Pub Date : 2024-08-07DOI: 10.1101/2024.08.05.606603
CB Canales-Aguirre, S Ferrada-Fuentes, R Galleguillos
The Trachurus murphyi have been studied for population genetic structure for decades, identifying only one large population across the South Pacific Ocean. Although all these studies have extensively examined the spatial genetic pattern, there remains a gap in understanding the potential role of temporality. Our study aims to elucidate temporal and spatial genetic patterns in T. murphyi populations in the South Pacific Ocean, examining genetic composition across seasons, including feeding and spawning seasons, where the latter was not previously investigated. Using 10 microsatellite loci, our study confirms a consistent and stable population genetic pattern in T. murphyi across its geographic distribution, observed over multiple years and seasons. Furthermore, we identify potential genetic markers for monitoring variability in the species.
几十年来，人们一直在研究墨鱼的种群遗传结构，但只发现了一个横跨南太平洋的大型种群。尽管所有这些研究都广泛考察了空间遗传模式，但在了解时间性的潜在作用方面仍存在差距。我们的研究旨在阐明南太平洋 T. murphyi 种群的时间和空间遗传模式，考察不同季节的遗传组成，包括觅食和产卵季节，而后者以前没有调查过。通过使用 10 个微卫星位点，我们的研究证实了 T. murphyi 在其地理分布范围内具有一致且稳定的种群遗传模式，并可在多个年份和季节观察到。此外，我们还发现了监测该物种变异性的潜在遗传标记。
{"title":"Temporal and spatial population genetic variation in Chilean jack mackerel, Trachurus murphyi","authors":"CB Canales-Aguirre, S Ferrada-Fuentes, R Galleguillos","doi":"10.1101/2024.08.05.606603","DOIUrl":"https://doi.org/10.1101/2024.08.05.606603","url":null,"abstract":"The <em>Trachurus murphyi</em> have been studied for population genetic structure for decades, identifying only one large population across the South Pacific Ocean. Although all these studies have extensively examined the spatial genetic pattern, there remains a gap in understanding the potential role of temporality. Our study aims to elucidate temporal and spatial genetic patterns in <em>T. murphyi</em> populations in the South Pacific Ocean, examining genetic composition across seasons, including feeding and spawning seasons, where the latter was not previously investigated. Using 10 microsatellite loci, our study confirms a consistent and stable population genetic pattern in <em>T. murphyi</em> across its geographic distribution, observed over multiple years and seasons. Furthermore, we identify potential genetic markers for monitoring variability in the species.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"366 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-06DOI: 10.1101/2024.08.04.605925
Erta Zykaj, Chelsea Abboud, Paria Asadi, Simane Warsame, Brittany Greco, Marcos López-Sánchez, Drago Bratkovic, Aashiq Kachroo, Luis Alberto Pérez-Jurado, Michael Sacher
Variants in membrane trafficking proteins are known to cause rare disorders with severe symptoms. The highly conserved transport protein particle (TRAPP) complexes are key membrane trafficking regulators that are also involved in autophagy. Pathogenic genetic variants in specific TRAPP subunits are linked to neurological disorders, muscular dystrophies, and skeletal dysplasias. Characterizing these variants and their phenotypes is important for understanding general and specialized roles of TRAPP subunits as well as for patient diagnosis. Patient-derived cells are not always available, which poses a limitation for the study of these diseases. Therefore, other systems, like the yeast Saccharomyces cerevisiae, can be used to dissect the mechanisms at the intracellular level underlying these disorders. The development of CRISPR/Cas9 technology in yeast has enabled a scar-less editing method that creates an efficient humanized yeast model. In this study, core yeast subunits were humanized by replacing their human orthologs, and TRAPPC1, TRAPPC2, TRAPPC2L, TRAPPC6A, and TRAPPC6B were found to successfully replace their yeast counterparts. This system was used for studying the first reported individual with an autosomal recessive disorder caused by biallelic TRAPPC1 variants, a girl with a severe neurodevelopmental disorder and myopathy. We show that the maternal variant (TRAPPC1 p.(Val121Alafs*3)) is non-functional while the paternal variant (TRAPPC1 p.(His22_Lys24del)) is conditional-lethal and affects secretion and non-selective autophagy in yeast. This parallels defects seen in fibroblasts derived from this individual which also showed membrane trafficking defects and altered Golgi morphology, all of which were rescued in the human system by wild type TRAPPC1. This study suggests that humanized yeast can be an efficient means to study TRAPP subunit variants in the absence of human cells, and can assign significance to variants of unknown significance (VUS). This study lays the foundation for characterizing further TRAPP variants through this system, rapidly contributing to disease diagnosis.
{"title":"A humanized yeast model for studying TRAPP complex mutations; proof-of-concept using variants from an individual with a TRAPPC1-associated neurodevelopmental syndrome","authors":"Erta Zykaj, Chelsea Abboud, Paria Asadi, Simane Warsame, Brittany Greco, Marcos López-Sánchez, Drago Bratkovic, Aashiq Kachroo, Luis Alberto Pérez-Jurado, Michael Sacher","doi":"10.1101/2024.08.04.605925","DOIUrl":"https://doi.org/10.1101/2024.08.04.605925","url":null,"abstract":"Variants in membrane trafficking proteins are known to cause rare disorders with severe symptoms. The highly conserved transport protein particle (TRAPP) complexes are key membrane trafficking regulators that are also involved in autophagy. Pathogenic genetic variants in specific TRAPP subunits are linked to neurological disorders, muscular dystrophies, and skeletal dysplasias. Characterizing these variants and their phenotypes is important for understanding general and specialized roles of TRAPP subunits as well as for patient diagnosis. Patient-derived cells are not always available, which poses a limitation for the study of these diseases. Therefore, other systems, like the yeast <em>Saccharomyces cerevisiae</em>, can be used to dissect the mechanisms at the intracellular level underlying these disorders. The development of CRISPR/Cas9 technology in yeast has enabled a scar-less editing method that creates an efficient humanized yeast model. In this study, core yeast subunits were humanized by replacing their human orthologs, and TRAPPC1, TRAPPC2, TRAPPC2L, TRAPPC6A, and TRAPPC6B were found to successfully replace their yeast counterparts. This system was used for studying the first reported individual with an autosomal recessive disorder caused by biallelic <em>TRAPPC1</em> variants, a girl with a severe neurodevelopmental disorder and myopathy. We show that the maternal variant (TRAPPC1 p.(Val121Alafs*3)) is non-functional while the paternal variant (TRAPPC1 p.(His22_Lys24del)) is conditional-lethal and affects secretion and non-selective autophagy in yeast. This parallels defects seen in fibroblasts derived from this individual which also showed membrane trafficking defects and altered Golgi morphology, all of which were rescued in the human system by wild type <em>TRAPPC1</em>. This study suggests that humanized yeast can be an efficient means to study TRAPP subunit variants in the absence of human cells, and can assign significance to variants of unknown significance (VUS). This study lays the foundation for characterizing further TRAPP variants through this system, rapidly contributing to disease diagnosis.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-06DOI: 10.1101/2024.08.03.605142
Yuriko Harigaya, Nana Matoba, Brandon D. Le, Jordan M. Valone, Jason L. Stein, Michael I. Love, William Valdar
Genetic variation can modulate response to treatment (G×T) or environmental stimuli (G×E), both of which may be highly consequential in biomedicine. An effective approach to identifying G×T signals and gaining insight into molecular mechanisms is mapping quantitative trait loci (QTL) of molecular count phenotypes, such as gene expression and chromatin accessibility, under multiple treatment conditions, which is termed response molecular QTL mapping. Although standard approaches evaluate the interaction between genetics and treatment conditions, they do not distinguish between meaningful interpretations such as whether a genetic effect is only observed in the treated condition or whether a genetic effect is observed but accentuated in the treated condition. To address this gap, we have developed a downstream method for classifying response molecular QTLs into subclasses with meaningful genetic interpretations. Our method uses Bayesian model selection and assigns posterior probabilities to different types of G×T interactions for a given feature-SNP pair. We compare linear and nonlinear regression of log-scale counts, noting that the latter accounts for an expected biological relationship between the genotype and the molecular count phenotype. Through simulation and application to existing datasets of molecular response QTLs, we show that our method provides an intuitive and well-powered framework to report and interpret G×T interactions. We provide a software package, ClassifyGxT, which is available at https://github.com/yharigaya/classifygxt.
{"title":"Probabilistic classification of gene-by-treatment interactions on molecular count phenotypes","authors":"Yuriko Harigaya, Nana Matoba, Brandon D. Le, Jordan M. Valone, Jason L. Stein, Michael I. Love, William Valdar","doi":"10.1101/2024.08.03.605142","DOIUrl":"https://doi.org/10.1101/2024.08.03.605142","url":null,"abstract":"Genetic variation can modulate response to treatment (G×T) or environmental stimuli (G×E), both of which may be highly consequential in biomedicine. An effective approach to identifying G×T signals and gaining insight into molecular mechanisms is mapping quantitative trait loci (QTL) of molecular count phenotypes, such as gene expression and chromatin accessibility, under multiple treatment conditions, which is termed response molecular QTL mapping. Although standard approaches evaluate the interaction between genetics and treatment conditions, they do not distinguish between meaningful interpretations such as whether a genetic effect is only observed in the treated condition or whether a genetic effect is observed but accentuated in the treated condition. To address this gap, we have developed a downstream method for classifying response molecular QTLs into subclasses with meaningful genetic interpretations. Our method uses Bayesian model selection and assigns posterior probabilities to different types of G×T interactions for a given feature-SNP pair. We compare linear and nonlinear regression of log-scale counts, noting that the latter accounts for an expected biological relationship between the genotype and the molecular count phenotype. Through simulation and application to existing datasets of molecular response QTLs, we show that our method provides an intuitive and well-powered framework to report and interpret G×T interactions. We provide a software package, ClassifyGxT, which is available at https://github.com/yharigaya/classifygxt.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"108 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-06DOI: 10.1101/2024.08.05.606594
Sébastien Lageix, Miguel Hernandez Sanchez-Rebato, Maria E. Gallego, Jérémy Verbeke, Yannick Bidet, Sandrine Viala, Charles I. White
Sequence-specific endonucleases have been key to the study of the mechanisms and control of DNA double-strand break (DSB) repair and recombination and the availability of CRISPR-Cas nucleases over the last decade has driven rapid progress in understanding and application of targeted recombination in many organisms, including plants. We present here an analysis of recombination at targeted chromosomal 5’overhang DSB generated by the FnCas12a endonuclease in the plant, Arabidopsis thaliana. The much-studied Cas9 nuclease cleaves DNA to generate blunt-ended, double-strand breaks (DSB), but relatively less is known about the repair of other types of breaks, such as those with 5’-overhanging ends. Sequencing the repaired breaks clearly shows that the majority of repaired DSB carry small deletions and are thus repaired locally by End-Joining recombination, confirmed by Nanopore sequencing of larger amplicons. Paired DSB generate deletions at one or both cut-sites, as well as deletions and reinsertions of the deleted segment between the two cuts, visible as inversions. While differences are seen in the details, overall the deletion patterns are similar between repair at single-cut and double-cut events, notwithstanding the fact that only the former involve cohesive DNA overhangs. A strikingly different repair pattern is however observed at breaks flanked by direct repeats. This change in sequence context results in the presence of an alternative class of repair events, corresponding to highly efficient repair by Single-strand Annealing recombination.
序列特异性内切酶是研究 DNA 双链断裂（DSB）修复和重组机制与控制的关键，过去十年中 CRISPR-Cas 核酸酶的出现推动了对包括植物在内的许多生物体中靶向重组的理解和应用的快速进展。我们在本文中分析了拟南芥（Arabidopsis thaliana）中由 FnCas12a 内切酶产生的靶向染色体 5'overhang DSB 重组。人们对 Cas9 核酸内切酶切割 DNA 产生钝端双链断裂（DSB）的情况研究颇多，但对其他类型断裂（如 5'overhanging end）的修复情况了解较少。对修复的断裂进行测序清楚地表明，大多数修复的 DSB 都带有小的缺失，因此是通过末端连接重组（End-Joining recombination）进行局部修复的，较大的扩增子的 Nanopore 测序也证实了这一点。成对的 DSB 会在一个或两个切割位点产生缺失，以及在两个切割位点之间的缺失片段的缺失和再插入，表现为倒位。虽然在细节上存在差异，但总的来说，单切和双切事件的缺失修复模式是相似的，尽管只有前者涉及内聚 DNA 悬垂。然而，在断裂两侧有直接重复序列的情况下，修复模式却截然不同。序列上下文的这种变化导致了另一类修复事件的出现，即单链退火重组的高效修复。
{"title":"Context effects on repair of 5’-overhang DSB induced by Cas12a in Arabidopsis","authors":"Sébastien Lageix, Miguel Hernandez Sanchez-Rebato, Maria E. Gallego, Jérémy Verbeke, Yannick Bidet, Sandrine Viala, Charles I. White","doi":"10.1101/2024.08.05.606594","DOIUrl":"https://doi.org/10.1101/2024.08.05.606594","url":null,"abstract":"Sequence-specific endonucleases have been key to the study of the mechanisms and control of DNA double-strand break (DSB) repair and recombination and the availability of CRISPR-Cas nucleases over the last decade has driven rapid progress in understanding and application of targeted recombination in many organisms, including plants. We present here an analysis of recombination at targeted chromosomal 5’overhang DSB generated by the FnCas12a endonuclease in the plant, <em>Arabidopsis thaliana</em>. The much-studied Cas9 nuclease cleaves DNA to generate blunt-ended, double-strand breaks (DSB), but relatively less is known about the repair of other types of breaks, such as those with 5’-overhanging ends. Sequencing the repaired breaks clearly shows that the majority of repaired DSB carry small deletions and are thus repaired locally by End-Joining recombination, confirmed by Nanopore sequencing of larger amplicons. Paired DSB generate deletions at one or both cut-sites, as well as deletions and reinsertions of the deleted segment between the two cuts, visible as inversions. While differences are seen in the details, overall the deletion patterns are similar between repair at single-cut and double-cut events, notwithstanding the fact that only the former involve cohesive DNA overhangs. A strikingly different repair pattern is however observed at breaks flanked by direct repeats. This change in sequence context results in the presence of an alternative class of repair events, corresponding to highly efficient repair by Single-strand Annealing recombination.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"366 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-06DOI: 10.1101/2024.08.02.606402
Ariella Coler-Reilly, Zachary Pincus, Erica L. Scheller, Roberto Civitelli
Many studies have compared gene expression in young and old samples to gain insights on aging, the primary risk factor for most major chronic diseases. However, these studies only describe associations, failing to distinguish drivers of aging from compensatory geroprotective responses and incidental downstream effects. Here, we introduce a workflow to characterize the causal effects of differentially expressed genes on lifespan. First, we performed a meta-analysis of 25 gene expression datasets comprising samples of various tissues from healthy, untreated adult mammals (humans, dogs, and rodents) at two distinct ages. We ranked each gene according to the number of distinct datasets in which the gene was differentially expressed with age in a consistent direction. The top age-upregulated genes were TMEM176A, EFEMP1, CP, and HLA-A; the top age-downregulated genes were CA4, SIAH, SPARC, and UQCR10. Second, the effects of the top ranked genes on lifespan were measured by applying post-developmental RNA interference of the corresponding ortholog in the nematode C. elegans (two trials, with roughly 100 animals per genotype per trial). Out of 10 age-upregulated and 9 age-downregulated genes that were tested, two age-upregulated genes (csp-3/CASP1 and spch-2/RSRC1) and four age-downregulated genes (C42C1.8/DIRC2, ost-1/SPARC, fzy-1/CDC20, and cah-3/CA4) produced significant and reproducible lifespan extension. Notably, the data do not suggest that the direction of differential expression with age is predictive of the effect on lifespan. Our study provides novel insight into the relationship between differential gene expression and aging phenotypes, pilots an unbiased workflow that can be easily repeated and expanded, and pinpoints six genes with evolutionarily conserved, causal roles in the aging process for further study.
{"title":"Six drivers of aging identified among genes differentially expressed with age","authors":"Ariella Coler-Reilly, Zachary Pincus, Erica L. Scheller, Roberto Civitelli","doi":"10.1101/2024.08.02.606402","DOIUrl":"https://doi.org/10.1101/2024.08.02.606402","url":null,"abstract":"Many studies have compared gene expression in young and old samples to gain insights on aging, the primary risk factor for most major chronic diseases. However, these studies only describe associations, failing to distinguish drivers of aging from compensatory geroprotective responses and incidental downstream effects. Here, we introduce a workflow to characterize the causal effects of differentially expressed genes on lifespan. First, we performed a meta-analysis of 25 gene expression datasets comprising samples of various tissues from healthy, untreated adult mammals (humans, dogs, and rodents) at two distinct ages. We ranked each gene according to the number of distinct datasets in which the gene was differentially expressed with age in a consistent direction. The top age-upregulated genes were TMEM176A, EFEMP1, CP, and HLA-A; the top age-downregulated genes were CA4, SIAH, SPARC, and UQCR10. Second, the effects of the top ranked genes on lifespan were measured by applying post-developmental RNA interference of the corresponding ortholog in the nematode C. elegans (two trials, with roughly 100 animals per genotype per trial). Out of 10 age-upregulated and 9 age-downregulated genes that were tested, two age-upregulated genes (<em>csp-3</em>/CASP1 and <em>spch-2</em>/RSRC1) and four age-downregulated genes (<em>C42C1.8</em>/DIRC2, <em>ost-1</em>/SPARC, <em>fzy-1</em>/CDC20, and <em>cah-3</em>/CA4) produced significant and reproducible lifespan extension. Notably, the data do not suggest that the direction of differential expression with age is predictive of the effect on lifespan. Our study provides novel insight into the relationship between differential gene expression and aging phenotypes, pilots an unbiased workflow that can be easily repeated and expanded, and pinpoints six genes with evolutionarily conserved, causal roles in the aging process for further study.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-06DOI: 10.1101/2024.08.05.606572
Manuel Tardaguila, Dominique Von Schiller, Michela Colombo, Ilaria Gori, Eve L. Coomber, Thomas Vanderstichele, Paola Benaglio, Chiara Chiereghin, Sebastian Gerety, Dragana Vuckovic, Arianna Landini, Giuditta Clerici, Patrick Albers, Helen Ray-Jones, Katie L. Burnham, Alex Tokolyi, Elodie Persyn, Mikhail Spivakov, Vijay G. Sankaran, Klaudia Walter, Kousik Kundu, Nicola Pirastu, Michael Inouye, Dirk S. Paul, Emma E. Davenport, Pelin Sahlén, Stephen Watt, Nicole Soranzo
Two decades of Genome Wide Association Studies (GWAS) have yielded hundreds of thousands of robust genetic associations to human complex traits and diseases. Nevertheless, the dissection of the functional consequences of variants lags behind, especially for non-coding variants (RNVs). Here we have characterised a set of rare, non-coding variants with large effects on haematological traits by integrating (i) a massively parallel reporter assay with (ii) a CRISPR/Cas9 screen and (iii) in vivo gene expression and transcript relative abundance analysis of whole blood and immune cells. After extensive manual curation we identify 22 RNVs with robust mechanistic hypotheses and perform an in-depth characterization of one of them, demonstrating its impact on megakaryopoiesis through regulation of the CUX1 transcriptional cascade. With this work we advance the understanding of the translational value of GWAS findings for variants implicated in blood and immunity.
{"title":"Variant-to-function dissection of rare non-coding GWAS loci with high impact on blood traits","authors":"Manuel Tardaguila, Dominique Von Schiller, Michela Colombo, Ilaria Gori, Eve L. Coomber, Thomas Vanderstichele, Paola Benaglio, Chiara Chiereghin, Sebastian Gerety, Dragana Vuckovic, Arianna Landini, Giuditta Clerici, Patrick Albers, Helen Ray-Jones, Katie L. Burnham, Alex Tokolyi, Elodie Persyn, Mikhail Spivakov, Vijay G. Sankaran, Klaudia Walter, Kousik Kundu, Nicola Pirastu, Michael Inouye, Dirk S. Paul, Emma E. Davenport, Pelin Sahlén, Stephen Watt, Nicole Soranzo","doi":"10.1101/2024.08.05.606572","DOIUrl":"https://doi.org/10.1101/2024.08.05.606572","url":null,"abstract":"Two decades of Genome Wide Association Studies (GWAS) have yielded hundreds of thousands of robust genetic associations to human complex traits and diseases. Nevertheless, the dissection of the functional consequences of variants lags behind, especially for non-coding variants (RNVs). Here we have characterised a set of rare, non-coding variants with large effects on haematological traits by integrating (i) a massively parallel reporter assay with (ii) a CRISPR/Cas9 screen and (iii) <em>in vivo</em> gene expression and transcript relative abundance analysis of whole blood and immune cells. After extensive manual curation we identify 22 RNVs with robust mechanistic hypotheses and perform an in-depth characterization of one of them, demonstrating its impact on megakaryopoiesis through regulation of the <em>CUX1</em> transcriptional cascade. With this work we advance the understanding of the translational value of GWAS findings for variants implicated in blood and immunity.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"86 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-05DOI: 10.1101/2024.08.05.606565
Mark Samuel Voorhies, Bastian Joehnk, Jessie Uehling, Keith Walcott, Claire Dubin, Heather Mead, Christina Homer, John Galgiani, Bridget Barker, Rachel Brem, Anita Sil
Next generation sequencing has unlocked a wealth of genotype information for microbial populations, but phenotyping remains a bottleneck for exploiting this information, particularly for pathogens that are difficult to manipulate. Here, we establish a method for high-throughput phenotyping of mixed cultures, in which the pattern of naturally occurring single-nucleotide polymorphisms in each isolate is used as intrinsic barcodes which can be read out by sequencing. We demonstrate that our method can correctly deconvolute strain proportions in simulated mixed-strain pools. As an experimental test of our method, we perform whole genome sequencing of 66 natural isolates of the thermally dimorphic pathogenic fungus Coccidioides posadasii and infer the strain compositions for large mixed pools of these strains after competition at 37 deg C and room temperature. We validate the results of these selection experiments by recapitulating the temperature-specific enrichment results in smaller pools. Additionally, we demonstrate that strain fitness estimated by our method can be used as a quantitative trait for genome-wide association studies. We anticipate that our method will be broadly applicable to natural populations of microbes and allow high-throughput phenotyping to match the rate of genomic data acquisition.
{"title":"Inferring the composition of a mixed culture of natural microbial isolates by deep sequencing","authors":"Mark Samuel Voorhies, Bastian Joehnk, Jessie Uehling, Keith Walcott, Claire Dubin, Heather Mead, Christina Homer, John Galgiani, Bridget Barker, Rachel Brem, Anita Sil","doi":"10.1101/2024.08.05.606565","DOIUrl":"https://doi.org/10.1101/2024.08.05.606565","url":null,"abstract":"Next generation sequencing has unlocked a wealth of genotype information for microbial populations, but phenotyping remains a bottleneck for exploiting this information, particularly for pathogens that are difficult to manipulate. Here, we establish a method for high-throughput phenotyping of mixed cultures, in which the pattern of naturally occurring single-nucleotide polymorphisms in each isolate is used as intrinsic barcodes which can be read out by sequencing. We demonstrate that our method can correctly deconvolute strain proportions in simulated mixed-strain pools. As an experimental test of our method, we perform whole genome sequencing of 66 natural isolates of the thermally dimorphic pathogenic fungus Coccidioides posadasii and infer the strain compositions for large mixed pools of these strains after competition at 37 deg C and room temperature. We validate the results of these selection experiments by recapitulating the temperature-specific enrichment results in smaller pools. Additionally, we demonstrate that strain fitness estimated by our method can be used as a quantitative trait for genome-wide association studies. We anticipate that our method will be broadly applicable to natural populations of microbes and allow high-throughput phenotyping to match the rate of genomic data acquisition.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-05DOI: 10.1101/2024.08.02.606433
Alyssa Kearly, Prontip Saelee, Jonathan Bard, Satrajit Sinha, Anne Satterthwaite, Lee Ann Garrett-Sinha
The levels of transcription factor Ets1 are high in resting B and T cells, but are downregulated by signaling through antigen receptors and Toll-like receptors (TLRs). Loss of Ets1 in mice leads to excessive immune cell activation and development of an autoimmune syndrome and reduced Ets1 expression has been observed in human PBMCs in the context of autoimmune diseases. In B cells, Ets1 serves to prevent premature activation and differentiation to antibody-secreting cells. Given these important roles for Ets1 in the immune response, stringent control of Ets1 gene expression levels is required for homeostasis. However, the genetic regulatory elements that control expression of the Ets1 gene remain relatively unknown. Here we identify a topologically-associating domain (TAD) in the chromatin of B cells that includes the mouse Ets1 gene locus and describe an interaction hub that extends over 100 kb upstream and into the gene body. Additionally, we compile epigenetic datasets to find several putative regulatory elements within the interaction hub by identifying regions of high DNA accessibility and enrichment of active enhancer histone marks. Using reporter constructs, we determine that DNA sequences within this interaction hub are sufficient to direct reporter gene expression in lymphoid tissues of transgenic mice. Further analysis indicates that the reporter construct drives faithful expression of the reporter gene in mouse B cells, but variegated expression in T cells, suggesting the existence of T cell regulatory elements outside this region. To investigate how the downregulation of Ets1 transcription is associated with alterations in the epigenetic landscape of stimulated B cells, we performed ATAC-seq in resting and BCR-stimulated primary B cells and identified four regions within and upstream of the Ets1 locus that undergo changes in chromatin accessibility that correlate to Ets1 gene expression. Interestingly, functional analysis of several putative Ets1 regulatory elements using luciferase constructs suggested a high level of functional redundancy. Taken together our studies reveal a complex network of regulatory elements and transcription factors that coordinate the B cell-specific expression of Ets1
静息的 B 细胞和 T 细胞中转录因子 Ets1 的水平很高，但通过抗原受体和 Toll 样受体（TLRs）发出信号时，Ets1 的水平会被下调。小鼠体内 Ets1 的缺失会导致免疫细胞过度活化和自身免疫综合症的发生，在自身免疫性疾病的情况下，也观察到人类 PBMCs 中 Ets1 的表达减少。在 B 细胞中，Ets1 的作用是防止过早活化和分化为分泌抗体的细胞。鉴于 Ets1 在免疫反应中的这些重要作用，需要对 Ets1 基因表达水平进行严格控制，以保持体内平衡。然而，控制 Ets1 基因表达的遗传调控元件仍然相对未知。在这里，我们确定了 B 细胞染色质中包括小鼠 Ets1 基因座的拓扑关联域（TAD），并描述了一个延伸至基因体上游 100 kb 以上的相互作用中心。此外，我们还汇编了表观遗传学数据集，通过识别高DNA可及性区域和活性增强子组蛋白标记的富集，在相互作用中心找到了几个推定的调控元件。利用报告基因构建体，我们确定该相互作用中枢内的 DNA 序列足以引导报告基因在转基因小鼠淋巴组织中的表达。进一步的分析表明，报告基因构建体在小鼠 B 细胞中能驱动报告基因的忠实表达，但在 T 细胞中的表达却参差不齐，这表明在该区域之外还存在 T 细胞调控元件。为了研究 Ets1 转录的下调如何与受刺激 B 细胞表观遗传景观的改变相关联，我们在静息和 BCR 刺激的原代 B 细胞中进行了 ATAC-seq 分析，发现 Ets1 基因座内和上游有四个区域的染色质可及性发生了变化，这些变化与 Ets1 基因的表达相关。有趣的是，利用荧光素酶构建物对几个假定的 Ets1 调控元件进行的功能分析表明，这些元件具有高度的功能冗余性。总之，我们的研究揭示了一个由调控元件和转录因子组成的复杂网络，它协调了 Ets1 的 B 细胞特异性表达。
{"title":"Sequences within and upstream of the mouse Ets1 gene drive high level expression in B cells, but are not sufficient for consistent expression in T cells","authors":"Alyssa Kearly, Prontip Saelee, Jonathan Bard, Satrajit Sinha, Anne Satterthwaite, Lee Ann Garrett-Sinha","doi":"10.1101/2024.08.02.606433","DOIUrl":"https://doi.org/10.1101/2024.08.02.606433","url":null,"abstract":"The levels of transcription factor Ets1 are high in resting B and T cells, but are downregulated by signaling through antigen receptors and Toll-like receptors (TLRs). Loss of Ets1 in mice leads to excessive immune cell activation and development of an autoimmune syndrome and reduced Ets1 expression has been observed in human PBMCs in the context of autoimmune diseases. In B cells, Ets1 serves to prevent premature activation and differentiation to antibody-secreting cells. Given these important roles for Ets1 in the immune response, stringent control of Ets1 gene expression levels is required for homeostasis. However, the genetic regulatory elements that control expression of the Ets1 gene remain relatively unknown. Here we identify a topologically-associating domain (TAD) in the chromatin of B cells that includes the mouse Ets1 gene locus and describe an interaction hub that extends over 100 kb upstream and into the gene body. Additionally, we compile epigenetic datasets to find several putative regulatory elements within the interaction hub by identifying regions of high DNA accessibility and enrichment of active enhancer histone marks. Using reporter constructs, we determine that DNA sequences within this interaction hub are sufficient to direct reporter gene expression in lymphoid tissues of transgenic mice. Further analysis indicates that the reporter construct drives faithful expression of the reporter gene in mouse B cells, but variegated expression in T cells, suggesting the existence of T cell regulatory elements outside this region. To investigate how the downregulation of Ets1 transcription is associated with alterations in the epigenetic landscape of stimulated B cells, we performed ATAC-seq in resting and BCR-stimulated primary B cells and identified four regions within and upstream of the Ets1 locus that undergo changes in chromatin accessibility that correlate to Ets1 gene expression. Interestingly, functional analysis of several putative Ets1 regulatory elements using luciferase constructs suggested a high level of functional redundancy. Taken together our studies reveal a complex network of regulatory elements and transcription factors that coordinate the B cell-specific expression of Ets1","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-05DOI: 10.1101/2024.08.01.606170
Edoardo Bertolini, Mohith Manjunath, Weihao Ge, Matthew D. Murphy, Mirai Inaoka, Christina Fliege, Andrea L. Eveland, Alexander E. Lipka
Plant architecture is a major determinant of planting density, which enhances productivity potential for crops per unit area. Genomic prediction is well-positioned to expedite genetic gain of plant architecture traits since they are typically highly heritable. Additionally, the adaptation of genomic prediction models to query predictive abilities of markers tagging certain genomic regions could shed light on the genetic architecture of these traits. Here, we leveraged transcriptional networks from a prior study that contextually described developmental progression during tassel and leaf organogenesis in maize (Z. mays) to inform genomic prediction models for architecture traits. Since these developmental processes underlie tassel branching and leaf angle, two important agronomic architecture traits, we tested whether genes prioritized from these networks quantitatively contribute to the genetic architecture of these traits. We used genomic prediction models to evaluate the ability of markers in the vicinity of prioritized network genes to predict breeding values of tassel branching and leaf angle traits for two diversity panels in maize, and diversity panels from sorghum (S. bicolor) and rice (O. sativa). Predictive abilities of markers near these prioritized network genes were similar to those using whole-genome marker sets. Notably, markers near highly connected transcription factors from core network motifs in maize yielded predictive abilities that were significantly greater than expected by chance in not only maize but also closely related sorghum. We expect that these highly connected regulators are key drivers of architectural variation that are conserved across closely related cereal crop species.
{"title":"Genomic prediction of cereal crop architecture traits using models informed by gene regulatory circuitries from maize","authors":"Edoardo Bertolini, Mohith Manjunath, Weihao Ge, Matthew D. Murphy, Mirai Inaoka, Christina Fliege, Andrea L. Eveland, Alexander E. Lipka","doi":"10.1101/2024.08.01.606170","DOIUrl":"https://doi.org/10.1101/2024.08.01.606170","url":null,"abstract":"Plant architecture is a major determinant of planting density, which enhances productivity potential for crops per unit area. Genomic prediction is well-positioned to expedite genetic gain of plant architecture traits since they are typically highly heritable. Additionally, the adaptation of genomic prediction models to query predictive abilities of markers tagging certain genomic regions could shed light on the genetic architecture of these traits. Here, we leveraged transcriptional networks from a prior study that contextually described developmental progression during tassel and leaf organogenesis in maize (<em>Z. mays</em>) to inform genomic prediction models for architecture traits. Since these developmental processes underlie tassel branching and leaf angle, two important agronomic architecture traits, we tested whether genes prioritized from these networks quantitatively contribute to the genetic architecture of these traits. We used genomic prediction models to evaluate the ability of markers in the vicinity of prioritized network genes to predict breeding values of tassel branching and leaf angle traits for two diversity panels in maize, and diversity panels from sorghum (<em>S. bicolor</em>) and rice (<em>O. sativa</em>). Predictive abilities of markers near these prioritized network genes were similar to those using whole-genome marker sets. Notably, markers near highly connected transcription factors from core network motifs in maize yielded predictive abilities that were significantly greater than expected by chance in not only maize but also closely related sorghum. We expect that these highly connected regulators are key drivers of architectural variation that are conserved across closely related cereal crop species.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-05DOI: 10.1101/2024.08.01.605863
Gennaro Volpe, Sarah Maria Mazzucchiello, Noemi Rosati, Francesca Lucibelli, Marianna Varone, Dora Baccaro, Ilaria Mattei, Ilaria Di Lelio, Andrea Becchimanzi, Ennio Giordano, Marco Salvemini, Serena Aceto, Francesco Pennacchio, Giuseppe Saccone
Ceratitis capitata, known as Mediterranean fruit fly (Medfly), is a major dipteran pest significantly impacting fruit and vegetable farming. Currently, its control heavily relies mainly on chemical insecticides, which pose health risks and have effects on pollinators. A friendly and species-specific alternative strategy involves providing double-stranded RNA (dsRNA) through feeding to disrupt essential functions in pest insects, which is poorly explored in dipteran species. Previous reports in Orthoptera and Coleoptera species suggested that dsRNA degradation by two specific nucleases in the intestinal lumen is among the major obstacle to feeding-mediated RNAi in insects. In our study, we experimented with three-day adult feeding using a combination of dsRNA molecules that target the expression of the ATPase vital gene and two intestinal dsRNA nucleases. These dsRNA molecules were recently tested separately in two Tephritidae species, showing limited effectiveness [1,2]. In contrast, we observed 79% mortality over seven days, which was associated with a decrease in mRNA levels of the three targeted genes. As expected, we also observed a reduction in dsRNA degradation following RNAi against nucleases. This research illustrates the potential of utilizing molecules as pesticides to achieve mortality rates in Medfly adults by targeting crucial genes and intestinal nucleases. Furthermore, it underscores the importance of exploring RNAi-based approaches for pest management
{"title":"Simultaneous silencing of gut nucleases and a vital target gene by adult dsRNA feeding enhances RNAi efficiency and mortality in Ceratitis capitata adults","authors":"Gennaro Volpe, Sarah Maria Mazzucchiello, Noemi Rosati, Francesca Lucibelli, Marianna Varone, Dora Baccaro, Ilaria Mattei, Ilaria Di Lelio, Andrea Becchimanzi, Ennio Giordano, Marco Salvemini, Serena Aceto, Francesco Pennacchio, Giuseppe Saccone","doi":"10.1101/2024.08.01.605863","DOIUrl":"https://doi.org/10.1101/2024.08.01.605863","url":null,"abstract":"<em>Ceratitis capitata</em>, known as Mediterranean fruit fly (Medfly), is a major dipteran pest significantly impacting fruit and vegetable farming. Currently, its control heavily relies mainly on chemical insecticides, which pose health risks and have effects on pollinators. A friendly and species-specific alternative strategy involves providing double-stranded RNA (dsRNA) through feeding to disrupt essential functions in pest insects, which is poorly explored in dipteran species. Previous reports in Orthoptera and Coleoptera species suggested that dsRNA degradation by two specific nucleases in the intestinal lumen is among the major obstacle to feeding-mediated RNAi in insects. In our study, we experimented with three-day adult feeding using a combination of dsRNA molecules that target the expression of the <em>ATPase</em> vital gene and two intestinal dsRNA nucleases. These dsRNA molecules were recently tested separately in two Tephritidae species, showing limited effectiveness [1,2]. In contrast, we observed 79% mortality over seven days, which was associated with a decrease in mRNA levels of the three targeted genes. As expected, we also observed a reduction in dsRNA degradation following RNAi against nucleases. This research illustrates the potential of utilizing molecules as pesticides to achieve mortality rates in Medfly adults by targeting crucial genes and intestinal nucleases. Furthermore, it underscores the importance of exploring RNAi-based approaches for pest management","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"65 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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