Genome research最新文献_第9页

Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR. 利用 MiXCR 从免疫谱系测序数据中进行超灵敏等位基因推断。

IF 6.2 2区生物学

Genome research Pub Date : 2024-12-23 DOI: 10.1101/gr.278775.123

Artem Mikelov, George Nefediev, Alexander Tashkeev, Oscar L Rodriguez, Diego Aguilar Ortmans, Valeriia Skatova, Mark Izraelson, Alexey N Davydov, Stanislav Poslavsky, Souad Rahmouni, Corey T Watson, Dmitriy Chudakov, Scott D Boyd, Dmitry Bolotin

{"title":"Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR.","authors":"Artem Mikelov, George Nefediev, Alexander Tashkeev, Oscar L Rodriguez, Diego Aguilar Ortmans, Valeriia Skatova, Mark Izraelson, Alexey N Davydov, Stanislav Poslavsky, Souad Rahmouni, Corey T Watson, Dmitriy Chudakov, Scott D Boyd, Dmitry Bolotin","doi":"10.1101/gr.278775.123","DOIUrl":"10.1101/gr.278775.123","url":null,"abstract":"Allelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), is of critical importance for immune responses to pathogens and vaccines. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread in immunology research making it the most readily available source of information about allelic diversity in immunoglobulin (IG) and T cell receptor (TR) loci. Here, we present a novel algorithm for extrasensitive and specific variable (V) and joining (J) gene allele inference, allowing the reconstruction of individual high-quality gene segment libraries. The approach can be applied for inferring allelic variants from peripheral blood lymphocyte BCR and TCR repertoire sequencing data, including hypermutated isotype-switched BCR sequences, thus allowing high-throughput novel allele discovery from a wide variety of existing data sets. The developed algorithm is a part of the MiXCR software. We demonstrate the accuracy of this approach using AIRR-seq paired with long-read genomic sequencing data, comparing it to a widely used algorithm, TIgGER. We applied the algorithm to a large set of IG heavy chain (IGH) AIRR-seq data from 450 donors of ancestrally diverse population groups, and to the largest reported full-length TCR alpha and beta chain (TRA and TRB) AIRR-seq data set, representing 134 individuals. This allowed us to assess the genetic diversity within the IGH, TRA, and TRB loci in different populations and to establish a database of alleles of V and J genes inferred from AIRR-seq data and their population frequencies with free public access through VDJ.online database.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":" ","pages":"2293-2303"},"PeriodicalIF":6.2,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models 在两种主要的CRX视网膜病变模型中，异常的同源结构域- dna合作二聚化是不同发育缺陷的基础

IF 7 2区生物学

Genome research Pub Date : 2024-12-23 DOI: 10.1101/gr.279340.124

Yiqiao Zheng, Gary D. Stormo, Shiming Chen

{"title":"Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models","authors":"Yiqiao Zheng, Gary D. Stormo, Shiming Chen","doi":"10.1101/gr.279340.124","DOIUrl":"https://doi.org/10.1101/gr.279340.124","url":null,"abstract":"Paired-class homeodomain transcription factors (HD TFs) play essential roles in vertebrate development, and their mutations are linked to human diseases. One unique feature of paired-class HD is cooperative dimerization on specific palindrome DNA sequences. Yet, the functional significance of HD cooperative dimerization in animal development and its dysregulation in diseases remain elusive. Using the retinal TF Cone-rod Homeobox (CRX) as a model, we have studied how blindness-causing mutations in the paired HD, p.E80A and p.K88N, alter CRX’s cooperative dimerization, lead to gene misexpression and photoreceptor developmental deficits in dominant manners. CRXE80A maintains binding at monomeric WT CRX motifs but is deficient in cooperative binding at dimeric motifs. CRXE80A’s cooperativity defect impacts the exponential increase of photoreceptor gene expression in terminal differentiation and produces immature, non-functional photoreceptors in the CrxE80A retinas. CRXK88N is highly cooperative and localizes to ectopic genomic sites with strong enrichment of dimeric HD motifs. CRXK88N’s altered biochemical properties disrupt CRX’s ability to direct dynamic chromatin remodeling during development to activate photoreceptor differentiation programs and silence progenitor programs. Our study here provides in vitro and in vivo molecular evidence that paired-class HD cooperative dimerization regulates neuronal development and dysregulation of cooperative binding contributes to severe dominant blinding retinopathies.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"13 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Reviewer Index, Volume 34, 2024. 审稿人索引，第34卷，2024年。

IF 6.2 2区生物学

Genome research Pub Date : 2024-12-23

引用次数: 0

Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development. 分析超级增强子的时间动态可揭示骨骼肌发育过程中潜在的关键增强子及其基因调控网络。

IF 6.2 2区生物学

Genome research Pub Date : 2024-12-23 DOI: 10.1101/gr.278344.123

Song Zhang, Chao Wang, Shenghua Qin, Choulin Chen, Yongzhou Bao, Yuanyuan Zhang, Lingna Xu, Qingyou Liu, Yunxiang Zhao, Kui Li, Zhonglin Tang, Yuwen Liu

{"title":"Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development.","authors":"Song Zhang, Chao Wang, Shenghua Qin, Choulin Chen, Yongzhou Bao, Yuanyuan Zhang, Lingna Xu, Qingyou Liu, Yunxiang Zhao, Kui Li, Zhonglin Tang, Yuwen Liu","doi":"10.1101/gr.278344.123","DOIUrl":"10.1101/gr.278344.123","url":null,"abstract":"Super-enhancers (SEs) govern the expression of genes defining cell identity. However, the dynamic landscape of SEs and their critical constituent enhancers involved in skeletal muscle development remains unclear. In this study, using pig as a model, we employed cleavage under targets and tagmentation (CUT&Tag) to profile the enhancer-associated histone modification marker H3K27ac in skeletal muscle across two prenatal and three postnatal stages, and investigated how SEs influence skeletal muscle development. We identify three SE families with distinct temporal dynamics: continuous (Con, 397), transient (TS, 434), and de novo (DN, 756). These SE families are associated with different temporal gene expression trajectories, biological functions, and DNA methylation levels. Notably, several lines of evidence suggest a potential prominent role of Con SEs in regulating porcine muscle development and meat traits. To pinpoint key cis-regulatory units in Con SEs, we developed an integrative approach that leverages information from eRNA annotation, genome-wide association study (GWAS) signals, and high-throughput capture self-transcribing active regulatory region sequencing (STARR-seq) experiments. Within Con SEs, we identify 20 candidate critical enhancers with meat and carcass-associated DNA variations that affect enhancer activity, and infer their upstream transcription factors and downstream target genes. As a proof of concept, we experimentally validate the role of one such enhancer and its potential target gene during myogenesis. Our findings reveal the dynamic regulatory features of SEs in skeletal muscle development and provide a general integrative framework for identifying critical enhancers underlying the formation of complex traits.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":" ","pages":"2190-2202"},"PeriodicalIF":6.2,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq 利用长读RNA-seq评估证据驱动的基因组注释策略

IF 7 2区生物学

Genome research Pub Date : 2024-12-23 DOI: 10.1101/gr.279864.124

Alejandro Paniagua, Cristina Agustin-García, Francisco J Pardo-Palacios, Thomas Brown, Maite De Maria, Nancy D Denslow, Camila Mazzoni, Ana Conesa

{"title":"Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq","authors":"Alejandro Paniagua, Cristina Agustin-García, Francisco J Pardo-Palacios, Thomas Brown, Maite De Maria, Nancy D Denslow, Camila Mazzoni, Ana Conesa","doi":"10.1101/gr.279864.124","DOIUrl":"https://doi.org/10.1101/gr.279864.124","url":null,"abstract":"While the production of a draft genome has become more accessible due to long-read sequencing, the annotation of these new genomes has not been developed at the same pace. Long-read RNA sequencing (lrRNA-seq) offers a promising solution for enhancing gene annotation. In this study, we explore how sequencing platforms, Oxford Nanopore R9.4.1 chemistry or PacBio Sequel II CCS, and data processing methods influence evidence-driven genome annotation using long reads. Incorporating PacBio transcripts into our annotation pipeline significantly outperformed traditional methods, such as ab initio predictions and short-read-based annotations. We applied this strategy to a nonmodel species, the Florida manatee, and compared our results to existing short-read-based annotation. At the loci level, both annotations were highly concordant, with 90% agreement. However, at the transcript level, the agreement was only 35%. We identified 4,906 novel loci, represented by 5,707 isoforms, with 64% of these isoforms matching known sequences in other mammalian species. Overall, our findings underscore the importance of using high-quality curated transcript models in combination with ab initio methods for effective genome annotation.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"32 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

MCHelper automatically curates transposable element libraries across eukaryotic species MCHelper自动管理跨真核生物物种的转座因子库

IF 7 2区生物学

Genome research Pub Date : 2024-12-09 DOI: 10.1101/gr.278821.123

Simon Orozco-Arias, Pío Sierra, Richard Durbin, Josefa González

{"title":"MCHelper automatically curates transposable element libraries across eukaryotic species","authors":"Simon Orozco-Arias, Pío Sierra, Richard Durbin, Josefa González","doi":"10.1101/gr.278821.123","DOIUrl":"https://doi.org/10.1101/gr.278821.123","url":null,"abstract":"The number of species with high-quality genome sequences continues to increase, in part due to the scaling up of multiple large-scale biodiversity sequencing projects. While the need to annotate genic sequences in these genomes is widely acknowledged, the parallel need to annotate transposable element (TE) sequences that have been shown to alter genome architecture, rewire gene regulatory networks, and contribute to the evolution of host traits is becoming ever more evident. However, accurate genome-wide annotation of TE sequences is still technically challenging. Several de novo TE identification tools are now available, but manual curation of the libraries produced by these tools is needed to generate high-quality genome annotations. Manual curation is time-consuming, and thus impractical for large-scale genomic studies, and lacks reproducibility. In this work, we present the Manual Curator Helper tool MCHelper, which automates the TE library curation process. By leveraging MCHelper's fully automated mode with the outputs from three de novo TE identification tools, RepeatModeler2, EDTA, and REPET, in the fruit fly, rice, hooded crow, zebrafish, maize, and human, we show a substantial improvement in the quality of the TE libraries and genome annotations. MCHelper libraries are less redundant, with up to 65% reduction in the number of consensus sequences, have up to 11.4% fewer false positive sequences, and up to ∼48% fewer “unclassified/unknown” TE consensus sequences. Genome-wide TE annotations are also improved, including larger unfragmented insertions. Moreover, MCHelper is an easy-to-install and easy-to-use tool.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"20 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142797141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Resolving the chromatin impact of mosaic variants with targeted Fiber-seq 利用靶向纤维序列分析镶嵌变异对染色质的影响

IF 7 2区生物学

Genome research Pub Date : 2024-12-09 DOI: 10.1101/gr.279747.124

Stephanie C. Bohaczuk, Zachary J. Amador, Chang Li, Benjamin J. Mallory, Elliott G. Swanson, Jane Ranchalis, Mitchell R. Vollger, Katherine M. Munson, Tom Walsh, Morgan O. Hamm, Yizi Mao, Andre Lieber, Andrew B. Stergachis

{"title":"Resolving the chromatin impact of mosaic variants with targeted Fiber-seq","authors":"Stephanie C. Bohaczuk, Zachary J. Amador, Chang Li, Benjamin J. Mallory, Elliott G. Swanson, Jane Ranchalis, Mitchell R. Vollger, Katherine M. Munson, Tom Walsh, Morgan O. Hamm, Yizi Mao, Andre Lieber, Andrew B. Stergachis","doi":"10.1101/gr.279747.124","DOIUrl":"https://doi.org/10.1101/gr.279747.124","url":null,"abstract":"Accurately quantifying the functional consequences of noncoding mosaic variants requires the pairing of DNA sequences with both accessible and closed chromatin architectures along individual DNA molecules—a pairing that cannot be achieved using traditional fragmentation-based chromatin assays. We demonstrate that targeted single-molecule chromatin fiber sequencing (Fiber-seq) achieves this, permitting single-molecule, long-read genomic, and epigenomic profiling across targeted >100 kb loci with ∼10-fold enrichment over untargeted sequencing. Targeted Fiber-seq reveals that pathogenic expansions of the DMPK CTG repeat that underlie Myotonic Dystrophy 1 are characterized by somatic instability and disruption of multiple nearby regulatory elements, both of which are repeat length-dependent. Furthermore, we reveal that therapeutic adenine base editing of the segmentally duplicated γ-globin (HBG1/HBG2) promoters in primary human hematopoietic cells induced toward an erythroblast lineage increases the accessibility of the HBG1 promoter as well as neighboring regulatory elements. Overall, we find that these non–protein coding mosaic variants can have complex impacts on chromatin architectures, including extending beyond the regulatory element harboring the variant.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"1 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142797142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation 人乳头瘤病毒整合事件中病毒和人类基因组的重排及其等位基因特异性对癌症基因组调控的影响

IF 7 2区生物学

Genome research Pub Date : 2024-12-05 DOI: 10.1101/gr.279041.124

Vanessa L. Porter, Michelle Ng, Kieran O'Neill, Signe MacLennan, Richard D. Corbett, Luka Culibrk, Zeid Hamadeh, Marissa Iden, Rachel Schmidt, Shirng-Wern Tsaih, Carolyn Nakisige, Martin Origa, Jackson Orem, Glenn Chang, Jeremy Fan, Ka Ming Nip, Vahid Akbari, Simon K. Chan, James Hopkins, Richard A. Moore, Eric Chuah, Karen L. Mungall, Andrew J. Mungall, Inanc Birol, Steven J.M. Jones, Janet S. Rader, Marco A. Marra

{"title":"Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation","authors":"Vanessa L. Porter, Michelle Ng, Kieran O'Neill, Signe MacLennan, Richard D. Corbett, Luka Culibrk, Zeid Hamadeh, Marissa Iden, Rachel Schmidt, Shirng-Wern Tsaih, Carolyn Nakisige, Martin Origa, Jackson Orem, Glenn Chang, Jeremy Fan, Ka Ming Nip, Vahid Akbari, Simon K. Chan, James Hopkins, Richard A. Moore, Eric Chuah, Karen L. Mungall, Andrew J. Mungall, Inanc Birol, Steven J.M. Jones, Janet S. Rader, Marco A. Marra","doi":"10.1101/gr.279041.124","DOIUrl":"https://doi.org/10.1101/gr.279041.124","url":null,"abstract":"Human papillomavirus (HPV) integration has been implicated in transforming HPV infection into cancer. To resolve genome dysregulation associated with HPV integration, we performed Oxford Nanopore long-read sequencing on 72 cervical cancer genomes from an Ugandan dataset that was previously characterized using short-read sequencing. We found recurrent structural rearrangement patterns at HPV integration events, which we categorized as: del(etion)-like, dup(lication)-like, translocation, multibreakpoint, or repeat region integrations. Integrations involving amplified HPV-human concatemers, particularly multibreakpoint events, frequently harbored heterogeneous forms and copy numbers of the viral genome. Transcriptionally active integrants were characterized by unmethylated regions in both the viral and human genomes downstream from the viral transcription start site, resulting in HPV-human fusion transcripts. In contrast, integrants without evidence of expression lacked consistent methylation patterns. Furthermore, whereas transcriptional dysregulation was limited to genes within 200 kilobases of an HPV integrant, dysregulation of the human epigenome in the form of allelic differentially methylated regions affected megabase expanses of the genome, irrespective of the integrant's transcriptional status. By elucidating the structural, epigenetic, and allele-specific impacts of HPV integration, we provide insight into the role of integrated HPV in cervical cancer.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"68 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142783300","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes 淋巴母细胞细胞系的整合TAD目录揭示了人类基因组中缺失和插入的功能影响

IF 7 2区生物学

Genome research Pub Date : 2024-12-05 DOI: 10.1101/gr.279419.124

Chong Li, Marc Jan Bonder, Sabriya Syed, Matthew Jensen, Human Genome Structural Variation Consortium (HGSVC), HGSVC Functional Analysis Working Group, Mark B. Gerstein, Michael C. Zody, Mark J.P. Chaisson, Michael E. Talkowski, Tobias Marschall, Jan O. Korbel, Evan E. Eichler, Charles Lee, Xinghua Shi

{"title":"An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes","authors":"Chong Li, Marc Jan Bonder, Sabriya Syed, Matthew Jensen, Human Genome Structural Variation Consortium (HGSVC), HGSVC Functional Analysis Working Group, Mark B. Gerstein, Michael C. Zody, Mark J.P. Chaisson, Michael E. Talkowski, Tobias Marschall, Jan O. Korbel, Evan E. Eichler, Charles Lee, Xinghua Shi","doi":"10.1101/gr.279419.124","DOIUrl":"https://doi.org/10.1101/gr.279419.124","url":null,"abstract":"The human genome is packaged within a three-dimensional (3D) nucleus and organized into structural units known as compartments, topologically associating domains (TADs), and loops. TAD boundaries, separating adjacent TADs, have been found to be well conserved across mammalian species and more evolutionarily constrained than TADs themselves. Recent studies show that structural variants (SVs) can modify 3D genomes through the disruption of TADs, which play an essential role in insulating genes from outside regulatory elements’ aberrant regulation. However, how SV affects the 3D genome structure and their association among different aspects of gene regulation and candidate cis-regulatory elements (cCREs) have rarely been studied systematically. Here, we assess the impact of SVs intersecting with TAD boundaries by developing an integrative Hi-C analysis pipeline, which enables the generation of an in-depth catalog of TADs and TAD boundaries in human lymphoblastoid cell lines (LCLs) to fill the gap of limited resources. Our catalog contains 18,865 TADs, including 4596 sub-TADs, with 185 SVs (TAD–SVs) that alter chromatin architecture. By leveraging the ENCODE registry of cCREs in humans, we determine that 34 of 185 TAD–SVs intersect with cCREs and observe significant enrichment of TAD–SVs within cCREs. This study provides a database of TADs and TAD–SVs in the human genome that will facilitate future investigations of the impact of SVs on chromatin structure and gene regulation in health and disease.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"199 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142783298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype 九头蛇具有类似哺乳动物的突变率，促进快速适应，尽管它的表型不老化

IF 7 2区生物学

Genome research Pub Date : 2024-12-04 DOI: 10.1101/gr.279025.124

Arne Sahm, Konstantin Riege, Marco Groth, Martin Bens, Johann Kraus, Martin Fischer, Hans Kestler, Christoph Englert, Ralf Schaible, Matthias Platzer, Steve Hoffmann

{"title":"Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype","authors":"Arne Sahm, Konstantin Riege, Marco Groth, Martin Bens, Johann Kraus, Martin Fischer, Hans Kestler, Christoph Englert, Ralf Schaible, Matthias Platzer, Steve Hoffmann","doi":"10.1101/gr.279025.124","DOIUrl":"https://doi.org/10.1101/gr.279025.124","url":null,"abstract":"Growing evidence suggests that somatic mutations may be a major cause of the aging process. However, it remains to be tested whether the predictions of the theory also apply to species with longer life spans than humans. Hydra is a genus of freshwater polyps with remarkable regeneration abilities and a potentially unlimited life span under laboratory conditions. By genome sequencing of single cells and whole animals, we found that the mutation rates in Hydra’s stem cells are even slightly higher than in humans or mice. A potential explanation for this deviation from the prediction of the theory may lie in the adaptability offered by a higher mutation rate, as we were able to show that the genome of the widely studied Hydra magnipapillata strain 105 has undergone a process of strong positive selection since the strain's cultivation 50 years ago. This most likely represents a rapid adaptation to the drastically altered environmental conditions associated with the transition from the wild to laboratory conditions. Processes under positive selection in captive animals include pathways associated with Hydra’s simple nervous system, its nucleic acid metabolic process, cell migration, and hydrolase activity.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"27 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142777005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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