also produce proteome-wide mismade proteins, which can disrupt proteostasis. To better understand the impact of mistranslating tRNA variants, we profile the proteome and phosphoproteome of yeast expressing three different mistranslating tRNAs. While the overall impacts were similar, the extent of growth defects and proteome changes varied with the substitution type. Although the global impacts were modest, mistranslation influenced key cellular processes, including proteostasis, cell cycle, and translation. These findings highlight the need to consider cellular consequences when developing mistranslating tRNAs for therapeutic applications.

The white-cheeked goby (Rhinogobius duospilus) is a small stream-dwelling fish endemic to southern China and Vietnam. With a sucker-like modified pelvic fin that helps it cling to substrate in fast-flowing water and vibrant breeding colors in males, R. duospilus is particularly appealing to aquarium enthusiasts. To investigate its distribution patterns, evolutionary history, and molecular adaptations to local environments, a high-quality genome assembly is critically needed. By employing PacBio HiFi sequencing combined with Hi-C-assisted assembly technology, we successfully obtained a chromosome-level genome assembly of R. duospilus. The final assembly yielded a genome size of 1,031.61 Mb with a scaffold N50 of 45.55 Mb. Approximately 991.84 Mb of genomic sequence was anchored onto 22 chromosome pairs. Benchmarking Universal Single-Copy Orthologs assessment indicated high genome completeness at 96.14%. Through gene prediction and functional annotation, we identified 24,418 protein-coding genes, with 23,660 (96.8%) successfully annotated. This work presents the first high-quality reference genome for R. duospilus, creating an essential genomic resource for investigating population differentiation and adaptive evolution through comparative genomics. Additionally, this dataset provides valuable support for taxonomy, evolution, and conservation genetics of genus Rhinogobius.

Poecilozonites bermudensis, the greater Bermuda land snail, is a critically endangered species and 1 of only 2 extant members in its genus. These snails are one of Bermuda's few endemic animal clades, and their rich fossil record was the basis for the punctuated equilibria model of speciation. Once thought extinct, recent conservation efforts have focused on the recovery of the species, yet no genomic information or other molecular sequences have been available to inform these initiatives. We present a high-quality, annotated genome for P. bermudensis generated using PacBio long reads and Hi-C long-range reads sequencing. The resulting assembly is approximately 1.36 Gb with a scaffold N50 of 44.8 Mb and 31 chromosome-length scaffolds. Nearly 43% of the genome was identified as repeat content. This assembly confirms that a whole genome duplication occurred near the base of Stylommatophora. The genome will serve as a resource for conservation efforts of the surviving Poecilozonites species and adds to the currently limited body of genomic data on gastropod evolution.