IF 3.3 3区生物学

Genetics Pub Date : 2025-06-27 DOI: 10.1093/genetics/iyaf124

Lucia Graziadio, Livia Scatolini, Elisabetta Bucciarelli, Grazia Daniela Raffa, Silvia Bonaccorsi, Maurizio Gatti

{"title":"Mutational analysis of the Drosophila CMG helicase reveals relationships among chromosome integrity and the maintenance of spindle and centrosome structure.","authors":"Lucia Graziadio, Livia Scatolini, Elisabetta Bucciarelli, Grazia Daniela Raffa, Silvia Bonaccorsi, Maurizio Gatti","doi":"10.1093/genetics/iyaf124","DOIUrl":"https://doi.org/10.1093/genetics/iyaf124","url":null,"abstract":"The CMG (Cdc45-MCM-GINS) complex is a conserved helicase that plays an essential DNA unwinding function at replication forks. Here we analyzed the mitotic phenotypes caused in Drosophila by knockdown of Cdc45, Mcm5 and the four GINS genes (Sld5, Psf1, Psf2 and Psf3). Silencing of these genes resulted in virtually identical mitotic phenotypes. Brain cells from mutant and RNAi larvae showed severe defects in chromosome condensation, chromosome breakage and frequent polyploid mitotic figures. In addition, mutant cells showed reduced Cid (Cenp-A) incorporation at centromeres and strong alterations in spindle and centrosome structures. Our cytological and genetic analyses suggest that replication-related DNA damage and Cid-dependent centromere/kinetochore defects trigger the spindle assembly checkpoint (SAC) that arrests the cells in a prometaphase-like stage. The arrested cells undergo mitotic slippage accompanied by Cyclin B degradation, and eventually return to G1 giving rise to polyploid cells. Our analyses further suggest that during the prolonged prometaphase arrest both the centrosomes and the spindles undergo severe structural degeneration, and that the spindle defects are not the consequence of the aberrant centrosome behavior. Most studies on mitotic slippage have been carried out in cells exposed to anti-microtubule agents and could not address the behavior of the spindle. Conversely, our results illuminate the complex consequences of replication stress and reveal what happens to the mitotic apparatus during the prolonged SAC-induced mitotic arrest. Because prolonged mitosis is a common event in human cancers, our results could provide useful information for studies on cancer etiology and therapy.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144512629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Alleles of Chaser, a dominant modifier of the Drosophila melanogaster foraging gene, are consistent with variegating alleles of the heterochromatic gene spookier. 黑腹果蝇觅食基因的显性修饰基因Chaser的等位基因与异色基因spookier的变异等位基因一致。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-26 DOI: 10.1093/genetics/iyaf123

Alistair B Coulthard, Richard Yuditskiy, Alexander R Molnar, Qaim Ali Ramazan, Marla B Sokolowski, Arthur J Hilliker

{"title":"Alleles of Chaser, a dominant modifier of the Drosophila melanogaster foraging gene, are consistent with variegating alleles of the heterochromatic gene spookier.","authors":"Alistair B Coulthard, Richard Yuditskiy, Alexander R Molnar, Qaim Ali Ramazan, Marla B Sokolowski, Arthur J Hilliker","doi":"10.1093/genetics/iyaf123","DOIUrl":"https://doi.org/10.1093/genetics/iyaf123","url":null,"abstract":"The relationship between genes and quantitative behavioral traits involves complex regulatory networks. Identifying genes that operate in these regulatory pathways can be challenging, especially when dealing with dominant genetic factors. Our work has focused on a naturally occurring behavioral polymorphism in larval foraging behavior in Drosophila melanogaster. This polymorphism in larval foraging behavior arises from variation in the foraging (for) gene with its rover and sitter naturally occurring variants. The dominant rover allele (forR) results in larvae which move longer distances while foraging compared to larvae with the recessive sitter (fors) alleles. In this article, we report the successful mapping of the Chaser (Csr) gene, a dominant modifier of larval foraging behavior which makes sitter larvae behave in a rover-like manner. We localized Csr by first mapping recessive phenotype tags closely linked to Csr. These phenotype tags mapped to the centromeric heterochromatin on the right arm of chromosome 3. We showed through a combination of deletion mapping, qRT-PCR and feeding of ecdysone hormone to larvae during development that the alleles of Csr are consistent with variegating alleles of the gene spookier (spok). With spok being an essential gene in the synthesis of the molting hormone ecdysone, we have established a link between ecdysone signaling and larval foraging behavior in D. melanogaster.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144508946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phospholipid biogenesis maintains neuronal integrity during aging and axon regeneration. 磷脂生物发生在衰老和轴突再生过程中维持神经元的完整性。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-25 DOI: 10.1093/genetics/iyaf122

Seungmee Park, Yishi Jin, Andrew D Chisholm

{"title":"Phospholipid biogenesis maintains neuronal integrity during aging and axon regeneration.","authors":"Seungmee Park, Yishi Jin, Andrew D Chisholm","doi":"10.1093/genetics/iyaf122","DOIUrl":"https://doi.org/10.1093/genetics/iyaf122","url":null,"abstract":"Neurons maintain their morphology over prolonged periods of adult life with limited regenerative capacity. Among the various factors that shape neuronal morphology, lipids function as membrane components, signaling molecules, and regulators of synaptic plasticity. Here, we tested genes involved in phospholipid biosynthesis and identified their roles in axon regrowth and maintenance. CEPT-2 and EPT-1 are enzymes catalyzing the final steps in the de novo phospholipid synthesis (Kennedy) pathway. Loss of function mutants of cept-2 or ept-1 show reduced axon regrowth and failure to maintain axon morphology. We demonstrate that CEPT-2 is required cell-autonomously to prevent age-related axonal morphology defects. We further investigated genetic interactions of cept-2 or ept-1 with dip-2, a conserved regulator of lipid metabolism that affects axon morphology maintenance and regrowth after injury. Loss of function in dip-2 led to suppression of axon regrowth defects observed in either cept-2 or ept-2 mutants, suggesting that DIP-2 acts to counterbalance phospholipid synthesis. Our findings reveal the genetic regulation of lipid metabolism as critical for axon maintenance following injury and during aging.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144486746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

How recombination and clonal evolution shape bacterial lineages and genomes. 重组和克隆进化如何塑造细菌谱系和基因组。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-24 DOI: 10.1093/genetics/iyaf115

Asher Preska Steinberg, Edo Kussell

{"title":"How recombination and clonal evolution shape bacterial lineages and genomes.","authors":"Asher Preska Steinberg, Edo Kussell","doi":"10.1093/genetics/iyaf115","DOIUrl":"https://doi.org/10.1093/genetics/iyaf115","url":null,"abstract":"Homologous recombination is a key process in bacterial genome evolution. By analyzing sequencing collections of 12 bacterial species encompassing >100,000 genomes, we determine how recombination and clonal evolution shape bacterial lineages and genome structures. Previous analyses proposed that for some bacterial species recombination is so dominant that almost no clonal genomic fraction remains. Further, it has been suggested that bacterial phylogenies are entirely structured by scale-free distributions of recombination rates, based on measurement of private SNP distributions that exhibit power-law tails. Using a coalescent model of populations that recombine with different gene pools, we find a substantial clonal signal in all global bacterial populations analyzed, and infer recombination rates that typically vary by less than an order of magnitude within species. Additionally, for a local population of Escherichia coli isolates that exhibit power-law private SNP distributions, we infer narrowly-distributed recombination rates and a substantial clonal signal, and show that their clonal genealogy exhibits a distribution of coalescence times spanning several orders of magnitude. Using simulations and theory, we demonstrate that power-law SNP distributions are not indicative of widely-varying recombination rates, and can be generated by a clonal genealogy recombining with an external pool at a constant rate. We use regression analysis to quantify the relative impact of recombination and clonal evolution on the diversity and lineage structure of local and global populations. Our findings have implications for how of bacterial phylogeny is interpreted, and lays key groundwork for understanding which evolutionary forces determine species diversity.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144486745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mentorship and acts of kindness. 指导和善意的行为。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-24 DOI: 10.1093/genetics/iyaf105

Brandon S Gaut

引用次数: 0

Revealing function-altering MECP2 mutations in individuals with autism spectrum disorder using yeast and Drosophila. 利用酵母和果蝇揭示自闭症谱系障碍个体功能改变的MECP2突变。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-23 DOI: 10.1093/genetics/iyaf121

Eric Chen, Jessica Schmitt, Graeme McIntosh, Barry P Young, Tianshun Lian, Jie Liu, Kexin K Chen, J Beatrice Liston, Lily MacDonald, Bill Wang, Sonia Medina Giro, Benjamin Boehme, Mriga Das, Seevasant Indran, Jesse T Chao, Sanja Rogic, Paul Pavlidis, Douglas W Allan, Christopher J R Loewen

{"title":"Revealing function-altering MECP2 mutations in individuals with autism spectrum disorder using yeast and Drosophila.","authors":"Eric Chen, Jessica Schmitt, Graeme McIntosh, Barry P Young, Tianshun Lian, Jie Liu, Kexin K Chen, J Beatrice Liston, Lily MacDonald, Bill Wang, Sonia Medina Giro, Benjamin Boehme, Mriga Das, Seevasant Indran, Jesse T Chao, Sanja Rogic, Paul Pavlidis, Douglas W Allan, Christopher J R Loewen","doi":"10.1093/genetics/iyaf121","DOIUrl":"10.1093/genetics/iyaf121","url":null,"abstract":"Pathogenic variants in MECP2 commonly lead to Rett syndrome, where MECP2's function as a DNA cytosine methylation reader is believed critical. MECP2 variants are also catalogued in individuals with autism spectrum disorder (ASD), including nine missense variants which had no known clinical significance at the start of this study. To assess these nine variants as risk alleles for ASD, we developed MECP2 variant functional assays using budding yeast and Drosophila. We calibrated these assays with known pathogenic and benign variants. Our data predict that four ASD variants are loss of function and five are functional. Protein destabilization offers insight into the altered function of some of these variants. Notably, yeast and Drosophila lack DNA methylation, yet all Rett pathogenic and ASD variants located in the methyl DNA binding domain that we analyzed proved to be loss of function, suggesting a clinically-relevant role for non-methyl DNA-binding by MECP2.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144369445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Combining ability of banana triploid hybrid progenitors and genomic prediction of cross performance for agro-morphological traits. 香蕉三倍体杂交祖先配合力及农业形态性状杂交性能的基因组预测。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-20 DOI: 10.1093/genetics/iyaf119

Lucile Toniutti, Simon Rio, Camille Madec, Sébastien Ricci, Chantal Guiougou, Franck Marius, Claude Mina, Jean-Marie Eric Delos, Frédéric Lambert, Jean-Claude Efile, Angélique D'Hont, Guillaume Martin, Jean-Yves Hoarau, Frédéric Salmon

{"title":"Combining ability of banana triploid hybrid progenitors and genomic prediction of cross performance for agro-morphological traits.","authors":"Lucile Toniutti, Simon Rio, Camille Madec, Sébastien Ricci, Chantal Guiougou, Franck Marius, Claude Mina, Jean-Marie Eric Delos, Frédéric Lambert, Jean-Claude Efile, Angélique D'Hont, Guillaume Martin, Jean-Yves Hoarau, Frédéric Salmon","doi":"10.1093/genetics/iyaf119","DOIUrl":"10.1093/genetics/iyaf119","url":null,"abstract":"Breeding disease-resistant cultivars that meet commercial criteria is essential to sustain banana production threatened by major diseases. Edible bananas are seedless triploid hybrids which represent end-breeding products. Hence, the crucial step in banana breeding is to improve and combine the parents. Currently, little information is available on parental combining abilities and on the inheritance of major traits to effectively guide banana breeding strategies. In this study, a breeding population of 2723 triploids individuals resulting from multiparental diploid-tetraploid crosses was characterized during three crop cycles for 23 traits relating to plant and fruit architecture and bunch yield components. The phenotypic variance was partitioned between non-genetic and genetic effects, the latter including the general combining ability of diploid and tetraploid parents, their specific combining ability and additional variance due to the within-cross genetic variability. Heritability was moderate to high depending on the trait and revealed the predominance of the tetraploid parent's contribution to hybrid performance for most traits. The use of parental genomic information enabled cross mean performance prediction through genomic relationship matrices of general and specific combining abilities, the latter being partitioned into dominance and across-population epistasis contributions. Predictive abilities often greater than 0.5 were obtained, particularly when the tetraploid parent was observed in other crosses and, for some traits, when neither parent was observed. Information on trait inheritance and genomic prediction of cross mean performance will help selecting and combining parents, facilitating the identification of promising hybrids.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144334210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Efficient epistasis inference via higher-order covariance matrix factorization. 基于高阶协方差矩阵分解的上位推理。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-20 DOI: 10.1093/genetics/iyaf118

Kai S Shimagaki, John P Barton

引用次数: 0

Functional Analysis of Human EED Variants Using Drosophila. 果蝇对人类EED变异的功能分析。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-20 DOI: 10.1093/genetics/iyaf120

Sharri S Cyrus, Sònia Medina Giró, Tianshun Lian, Douglas W Allan, William T Gibson

引用次数: 0

Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis. 反调控位点塑造拟南芥基因表达可塑性的自然变异。

IF 3.3 3区生物学

Genetics Pub Date : 2025-06-19 DOI: 10.1093/genetics/iyaf116

Mariele Lensink, Grey Monroe, Dan Kliebenstein

{"title":"Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis.","authors":"Mariele Lensink, Grey Monroe, Dan Kliebenstein","doi":"10.1093/genetics/iyaf116","DOIUrl":"https://doi.org/10.1093/genetics/iyaf116","url":null,"abstract":"Organisms regulate gene expression in response to environmental cues, a process known as plasticity, to adjust to changing environments. Research into natural variation and the evolution of plasticity frequently studies cis-regulatory elements with theory suggesting they are more important evolutionarily than trans-regulatory elements. Genome-wide association studies have supported this idea, observing a predominance of cis-loci affecting plasticity. However, studies in structured populations provide a contrasting image, raising questions about the genetic architecture of natural variation in plasticity. To circumvent potential statistical difficulties present in genome-wide association studies, we mapped loci underlying transcriptomic plasticity in response to salicylic acid using recombinant inbred lines generated from two random Arabidopsis thaliana accessions. We detected extensive transgressive segregation in the salicylic acid response, suggesting that plasticity to salicylate in Arabidopsis is polygenic. Most loci (>75%) underlying this variation act in trans, especially for loci influencing plasticity. Trans-acting loci were enriched in genome hotspots, with predominantly small effect sizes distributed across many genes. This could potentially explain their under-discovery in genome-wide association studies. This work reveals a potentially important role for trans-acting loci in plastic expression responses, with implications for understanding plant adaptation to different environments.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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