bioRxiv - Genetics最新文献

{"title":"Universal dynamics of cohesin-mediated loop extrusion","authors":"Thomas Sabate, Benoit Lelandais, Marie-Cecile Robert, Michael Szalay, Jean-Yves Tinevez, Edouard Bertrand, Christophe Zimmer","doi":"10.1101/2024.08.09.605990","DOIUrl":"https://doi.org/10.1101/2024.08.09.605990","url":null,"abstract":"Most animal genomes are partitioned into Topologically Associating Domains (TADs), created by cohesin-mediated loop extrusion and defined by convergently oriented CTCF sites. The dynamics of loop extrusion and its regulation remains poorly characterized in vivo. Here, we tracked TAD anchors in living human cells to visualize and quantify cohesin-dependent loop extrusion across multiple endogenous genomic regions. We show that TADs are dynamic structures whose anchors are brought in proximity about once per hour and for 6-19 min (~16% of the time). TADs are continuously subjected to extrusion by multiple cohesin complexes, extruding loops at ~0.1 kb/s. Remarkably, despite strong differences of Hi-C patterns between the chromatin regions, their dynamics is consistent with the same density, residence time and speed of cohesin. Our results suggest that TAD dynamics is governed primarily by CTCF site location and affinity, which allows genome-wide predictive models of cohesin-dependent interactions.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934455","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}

{"title":"Non-destructive DNA extraction from specimens and environmental samples using DESS preservation solution for DNA barcoding","authors":"Eri Ogiso-Tanaka, Minako Abe Ito, Daisuke Shimada","doi":"10.1101/2024.08.09.607403","DOIUrl":"https://doi.org/10.1101/2024.08.09.607403","url":null,"abstract":"DESS is a widely used storage solution for the preservation of DNA from biological tissue samples. DESS comprises 20% dimethyl sulfoxide, 250 mM ethylenediaminetetraacetic acid, and saturated sodium chloride, and its efficacy has been confirmed in various taxa and tissues. DESS enables the stable, long-term preservation of both sample morphology and DNA. However, to access the DNA, excising a portion of the sample was necessary. Although DNA is a valuable source of information for species identification, DNA extraction can result in the loss of an entire sample or segment, especially in small-sized organisms, thereby compromising specimen value. Therefore, establishing non-destructive DNA extraction techniques is imperative. Thus, this paper presents a protocol for conducting non-destructive DNA extraction and DNA barcoding using a portion of the DESS supernatant obtained from a nematode specimen. This method was successfully employed for DNA barcoding of nematodes that were stored in DESS at room temperature (-10~35˚C) for ten years. Moreover, the method can be potentially applied in the preservation and non-destructive extraction of DNA from specimens of various species. Following sample collection, a bulk environmental sample from sediment and seagrass is immediately immersed in DESS in the field. Subsequently, DNA is extracted from the supernatant solution, allowing non-destructive DNA barcoding. Overall, this paper presents comprehensive protocols for DNA extraction from DESS supernatants and demonstrates their practical application using meiofauna (small animals) and diatoms as examples.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934454","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}

{"title":"Optimising future rhino population management strategies using insights from genetic health assessments across India","authors":"Tista Ghosh, Parikshit Kakati, Amit Sharma, Samrat Mondol","doi":"10.1101/2024.08.09.607316","DOIUrl":"https://doi.org/10.1101/2024.08.09.607316","url":null,"abstract":"Various species conservation paradigms are facing enormous challenges during the ongoing Anthropocene. While the widely-used reintroduction/translocation-based approaches have supported many endangered species population recoveries, they seldom use detailed genetic information during initial planning. The Indian greater one-horned rhino typifies such assisted migration-driven species recovery, but currently facing long-term survival concerns due to their mostly small, isolated populations reaching respective carrying capacities. We assessed nation-wide rhino genetic health, identified suitable source populations and provided future translocation scenarios for all extant and proposed rhino habitats. Analyses with 504 unique rhino genotypes across all seven Indian rhino-bearing parks revealed six genetically-isolated populations with overall moderately low genetic diversity. Our results showed that Kaziranga and Manas NPs (Assam) to have the best rhino genetic health, whereas Jaldapara and Gorumara NPs (West Bengal) undergoing strong genetic erosions. Forward genetic simulations suggested that annual supplementation efforts from only few Assam rhino populations (Kaziranga NP, Orang NP and Pobitora WLS) are best suited for genetic rescue of most of the extant populations. Overall, the genetic diversity and differentiation patterns mimics the complex evolutionary history and individual recovery histories. We suggest park-specific management solutions (ranging from protection measures, grassland restoration, livestock and conflict management, regular supplementation events etc.) to ensure the species long-term persistence and prevent the alarming loss of grassland habitats and its associated biodiversity. We insist on utilising such genetic health indices-driven population management solutions to identify targeted mitigative measures in other species.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934456","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}

{"title":"Whole genome sequence improvement with pedigree information and reference genotypic profiles, demonstrated in outcrossing apple","authors":"Stijn Vanderzande, Cameron Peace, Eric van de Weg","doi":"10.1101/2024.08.08.607141","DOIUrl":"https://doi.org/10.1101/2024.08.08.607141","url":null,"abstract":"Understanding the quality of a whole genome sequence (WGS) is important for its further use. Most WGS quality evaluations are based on bioinformatic quality metrics such as the N50 score, BUSCO score, and number of contigs and scaffolds present, yet genetic information considering principles of inheritance could be used to evaluate and improve assembly and phasing. Furthermore, WGS and genome resequencing data of related individuals could provide useful information when large chromosomal segments are shared with the target individual through common ancestry. Here, we show how high-quality, phased, genome-wide genotypic information is useful to evaluate the quality of a WGS. We provide an R-tool to routinely conduct such quality evaluations. The script also provides a method to accurately determine the WGS positions of reference SNP markers, which is needed for integration of SNP array-based genotypic data sets with WGS data, and the identification and comparison of segments across WGSs that are shared by descent. Finally, we provide suggestions on how such sharing can be used to evaluate and improve new WGSs. The approach is demonstrated in apple, for which improvements in WGS quality are evident from the first collapsed WGS with many inconsistencies in genetic marker order and genotype scores, through well-assembled haploid WGSs, to incorrectly and correctly phased diploid WGSs. This study shows that homozygous regions might need extra attention in phased WGSs and that further improvements to phased WGSs can be achieved by grouping chromosomes of single parental origin into the same haplome.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934457","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}

{"title":"A newly evolved gene is essential for efficient sperm entry into eggs in Drosophila melanogaster","authors":"Sara Y Guay, Prajal H Patel, Jonathon M Thomalla, Kerry L McDermott, Jillian M O'Toole, Sarah E Arnold, Sarah J Obrycki, Mariana F Wolfner, Geoffrey D Findlay","doi":"10.1101/2024.08.08.607187","DOIUrl":"https://doi.org/10.1101/2024.08.08.607187","url":null,"abstract":"New genes arise through a variety of evolutionary processes and provide raw material for adaptation in the face of both natural and sexual selection. <em>De novo</em> evolved genes emerge from previously non-protein-coding DNA sequences, and many such genes are expressed in male reproductive structures. In <em>Drosophila melanogaster</em>, several putative <em>de novo</em> genes have evolved essential roles in spermatogenesis, but whether such genes can also impact sperm function beyond the male has not been investigated. We identified a putative <em>de novo</em> gene, <em>katherine johnson</em> (<em>kj</em>), that is required for high levels of male fertility. Males that do not express <em>kj</em> produce and transfer sperm that are stored normally in females, but sperm from these males enter eggs with severely reduced efficiency. Using a tagged transgenic rescue construct, we observed that KJ protein localizes to the nuclear periphery in various stages of spermatogenesis, but is not detectable in mature sperm. These data suggest that <em>kj</em> exerts an effect on sperm development, the loss of which results in reduced fertilization ability. While previous bioinformatic analyses suggested the <em>kj</em> gene was restricted to the <em>melanogaster</em> group of <em>Drosophila</em>, we identified putative orthologs with conserved synteny, male-biased expression, and predicted protein features across the genus, as well as instances of gene loss in some lineages. Thus, <em>kj</em> potentially arose in the <em>Drosophila</em> common ancestor and subsequently evolved an essential role in <em>D. melanogaster</em>. Our results demonstrate a new aspect of male reproduction that has been shaped by new gene evolution and provide a molecular foothold for further investigating the mechanism of sperm entry into eggs in <em>Drosophila</em>.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934459","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}

{"title":"Drosophila ring chromosomes interact with sisters and homologs to produce anaphase bridges in mitosis.","authors":"Ho-Chen Lin, Mary M Golic, Hunter J Hill, Katherine F Lemons, Truc T Vuong, Madison Smith, Forrest T Golic, Kent G Golic","doi":"10.1101/2024.08.08.607186","DOIUrl":"https://doi.org/10.1101/2024.08.08.607186","url":null,"abstract":"Ring chromosomes are known in many eukaryotic organisms, including humans. They are typically associated with a variety of maladies, including abnormal development and lethality. Underlying these phenotypes are anaphase chromatin bridges that can lead to chromosome loss, nondisjunction and breakage. By cytological examination of ring chromosomes in Drosophila melanogaster we identified five causes for anaphase bridges produced by ring chromosomes. Catenation of sister chromatids is the most common cause and these bridges frequently resolve during anaphase, presumably by the action of topoisomerase II. Sister chromatid exchange and chromosome breakage followed by sister chromatid union also produce anaphase bridges. Mitotic recombination with the homolog was rare, but was another route to generation of anaphase bridges. Most surprising, was the discovery of homolog capture, where the ring chromosome was connected to its linear homolog in anaphase. We hypothesize that this is a remnant of mitotic pairing and that the linear chromosome is connected to the ring by multiple wraps produced through the action of topoisomerase II during establishment of homolog pairing. In support, we showed that in a ring/ring homozygote the two rings are frequently catenated in mitotic metaphase, a configuration that requires breaking and rejoining of at least one chromosome.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934458","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}

{"title":"Epigenetic heterogeneity shapes the transcriptional landscape of regional microglia","authors":"Alexander Ve Margetts, Samara Jo Vilca, Florence Bourgain-Guglielmetti, Luis Miguel Tuesta","doi":"10.1101/2024.08.08.607229","DOIUrl":"https://doi.org/10.1101/2024.08.08.607229","url":null,"abstract":"Microglia, the innate immune cells in the central nervous system, exhibit distinct transcriptional profiles across brain regions that are important for facilitating their specialized function. There has been recent interest in identifying the epigenetic modifications associated with these distinct transcriptional profiles, as these may improve our understanding of the underlying mechanisms governing the functional specialization of microglia. One obstacle to achieving this goal is the large number of microglia required to obtain a genome-wide profile for a single histone modification. Given the cellular and regional heterogeneity of the brain, this would require pooling many samples which would impede biological applications that are limited by numbers of available animals. To overcome this obstacle, we have adapted a method of chromatin profiling known as Cleavage Under Targets and Tagmentation (CUT&amp;Tag-Direct) to profile histone modifications associated with regional differences in gene expression throughout the brain reward system. Consistent with previous studies, we find that transcriptional profiles of microglia vary by brain region. However, here we report that these regional differences also exhibit transcriptional network signatures specific to each region. Additionally, we find that these region-dependent network signatures are associated with differential deposition of H3K27ac and H3K7me3, and while the H3K27me3 landscape is remarkably stable across brain regions, the H3K27ac landscape is most consistent with the anatomical location of microglia which explain their distinct transcriptional profiles. Altogether, these findings underscore the established role of H3K27me3 in cell fate determination and support the active role of H3K27ac in the dynamic regulation of microglial gene expression. In this study, we report a molecular and computational framework that can be applied to improve our understanding of the role of epigenetic regulation in microglia in both health and disease, using as few as 2,500 cells per histone mark.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934460","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}

{"title":"Genetic estimates and genome-wide association studies of antibody response in Tanzanian dairy cattle","authors":"Luis E Hernandez-Castro, Elizabeth Anne Jessie Cook, Oswald Matika, Isaac Joseph Mengele, Shabani Kiyabo Motto, Shedrack Festo Bwatota, Bibiana Zirra-Shallangwa, Ricardo Pong-Wong, James Prendergast, Raphael Mrode, Philip G. Toye, Daniel Mushumbusi Komwihangilo, Eliamoni Lyatuu, Benedict E. Karani, Getrude Nangekhe, Okeyo Ally Mwai, Gabriel Mkilema Shirima, Barend Mark de Clare Bronsvoort","doi":"10.1101/2024.08.05.606566","DOIUrl":"https://doi.org/10.1101/2024.08.05.606566","url":null,"abstract":"Identifying the genetic determinants of host defence against infectious pathogens is central to enhancing disease resilience and therapeutic efficacy in livestock. Here we have taken a genome-wide association approach to identify genetic variants associated with the presence of serological markers for important infectious diseases affecting dairy cattle in smallholder farms. Assessing 668,911 single-nucleotide polymorphisms in 1977 crossbreed cattle sampled from six regions of Tanzania, we identified high levels of interregional admixture and European introgression which may increase infectious disease susceptibility relative to indigenous breeds. Heritability estimates ranged from 0.03 (SE ± 0.06) to 0.44 (SE ± 0.07) depending on the pathogen assayed. Preliminary genome scans revealed several loci associated with seropositivity to the viral diseases Rift Valley fever and bovine viral diarrhoea, the protozoan parasites <em>Neospora caninum</em> and <em>Toxoplasma gondii</em>, and the bacterial pathogens <em>Brucella sp, Leptospira hardjo</em> and <em>Coxiella burnetti</em>. The associated loci mapped to genes involved in immune defence, tumour suppression, neurological processes, and cell exocytosis. We discuss future work to clarify the cellular pathways contributing to general and taxon-specific infection responses and to advance selective breeding and therapeutic target designs.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934541","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}

{"title":"Using phylogenetic summary statistics for epidemiological inference","authors":"Rafael C. Núñez, Gregory R. Hart, Michael Famulare, Christopher Lorton, Joshua T. Herbeck","doi":"10.1101/2024.08.07.607080","DOIUrl":"https://doi.org/10.1101/2024.08.07.607080","url":null,"abstract":"Since the coining of the term phylodynamics, the use of phylogenies to understand infectious disease dynamics has steadily increased. As methods for phylodynamics and genomic epidemiology have proliferated and grown more computationally expensive, the epidemiological information they extract has also evolved to better complement what can be learned through traditional epidemiological data. However, for genomic epidemiology to continue to grow, and for the accumulating number of pathogen genetic sequences to fulfill their potential widespread utility, the extraction of epidemiological information from phylogenies needs to be simpler and more efficient. Summary statistics provide a straightforward way of extracting information from a phylogenetic tree, but the relationship between these statistics and epidemiological quantities needs to be better understood. In this work we address this need via simulation. Using two different benchmark scenarios, we evaluate 74 tree summary statistics and their relationship to epidemiological quantities. In addition to evaluating the epidemiological information that can be inferred from each summary statistic, we also assess the computational cost of each statistic. This helps us optimize the selection of summary statistics for specific applications. Our study offers guidelines on essential considerations for designing or choosing summary statistics. The evaluated set of summary statistics, along with additional helpful functions for phylogenetic analysis, is accessible through an open-source Python library. Our research not only illuminates the main characteristics of many tree summary statistics but also provides valuable computational tools for real-world epidemiological analyses. These contributions aim to enhance our understanding of disease spread dynamics and advance the broader utilization of genomic epidemiology in public health efforts.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934547","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}

{"title":"Improved vectors for retron-mediated CRISPR-Cas9 genome editing in Saccharomyces cerevisiae","authors":"Tara N. Stuecker, Stephanie E. Hood, Julio Molina Pineda, Sonali Lenaduwe, Joshua Winter, Meru J. Sadhu, Jeffrey A. Lewis","doi":"10.1101/2024.08.06.606807","DOIUrl":"https://doi.org/10.1101/2024.08.06.606807","url":null,"abstract":"<em>In vivo</em> site-directed mutagenesis is a powerful genetic tool for testing the effects of specific alleles in their normal genomic context. While the budding yeast <em>Saccharomyces cerevisiae</em> possesses classical tools for site-directed mutagenesis, more efficient recent CRISPR-based approaches use Cas ‘cutting’ combined with homologous recombination of a ‘repair’ template that introduces the desired edit. However, current approaches are limited for fully prototrophic yeast strains, and rely on relatively low efficiency cloning of short gRNAs. We were thus motivated to simplify the process by combining the gRNA and its cognate repair template in <em>cis</em> on a single oligonucleotide. Moreover, we wished to take advantage of a new approach that uses an <em>E. coli</em> retron (EcRT) to amplify repair templates as multi-copy single-stranded (ms)DNA <em>in vivo</em>, which are more efficient templates for homologous recombination. To this end, we have created a set of plasmids that express Cas9-EcRT, allowing for co-transformation with the gRNA-repair template plasmid in a single step. Our suite of plasmids contains different antibiotic (Nat, Hyg, Kan) or auxotrophic (<em>HIS3, URA3</em>) selectable markers, allowing for editing of fully prototrophic wild yeast strains. In addition to classic galactose induction, we generated a β-estradiol-inducible version of each plasmid to facilitate editing in yeast strains that grow poorly on galactose. The plasmid-based system results in &gt;95% editing efficiencies for point mutations and &gt;50% efficiencies for markerless deletions, in a minimum number of steps and time. We provide a detailed step-by-step guide for how to use this system.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141934543","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}