Pub Date : 2024-09-07DOI: 10.1101/2024.09.04.611234
Francesc Montardit-Tarda, Ana M Casas, William Thomas, Florian Schnaithmann, Rajiv Sharma, Salar Shaaf, Chiara Campoli, Joanne Russell, Luke Ramsay, Stefano Delbono, Marko Jääskeläinen, Maitry Paul, Fred Stoddard, Andrea Visioni, Andrew J Flavell, Klaus Pillen, Benjamin Kilian, A Graner, Laura Rossini, Robbie Waugh, Luigi Cattivelli, Alan H Schulman, Alessandro Tondelli, Ernesto Igartua
This study contributes new knowledge on quantitative trait loci (QTLs) and candidate genes for adaptive traits and yield in two-rowed spring barley. A meta-analysis of a network of field trials, varying in latitude and sowing date, with 151 cultivars across several European countries, increased QTL detection power compared to single-trial analyses. The traits analysed were heading date (HD), plant height (PH), thousand-grain weight (TGW), and grain yield (GY). Breaking down the analysis by the main genotype-by-environment trends revealed QTLs and candidate genes specific to conditions like sowing date and latitude. A historical look on the evolution of QTL frequencies revealed that early selection focused on PH and TGW, likely due to their high heritability. GY selection occurred later, facilitated by reduced variance in other traits. The study observed that favourable alleles for plant height were often fixed before those for grain yield and TGW. Some regions showed linkage in repulsion, suggesting targets for future breeding. Several candidate genes were identified, including known genes and new candidates based on orthology with rice. Remarkably, the deficiens allele of gene Vrs1, appears associated to higher GY. These findings provide valuable insights for barley breeders aiming to improve yield, and other agronomic traits.
{"title":"New loci and candidate genes in spring two-rowed barley detected through meta-analysis of a field trial European network","authors":"Francesc Montardit-Tarda, Ana M Casas, William Thomas, Florian Schnaithmann, Rajiv Sharma, Salar Shaaf, Chiara Campoli, Joanne Russell, Luke Ramsay, Stefano Delbono, Marko Jääskeläinen, Maitry Paul, Fred Stoddard, Andrea Visioni, Andrew J Flavell, Klaus Pillen, Benjamin Kilian, A Graner, Laura Rossini, Robbie Waugh, Luigi Cattivelli, Alan H Schulman, Alessandro Tondelli, Ernesto Igartua","doi":"10.1101/2024.09.04.611234","DOIUrl":"https://doi.org/10.1101/2024.09.04.611234","url":null,"abstract":"This study contributes new knowledge on quantitative trait loci (QTLs) and candidate genes for adaptive traits and yield in two-rowed spring barley. A meta-analysis of a network of field trials, varying in latitude and sowing date, with 151 cultivars across several European countries, increased QTL detection power compared to single-trial analyses. The traits analysed were heading date (HD), plant height (PH), thousand-grain weight (TGW), and grain yield (GY). Breaking down the analysis by the main genotype-by-environment trends revealed QTLs and candidate genes specific to conditions like sowing date and latitude. A historical look on the evolution of QTL frequencies revealed that early selection focused on PH and TGW, likely due to their high heritability. GY selection occurred later, facilitated by reduced variance in other traits. The study observed that favourable alleles for plant height were often fixed before those for grain yield and TGW. Some regions showed linkage in repulsion, suggesting targets for future breeding. Several candidate genes were identified, including known genes and new candidates based on orthology with rice. Remarkably, the <em>deficiens</em> allele of gene <em>Vrs1</em>, appears associated to higher GY. These findings provide valuable insights for barley breeders aiming to improve yield, and other agronomic traits.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179753","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 : 2024-09-07DOI: 10.1101/2024.09.07.611789
Emil Karpinski, Nikil Badey, Esther Mintzer, Asaf Ashkenazy-Titelman, George M Church
TP53 functions as a central regulator in response to DNA damage and other cell stressors by inducing the expression of many protective pathways such as cell cycle arrest and apoptosis. Consequently, this gene is often found disrupted in human cancers. Elephants are a particularly interesting species for the study of cancer, by virtue of their large number of cell divisions and long lives yet low incidence of cancer. Elephants also possess multiple retrogene copies of TP53, which have previously been shown to induce strong cellular responses to DNA damage. However, most previous studies have largely focused only on African elephant TP53 retrogenes and often in non-native backgrounds. Here we generated CRISPR-Cas9 knockouts of TP53, all 29 TP53 retrogenes, or both in combination in Asian elephant fibroblasts. We find that while there is considerable overlap in the DNA damage responses of the TP53 and retrogene knockouts, there are also many unique pathways enriched in both. In particular, the retrogene knockouts exhibit strong enrichment of many extracellular pathways suggesting they may play a large role in the tumor microenvironment and mitigating metastatic growth. We also find that only a small fraction of these 29 retrogenes appear to be expressed across a variety of tissues and identify three loci that are likely driving this response. This work shows for the first time the transcriptomic effect of these retrogenes within their native background and establishes a foundation for future research into the relative contributions of these genes.
TP53 通过诱导细胞周期停滞和细胞凋亡等多种保护性途径的表达，在应对 DNA 损伤和其他细胞应激源时发挥核心调节作用。因此，在人类癌症中，该基因经常被破坏。大象细胞分裂次数多，寿命长，但癌症发病率低，因此是研究癌症的一个特别有趣的物种。大象还拥有多个 TP53 的逆转录基因拷贝，以前的研究表明，TP53 能诱导细胞对 DNA 损伤做出强烈反应。然而，以前的研究大多只关注非洲象的 TP53 逆基因，而且往往是在非本地背景下进行的。在这里，我们在亚洲象成纤维细胞中产生了TP53的CRISPR-Cas9基因敲除、全部29个TP53逆源基因敲除或两者结合的基因敲除。我们发现，虽然TP53基因敲除和逆转录基因敲除的DNA损伤反应有相当多的重叠，但两者也有许多独特的途径。特别是，逆转录基因敲除子在许多细胞外通路中表现出很强的富集性，这表明它们可能在肿瘤微环境和减轻转移性生长中发挥了很大作用。我们还发现，这 29 个逆转录基因中只有一小部分似乎在各种组织中表达，并确定了可能驱动这种反应的三个位点。这项工作首次显示了这些逆源基因在其原生背景下的转录组效应，并为今后研究这些基因的相对贡献奠定了基础。
{"title":"Engineering Asian elephant TP53: TP53 retrogene knockouts activate common and unique cancer-relevant pathways","authors":"Emil Karpinski, Nikil Badey, Esther Mintzer, Asaf Ashkenazy-Titelman, George M Church","doi":"10.1101/2024.09.07.611789","DOIUrl":"https://doi.org/10.1101/2024.09.07.611789","url":null,"abstract":"TP53 functions as a central regulator in response to DNA damage and other cell stressors by inducing the expression of many protective pathways such as cell cycle arrest and apoptosis. Consequently, this gene is often found disrupted in human cancers. Elephants are a particularly interesting species for the study of cancer, by virtue of their large number of cell divisions and long lives yet low incidence of cancer. Elephants also possess multiple retrogene copies of TP53, which have previously been shown to induce strong cellular responses to DNA damage. However, most previous studies have largely focused only on African elephant TP53 retrogenes and often in non-native backgrounds. Here we generated CRISPR-Cas9 knockouts of TP53, all 29 TP53 retrogenes, or both in combination in Asian elephant fibroblasts. We find that while there is considerable overlap in the DNA damage responses of the TP53 and retrogene knockouts, there are also many unique pathways enriched in both. In particular, the retrogene knockouts exhibit strong enrichment of many extracellular pathways suggesting they may play a large role in the tumor microenvironment and mitigating metastatic growth. We also find that only a small fraction of these 29 retrogenes appear to be expressed across a variety of tissues and identify three loci that are likely driving this response. This work shows for the first time the transcriptomic effect of these retrogenes within their native background and establishes a foundation for future research into the relative contributions of these genes.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179743","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 : 2024-09-07DOI: 10.1101/2024.09.03.611097
Alex J. Shamoun, Gisienne Reis, Malaica Ashley, Anatalia Labilloy, Leonardo F. Ferreira
Mucopolysaccharidosis Type II is a hereditary lysosomal storage disease characterized by deficiency in the enzyme iduronate 2-sulfatase (IDS). IDS is critical in the breakdown of sulfated glycosaminoglycans and its deficiency leads to an accumulation of these compounds across various tissue types resulting in multisystemic dysfunction. Intravenous administration of recombinant IDS (idursulfase) substantially improves patients’ quality and length of life. However, recombinant IDS delivered intravenously is sequestered in the liver and respiratory failure remains as the leading cause of death for patients independent of idursulfase treatment, which suggests insufficient delivery to the lungs. This study aimed to assess a novel method of idursulfase administration using a nebulizer in combination with intravenous treatment and determine if this combination may improve lung delivery of idursulfase and overall pathology. Whole body IDS knockout mice underwent twelve weeks of intravenous, combination treatment, or vehicle injection and we harvested liver and lungs seven days after the last treatment for assessment of IDS activity, histological markers, and global proteomics for comparison with wild-type mice. Combination treatment increased IDS enzyme activity in the liver but not lungs Proteomics data demonstrated attenuation of key features of the disease in liver (metabolic pathways) and lungs (glycosaminoglycan pathways) with both treatments. Overall, adding nebulized administration of IDS did not lead to sustained increase in enzyme activity in the lungs but caused persistent modifications in glycosaminoglycan degradation pathway suggesting additional benefits to intravenous administration alone.
{"title":"Nebulized and intravenous enzyme replacement therapy in mice with mucopolysaccharidosis type II","authors":"Alex J. Shamoun, Gisienne Reis, Malaica Ashley, Anatalia Labilloy, Leonardo F. Ferreira","doi":"10.1101/2024.09.03.611097","DOIUrl":"https://doi.org/10.1101/2024.09.03.611097","url":null,"abstract":"Mucopolysaccharidosis Type II is a hereditary lysosomal storage disease characterized by deficiency in the enzyme iduronate 2-sulfatase (IDS). IDS is critical in the breakdown of sulfated glycosaminoglycans and its deficiency leads to an accumulation of these compounds across various tissue types resulting in multisystemic dysfunction. Intravenous administration of recombinant IDS (idursulfase) substantially improves patients’ quality and length of life. However, recombinant IDS delivered intravenously is sequestered in the liver and respiratory failure remains as the leading cause of death for patients independent of idursulfase treatment, which suggests insufficient delivery to the lungs. This study aimed to assess a novel method of idursulfase administration using a nebulizer in combination with intravenous treatment and determine if this combination may improve lung delivery of idursulfase and overall pathology. Whole body IDS knockout mice underwent twelve weeks of intravenous, combination treatment, or vehicle injection and we harvested liver and lungs seven days after the last treatment for assessment of IDS activity, histological markers, and global proteomics for comparison with wild-type mice. Combination treatment increased IDS enzyme activity in the liver but not lungs Proteomics data demonstrated attenuation of key features of the disease in liver (metabolic pathways) and lungs (glycosaminoglycan pathways) with both treatments. Overall, adding nebulized administration of IDS did not lead to sustained increase in enzyme activity in the lungs but caused persistent modifications in glycosaminoglycan degradation pathway suggesting additional benefits to intravenous administration alone.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179739","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 : 2024-09-07DOI: 10.1101/2024.09.03.611011
Katherine M Widmer, Faith Rahic-Seggerman, Ahlea Forster, Amanda Ahrens-Kress, Mary Sauer, Shankumar Mooyottu, Akhil Vinithakumari, Aaron Dunkerson-Kurzhumov, Brett Sponseller, Matti Kiupel, Stephan Schmitz-Esser, Christopher K Tuggle
Severe combined immunodeficient (SCID) individuals lack functional T and B lymphocytes, leading to a deficient adaptive immune system. SCID pigs are a unique large animal biomedical model as they possess many similarities to humans, allowing for the collection of translatable data in regenerative medicine, cancer, and other biomedical research topics. While many studies suggest early gut microbiota development is necessary for developing the intestinal barrier and immune system, these animals are often cesarian section derived, leaving them uncolonized for normal intestinal microflora. The hypothesis was that an increase in complexity of microbiota inoculum will allow for more stability in the composition of the gut microbiota of SCID piglets. This was tested across multiple litters of SCID piglets with three different defined microbiota consortium (2-strain, 6-strain, 7-strain). All piglets received their designated defined microbiota by oral gavage immediately after birth and again 24 hours later. There was no effect of SCID genotype on the composition of the gut microbiota, but there was a significant effect due to piglet age. Additionally, all three defined microbiota consortia were deemed safe to use in SCID piglets, and the 7-strain microbiota was the most stable over time. Based on these results, the 7-strain defined microbiota will be added to the SCID pig husbandry protocol, allowing for a more reproducible model.
严重联合免疫缺陷（SCID）个体缺乏功能性 T 淋巴细胞和 B 淋巴细胞，导致适应性免疫系统缺陷。SCID 猪是一种独特的大型动物生物医学模型，因为它们与人类有许多相似之处，可以收集再生医学、癌症和其他生物医学研究课题的可转化数据。许多研究表明，早期肠道微生物群的发育对肠道屏障和免疫系统的发育十分必要，但这些动物通常是剖腹产，正常的肠道微生物菌群尚未覆盖。我们的假设是，增加微生物群接种物的复杂性将使 SCID 仔猪肠道微生物群的组成更加稳定。我们在多窝 SCID 仔猪中使用三种不同的定义微生物群（2-菌株、6-菌株、7-菌株）进行了测试。所有仔猪在出生后立即口服指定的微生物群，24 小时后再次口服。SCID 基因型对肠道微生物群的组成没有影响，但仔猪年龄有显著影响。此外，在 SCID 仔猪中使用所有三种确定的微生物群都被认为是安全的，而 7 菌株微生物群随着时间的推移最为稳定。基于这些结果，7 种菌株定义的微生物群将被添加到 SCID 仔猪饲养方案中，从而建立一个可重复性更强的模型。
{"title":"Effect of Genotype and Age on a Defined Microbiota in Gnotobiotic SCID Piglets","authors":"Katherine M Widmer, Faith Rahic-Seggerman, Ahlea Forster, Amanda Ahrens-Kress, Mary Sauer, Shankumar Mooyottu, Akhil Vinithakumari, Aaron Dunkerson-Kurzhumov, Brett Sponseller, Matti Kiupel, Stephan Schmitz-Esser, Christopher K Tuggle","doi":"10.1101/2024.09.03.611011","DOIUrl":"https://doi.org/10.1101/2024.09.03.611011","url":null,"abstract":"Severe combined immunodeficient (SCID) individuals lack functional T and B lymphocytes, leading to a deficient adaptive immune system. SCID pigs are a unique large animal biomedical model as they possess many similarities to humans, allowing for the collection of translatable data in regenerative medicine, cancer, and other biomedical research topics. While many studies suggest early gut microbiota development is necessary for developing the intestinal barrier and immune system, these animals are often cesarian section derived, leaving them uncolonized for normal intestinal microflora. The hypothesis was that an increase in complexity of microbiota inoculum will allow for more stability in the composition of the gut microbiota of SCID piglets. This was tested across multiple litters of SCID piglets with three different defined microbiota consortium (2-strain, 6-strain, 7-strain). All piglets received their designated defined microbiota by oral gavage immediately after birth and again 24 hours later. There was no effect of SCID genotype on the composition of the gut microbiota, but there was a significant effect due to piglet age. Additionally, all three defined microbiota consortia were deemed safe to use in SCID piglets, and the 7-strain microbiota was the most stable over time. Based on these results, the 7-strain defined microbiota will be added to the SCID pig husbandry protocol, allowing for a more reproducible model.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"109 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179758","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 : 2024-09-05DOI: 10.1101/2024.09.05.611529
Pankaj Agrawal, Klaus E Schmitz-Abe, Qifei Li, Sunny Greene, Michela Borrelli, Shiyu Luo, Madesh Ramesh
Publicly available genomic databases and genetic constraint scores are crucial in understanding human population variation and the identification of variants that are likely to have a deleterious impact causing human disease. We utilized the one of largest publicly available databases, gnomAD, to determine genes that are highly constrained for only LoF, only missense, and both LoF/missense variants, identified their unique signatures, and explored their causal relationship with human conditions. Those genes were evaluated for unique patterns including their chromosomal location, tissue level expression, gene ontology analysis, and gene family categorization using multiple publicly available databases. Those highly constrained genes associated with human disease, we identified unique patterns of inheritance, protein size, and enrichment in distinct molecular pathways. In addition, we identified a cohort of highly constrained genes that are currently not known to cause human disease, that we suggest will be candidates to pursue as novel disease-associated genes. In summary, these insights not only elucidate biological pathways of highly constrained genes that expand our understanding of critical cellular proteins but also advance research in rare diseases.
{"title":"Unique Signatures of Highly Constrained Genes Across Publicly Available Genomic Databases","authors":"Pankaj Agrawal, Klaus E Schmitz-Abe, Qifei Li, Sunny Greene, Michela Borrelli, Shiyu Luo, Madesh Ramesh","doi":"10.1101/2024.09.05.611529","DOIUrl":"https://doi.org/10.1101/2024.09.05.611529","url":null,"abstract":"Publicly available genomic databases and genetic constraint scores are crucial in understanding human population variation and the identification of variants that are likely to have a deleterious impact causing human disease. We utilized the one of largest publicly available databases, gnomAD, to determine genes that are highly constrained for only LoF, only missense, and both LoF/missense variants, identified their unique signatures, and explored their causal relationship with human conditions. Those genes were evaluated for unique patterns including their chromosomal location, tissue level expression, gene ontology analysis, and gene family categorization using multiple publicly available databases. Those highly constrained genes associated with human disease, we identified unique patterns of inheritance, protein size, and enrichment in distinct molecular pathways. In addition, we identified a cohort of highly constrained genes that are currently not known to cause human disease, that we suggest will be candidates to pursue as novel disease-associated genes. In summary, these insights not only elucidate biological pathways of highly constrained genes that expand our understanding of critical cellular proteins but also advance research in rare diseases.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179778","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 : 2024-09-03DOI: 10.1101/2024.09.03.611048
Mahendra K. Prajapat, Joana A Vidigal
Non-coding regulatory sequences play essential roles in adjusting gene output to cellular needs and are thus critical to animal development and health. Numerous such sequences have been identified in mammalian genomes ranging from transcription factors binding motifs to recognition sites for RNA-binding proteins and non-coding RNAs. The advent of CRISPR has raised the possibility of assigning functionality to individual endogenous regulatory sites by facilitating the generation of isogenic cell lines that differ by a defined set of genetic modifications. Here we investigate the usefulness of this approach to assign function to individual miRNA binding sites. We find that the process of generating isogenic pairs of mammalian cell lines with CRISPR-mediated mutations introduces extensive molecular and phenotypic variability between biological replicates making any attempt of assigning function to the binding site essentially impossible. Our work highlights an important consideration when employing CRISPR editing to characterize non-coding regulatory sequences in cell lines and calls for the development and adoption of alternative strategies to address this question in the future.
{"title":"CRISPR-based dissection of miRNA binding sites using isogenic cell lines is hampered by pervasive noise.","authors":"Mahendra K. Prajapat, Joana A Vidigal","doi":"10.1101/2024.09.03.611048","DOIUrl":"https://doi.org/10.1101/2024.09.03.611048","url":null,"abstract":"Non-coding regulatory sequences play essential roles in adjusting gene output to cellular needs and are thus critical to animal development and health. Numerous such sequences have been identified in mammalian genomes ranging from transcription factors binding motifs to recognition sites for RNA-binding proteins and non-coding RNAs. The advent of CRISPR has raised the possibility of assigning functionality to individual endogenous regulatory sites by facilitating the generation of isogenic cell lines that differ by a defined set of genetic modifications. Here we investigate the usefulness of this approach to assign function to individual miRNA binding sites. We find that the process of generating isogenic pairs of mammalian cell lines with CRISPR-mediated mutations introduces extensive molecular and phenotypic variability between biological replicates making any attempt of assigning function to the binding site essentially impossible. Our work highlights an important consideration when employing CRISPR editing to characterize non-coding regulatory sequences in cell lines and calls for the development and adoption of alternative strategies to address this question in the future.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"109 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179742","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 : 2024-09-03DOI: 10.1101/2024.09.02.610808
Victor A. Shamanskiy, Konstantin V. Gunbin, Evgenii O. Tretiakov, Ilia O. Mazunin, Victoria Skripskaya, Alina A. Mihailova, Alina G. Mikhailova, Natalia Ree, Valeriia Timonina, Dmitry Knorre, Wolfram S. Kunz, Yukinori Okada, Nathan Fiorell, Alexandre Reymond, Georgii A. Bazykin, Jacques Fellay, Masashi Tanaka, Konstantin Khrapko, Konstantin Popadin
Aging, characterized by a series of functional declines correlated with advancing chronological age, has a significant mitochondrial DNA (mtDNA) component, with somatic mtDNA deletions playing a central role. In post-mitotic or slow-dividing cells like neurons and skeletal muscles, selfish mtDNA deletions clonally expand within a cell, ultimately leading to the deterioration and death of host cells and appearence of age-related phenotypes. Thus reducing the burden of somatic deletions could have far-reaching systemic benefits for the entire human body. Given the crucial role of direct nucleotide repeats in the formation of mitochondrial deletions, we hypothesize that minimizing these repeats in the human mitochondrial genome could enhance healthspan by decreasing somatic deletions. To investigate this hypothesis, we focus on the "common repeat", a 13-base pair perfect direct repeat sequence (ACCTCCCTCACCA) located at positions 8470-8482 and 13447-13459, respectively. This perfect repeat: (i) is highly prevalent, with its potential deleterious consequences affecting the majority of humans; (ii) represents one of the most fragile sites, highly prone to forming deletions; (iii) when disrupted, is associated with a decreased somatic deletion load and enhanced human healthspan; (iv) is likely to experience positive selection in the present or near future due to indirect fitness effects, such as the "grandmother effect", and direct fitness effects, such as (v) a decreased mutation rate. These observations support the argument that reducing the mtDNA somatic deletion load through targeted disruption of these repeats, or by using naturally occurring polymorphisms with disrupted repeats in mitochondrial medicine, could be an effective approach to increasing human longevity.
{"title":"Mitochondrial direct repeat reduction as a strategy for enhancing human longevity: the case of the common repeat","authors":"Victor A. Shamanskiy, Konstantin V. Gunbin, Evgenii O. Tretiakov, Ilia O. Mazunin, Victoria Skripskaya, Alina A. Mihailova, Alina G. Mikhailova, Natalia Ree, Valeriia Timonina, Dmitry Knorre, Wolfram S. Kunz, Yukinori Okada, Nathan Fiorell, Alexandre Reymond, Georgii A. Bazykin, Jacques Fellay, Masashi Tanaka, Konstantin Khrapko, Konstantin Popadin","doi":"10.1101/2024.09.02.610808","DOIUrl":"https://doi.org/10.1101/2024.09.02.610808","url":null,"abstract":"Aging, characterized by a series of functional declines correlated with advancing chronological age, has a significant mitochondrial DNA (mtDNA) component, with somatic mtDNA deletions playing a central role. In post-mitotic or slow-dividing cells like neurons and skeletal muscles, selfish mtDNA deletions clonally expand within a cell, ultimately leading to the deterioration and death of host cells and appearence of age-related phenotypes. Thus reducing the burden of somatic deletions could have far-reaching systemic benefits for the entire human body. Given the crucial role of direct nucleotide repeats in the formation of mitochondrial deletions, we hypothesize that minimizing these repeats in the human mitochondrial genome could enhance healthspan by decreasing somatic deletions. To investigate this hypothesis, we focus on the \"common repeat\", a 13-base pair perfect direct repeat sequence (ACCTCCCTCACCA) located at positions 8470-8482 and 13447-13459, respectively. This perfect repeat: (i) is highly prevalent, with its potential deleterious consequences affecting the majority of humans; (ii) represents one of the most fragile sites, highly prone to forming deletions; (iii) when disrupted, is associated with a decreased somatic deletion load and enhanced human healthspan; (iv) is likely to experience positive selection in the present or near future due to indirect fitness effects, such as the \"grandmother effect\", and direct fitness effects, such as (v) a decreased mutation rate. These observations support the argument that reducing the mtDNA somatic deletion load through targeted disruption of these repeats, or by using naturally occurring polymorphisms with disrupted repeats in mitochondrial medicine, could be an effective approach to increasing human longevity.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"83 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179755","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 : 2024-09-02DOI: 10.1101/2024.08.31.610248
Árni Freyr Gunnarsson, Jiazheng Zhu, Brian C. Zhang, Zoi Tsangalidou, Alex Allmont, Pier Francesco Palamara
The ancestral recombination graph (ARG) is a graph-like structure that encodes a detailed genealogical history of a set of individuals along the genome. ARGs that are accurately reconstructed from genomic data have several downstream applications, but inference from data sets comprising millions of samples and variants remains computationally challenging. We introduce Threads, a threading-based method that significantly reduces the computational costs of ARG inference while retaining high accuracy. We apply Threads to infer the ARG of 487,409 genomes from the UK Biobank using ~10 million high-quality imputed variants, reconstructing a detailed genealogical history of the samples while compressing the input genotype data. Additionally, we develop ARG-based imputation strategies that increase genotype imputation accuracy for ultra-rare variants (MAC ≤ 10) from UK Biobank exome sequencing data by 5-10%. We leverage ARGs inferred by Threads to detect associations with 52 quantitative traits in non-European UK Biobank samples, identifying 22.5% more signals than ARG-Needle. These analyses underscore the value of using computationally efficient genealogical modeling to improve and complement genotype imputation in large-scale genomic studies.
{"title":"A scalable approach for genome-wide inference of ancestral recombination graphs","authors":"Árni Freyr Gunnarsson, Jiazheng Zhu, Brian C. Zhang, Zoi Tsangalidou, Alex Allmont, Pier Francesco Palamara","doi":"10.1101/2024.08.31.610248","DOIUrl":"https://doi.org/10.1101/2024.08.31.610248","url":null,"abstract":"The ancestral recombination graph (ARG) is a graph-like structure that encodes a detailed genealogical history of a set of individuals along the genome. ARGs that are accurately reconstructed from genomic data have several downstream applications, but inference from data sets comprising millions of samples and variants remains computationally challenging. We introduce Threads, a threading-based method that significantly reduces the computational costs of ARG inference while retaining high accuracy. We apply Threads to infer the ARG of 487,409 genomes from the UK Biobank using ~10 million high-quality imputed variants, reconstructing a detailed genealogical history of the samples while compressing the input genotype data. Additionally, we develop ARG-based imputation strategies that increase genotype imputation accuracy for ultra-rare variants (MAC ≤ 10) from UK Biobank exome sequencing data by 5-10%. We leverage ARGs inferred by Threads to detect associations with 52 quantitative traits in non-European UK Biobank samples, identifying 22.5% more signals than ARG-Needle. These analyses underscore the value of using computationally efficient genealogical modeling to improve and complement genotype imputation in large-scale genomic studies.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179752","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}
This study presents the development of a simple DNA extraction method and a novel PCR-RFLP technique for genotyping the MALE STERILITY 4 (MS4) gene in Cryptomeria japonica. Traditional CTAB-based DNA extraction methods, while effective, involve hazardous chemicals and require high-speed centrifugation, which are impractical in many field settings. Our approach utilizes a household dish detergent-based buffer, sodium chloride, and polyvinylpyrrolidone K-30 to extract DNA from C. japonica needle leaf tissues. The simplicity of this method makes it more accessible and environmentally friendly. The extracted DNA was successfully used in PCR-RFLP analysis, targeting a single nucleotide polymorphism in the MS4 gene, demonstrating its efficacy for genotyping. The PCR-RFLP markers reliably discriminated between individual genotypes, confirming the practical application of our simple extraction method, even for conifers containing inhibitory substances. This technique is particularly advantageous for use in arboretums and field stations, where the use of hazardous chemicals and specialized equipment is limited. Our study contributes to genetic resource management by providing an easy, reliable, and safer method for DNA extraction and genetic analysis.
本研究介绍了一种简单的 DNA 提取方法和一种新型 PCR-RFLP 技术，用于对日本隐花植物的雄性不育性 4（MS4）基因进行基因分型。传统的基于 CTAB 的 DNA 提取方法虽然有效，但涉及有害化学物质，而且需要高速离心，这在许多野外环境中不切实际。我们的方法是利用家用洗洁精缓冲液、氯化钠和聚乙烯吡咯烷酮 K-30 从隐杆线虫针叶组织中提取 DNA。这种方法简便易行，对环境更加友好。提取的 DNA 被成功用于针对 MS4 基因单核苷酸多态性的 PCR-RFLP 分析，证明了其基因分型的有效性。PCR-RFLP 标记可靠地区分了不同的基因型，证实了我们的简单提取方法的实际应用价值，即使对含有抑制物质的针叶树也是如此。这项技术尤其适合在植物园和野外站使用，因为在这些地方使用危险化学品和专业设备的可能性有限。我们的研究为 DNA 提取和遗传分析提供了一种简便、可靠、安全的方法，有助于遗传资源管理。
{"title":"Developing simple DNA extraction and PCR-RFLP for MALE STERILITY 4 (MS4) gene in Cryptomeria japonica D. Don: Toward an environmentally friendly protocol","authors":"Saneyoshi Ueno, Yukiko Ito, Yoichi Hasegawa, Yoshinari Moriguchi","doi":"10.1101/2024.08.31.610595","DOIUrl":"https://doi.org/10.1101/2024.08.31.610595","url":null,"abstract":"This study presents the development of a simple DNA extraction method and a novel PCR-RFLP technique for genotyping the <em>MALE STERILITY 4</em> (<em>MS4</em>) gene in <em>Cryptomeria japonica</em>. Traditional CTAB-based DNA extraction methods, while effective, involve hazardous chemicals and require high-speed centrifugation, which are impractical in many field settings. Our approach utilizes a household dish detergent-based buffer, sodium chloride, and polyvinylpyrrolidone K-30 to extract DNA from <em>C. japonica</em> needle leaf tissues. The simplicity of this method makes it more accessible and environmentally friendly. The extracted DNA was successfully used in PCR-RFLP analysis, targeting a single nucleotide polymorphism in the <em>MS4</em> gene, demonstrating its efficacy for genotyping. The PCR-RFLP markers reliably discriminated between individual genotypes, confirming the practical application of our simple extraction method, even for conifers containing inhibitory substances. This technique is particularly advantageous for use in arboretums and field stations, where the use of hazardous chemicals and specialized equipment is limited. Our study contributes to genetic resource management by providing an easy, reliable, and safer method for DNA extraction and genetic analysis.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179756","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 : 2024-09-02DOI: 10.1101/2024.08.30.609799
Rikuou Yokosaka, Kentaro Noma
A decline in food-searching behavior of post-reproductive animals can be beneficial for the population and possibly programmed by the genome. We investigated the genetic program of age-dependent decline in chemotaxis behavior toward an odorant secreted from bacterial food in C. elegans. Through a forward genetic screen, we identified a nuclear hormone receptor, nhr-76, whose mutants ameliorate the age-dependent chemotaxis decline. We found that nhr-76 downregulates the expression of the odorant receptor during aging. Because NHR-76 expression and localization did not change during aging, secretion of its hydrophobic ligands might alter the activity of NHR-76 to cause age-dependent chemotaxis decline. Our findings imply that post-reproductive behavioral decline can be genetically programmed.
{"title":"A nuclear hormone receptor nhr-76 programs age-dependent chemotaxis decline in C. elegans","authors":"Rikuou Yokosaka, Kentaro Noma","doi":"10.1101/2024.08.30.609799","DOIUrl":"https://doi.org/10.1101/2024.08.30.609799","url":null,"abstract":"A decline in food-searching behavior of post-reproductive animals can be beneficial for the population and possibly programmed by the genome. We investigated the genetic program of age-dependent decline in chemotaxis behavior toward an odorant secreted from bacterial food in C. elegans. Through a forward genetic screen, we identified a nuclear hormone receptor, nhr-76, whose mutants ameliorate the age-dependent chemotaxis decline. We found that nhr-76 downregulates the expression of the odorant receptor during aging. Because NHR-76 expression and localization did not change during aging, secretion of its hydrophobic ligands might alter the activity of NHR-76 to cause age-dependent chemotaxis decline. Our findings imply that post-reproductive behavioral decline can be genetically programmed.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"50 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179754","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：