bioRxiv - Genomics最新文献_第2页

Transcriptomic and multi-scale network analyses reveal key drivers of cardiovascular disease 转录组和多尺度网络分析揭示心血管疾病的关键驱动因素

bioRxiv - Genomics Pub Date : 2024-09-16 DOI: 10.1101/2024.09.11.612437

Bat-Ider Tumenbayar, Khanh Pham, John C Biber, Rhonda Drewes, Yongho Bae

{"title":"Transcriptomic and multi-scale network analyses reveal key drivers of cardiovascular disease","authors":"Bat-Ider Tumenbayar, Khanh Pham, John C Biber, Rhonda Drewes, Yongho Bae","doi":"10.1101/2024.09.11.612437","DOIUrl":"https://doi.org/10.1101/2024.09.11.612437","url":null,"abstract":"Cardiovascular diseases (CVDs) and pathologies are often driven by changes in molecular signaling and communication, as well as in cellular and tissue components, particularly those involving the extracellular matrix (ECM), cytoskeleton, and immune response. The fine-wire vascular injury model is commonly used to study neointimal hyperplasia and vessel stiffening, but it is not typically considered a model for CVDs. In this paper, we hypothesize that vascular injury induces changes in gene expression, molecular communication, and biological processes similar to those observed in CVDs at both the transcriptome and protein levels. To investigate this, we analyzed gene expression in microarray datasets from injured and uninjured femoral arteries in mice two weeks post-injury, identifying 1,467 significantly and differentially expressed genes involved in several CVDs such as including vaso-occlusion, arrhythmia, and atherosclerosis. We further constructed a protein-protein interaction network with seven functionally distinct clusters, with notable enrichment in ECM, metabolic processes, actin-based process, and immune response. Significant molecular communications were observed between the clusters, most prominently among those involved in ECM and cytoskeleton organizations, inflammation, and cell cycle. Machine Learning Disease pathway analysis revealed that vascular injury-induced crosstalk between ECM remodeling and immune response clusters contributed to aortic aneurysm, neovascularization of choroid, and kidney failure. Additionally, we found that interactions between ECM and actin cytoskeletal reorganization clusters were linked to cardiac damage, carotid artery occlusion, and cardiac lesions. Overall, through multi-scale bioinformatic analyses, we demonstrated the robustness of the vascular injury model in eliciting transcriptomic and molecular network changes associated with CVDs, highlighting its potential for use in cardiovascular research.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"32 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260812","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}

引用次数: 0

Pervasive Induction of Regulatory Mutation Microclones in Sun-exposed Skin 暴露于阳光下的皮肤普遍诱导调节突变微克隆

bioRxiv - Genomics Pub Date : 2024-09-16 DOI: 10.1101/2024.09.12.612526

Vijay Menon, Alejandro Garcia-Ruiz, Susan Neveu, Brenda Cartmel, Leah M Ferrucci, Meg Palmatier, Christine Ko, Kenneth Y Tsai, Mio Nakamura, Sa Rang Kim, Michael Girardi, Karl Kornacker, Douglas Brash

{"title":"Pervasive Induction of Regulatory Mutation Microclones in Sun-exposed Skin","authors":"Vijay Menon, Alejandro Garcia-Ruiz, Susan Neveu, Brenda Cartmel, Leah M Ferrucci, Meg Palmatier, Christine Ko, Kenneth Y Tsai, Mio Nakamura, Sa Rang Kim, Michael Girardi, Karl Kornacker, Douglas Brash","doi":"10.1101/2024.09.12.612526","DOIUrl":"https://doi.org/10.1101/2024.09.12.612526","url":null,"abstract":"Carcinogen-induced mutations are thought near-random, with rare cancer-driver mutations underlying clonal expansion. Using high-fidelity Duplex Sequencing to reach a mutation frequency sensitivity of 4x10-9 per nt, we report that sun exposure creates pervasive mutations at sites with ~100-fold UV-sensitivity in RNA-processing gene promoters-cyclobutane pyrimidine dimer (CPD) hyperhotspots-and these mutations have a mini-driver clonal expansion phenotype. Numerically, human skin harbored 10-fold more genuine mutations than previously reported, with neonatal skin containing 90,000 per cell; UV signature mutations increased 8,000-fold in sun-exposed skin, averaging 3x10-5 per nt. Clonal expansion by neutral drift or passenger formation was nil. Tumor suppressor gene hotspots reached variant allele frequency 0.1-10% via 30-3,000 fold clonal expansion, in occasional biopsies. CPD hyperhotspots reached those frequencies in every biopsy, with modest clonal expansion. In vitro, tumor hotspot mutations arose occasionally over weeks of chronic low-dose exposure, whereas CPD hyperhotspot mutations arose in days at 1000-fold higher frequencies, growing exponentially. UV targeted mini-drivers in every skin cell.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260809","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}

引用次数: 0

Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm 通过有丝分裂染色体或细胞质遗传的不同折叠程序规定了染色体间期的构象

bioRxiv - Genomics Pub Date : 2024-09-16 DOI: 10.1101/2024.09.16.613305

Allana Schooley, Sergey V Venev, Vasilisa Aksenova, Emily Navarrete, Mary Dasso, Job Dekker

{"title":"Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm","authors":"Allana Schooley, Sergey V Venev, Vasilisa Aksenova, Emily Navarrete, Mary Dasso, Job Dekker","doi":"10.1101/2024.09.16.613305","DOIUrl":"https://doi.org/10.1101/2024.09.16.613305","url":null,"abstract":"Identity-specific interphase chromosome conformation must be re-established each time a cell divides. To understand how interphase folding is inherited, we developed an experimental approach that physically segregates mediators of G1 folding that are intrinsic to mitotic chromosomes from cytoplasmic factors. Proteins essential for nuclear transport, RanGAP1 and Nup93, were degraded in pro-metaphase arrested DLD-1 cells to prevent the establishment of nucleo-cytoplasmic transport during mitotic exit and isolate the decondensing mitotic chromatin of G1 daughter cells from the cytoplasm. Using this approach, we discover a transient folding intermediate entirely driven by chromosome-intrinsic factors. In addition to conventional compartmental segregation, this chromosome-intrinsic folding program leads to prominent genome-scale microcompartmentalization of mitotically bookmarked and cell type-specific cis-regulatory elements. This microcompartment conformation is formed during telophase and subsequently modulated by a second folding program driven by factors inherited through the cytoplasm in G1. This nuclear import-dependent folding program includes cohesin and factors involved in transcription and RNA processing. The combined and inter-dependent action of chromosome-intrinsic and cytoplasmic inherited folding programs determines the interphase chromatin conformation as cells exit mitosis.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"29 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260810","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}

引用次数: 0

Towards large-scale museomics projects: a cost-effective and high-throughput extraction method for obtaining historical DNA from museum insect specimens 迈向大规模博物馆组学项目：从博物馆昆虫标本中获取历史 DNA 的高性价比高通量提取方法

bioRxiv - Genomics Pub Date : 2024-09-16 DOI: 10.1101/2024.09.11.612573

Anna J Holmquist, Holly Tavris, Grace Kim, Lauren A Esposito, Brian L Fisher, Athena Lam

{"title":"Towards large-scale museomics projects: a cost-effective and high-throughput extraction method for obtaining historical DNA from museum insect specimens","authors":"Anna J Holmquist, Holly Tavris, Grace Kim, Lauren A Esposito, Brian L Fisher, Athena Lam","doi":"10.1101/2024.09.11.612573","DOIUrl":"https://doi.org/10.1101/2024.09.11.612573","url":null,"abstract":"Natural history collections serve as invaluable repositories of biodiversity data. Large-scale genomic analysis would greatly expand the utility and accessibility of museum collections but the high cost and time-intensive nature of genomic methods limit such projects, particularly for invertebrate specimens. This paper presents an innovative, cost-effective and high-throughput approach to extracting genomic DNA from diverse insect specimens using single-phase reverse immobilization (SPRI) beads. We optimized PEG-8000 and NaCl concentrations to balance DNA yield and purity, reducing reagent cost to 6-11 cents per sample. Our method was validated against three widely used extraction protocols, and showed comparable DNA yield and amplification success to the widely used Qiagen DNeasy kit. We successfully applied the protocol in a high-throughput manner, extracting DNA from 3,786 insect specimens across a broad range of ages, taxonomies, and tissue types. A detailed protocol is provided to facilitate the adoption of the method by other researchers. By improving one of the most crucial steps in any molecular project, this SPRI bead-based DNA extraction approach has significant potential for enabling large-scale museomics projects, thereby increasing the utility of historical collections for biodiversity research and conservation efforts.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"85 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260811","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}

引用次数: 0

Subcellular Level Spatial Transcriptomics with PHOTON 利用 PHOTON 进行亚细胞级空间转录组学研究

bioRxiv - Genomics Pub Date : 2024-09-14 DOI: 10.1101/2024.09.10.612328

Shreya Rajachandran, Qianlan Xu, Qiqi Cao, Xin Zhang, Fei Chen, Sarah M. Mangiameli, Haiqi Chen

引用次数: 0

DiatOmicBase, a gene-centered platform to mine functional omics data across diatom genomes DiatOmicBase 是一个以基因为中心的平台，用于挖掘硅藻基因组中的功能性 omics 数据

bioRxiv - Genomics Pub Date : 2024-09-14 DOI: 10.1101/2024.09.12.612655

Emilie Villar, Nathanael Zweig, Pierre Vincens, Helena Cruz de Carvalho, Carole Duchene, Shun Liu, Raphael Monteil, Richard G Dorrell, Michele Fabris, Klaas Vandepoele, Chris Bowler, Angela Falciatore

{"title":"DiatOmicBase, a gene-centered platform to mine functional omics data across diatom genomes","authors":"Emilie Villar, Nathanael Zweig, Pierre Vincens, Helena Cruz de Carvalho, Carole Duchene, Shun Liu, Raphael Monteil, Richard G Dorrell, Michele Fabris, Klaas Vandepoele, Chris Bowler, Angela Falciatore","doi":"10.1101/2024.09.12.612655","DOIUrl":"https://doi.org/10.1101/2024.09.12.612655","url":null,"abstract":"Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology and biotechnology. Since the first genome sequencing in 2008, numerous genome-enabled datasets have been generated, based on RNA-Seq and proteomics, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and two other diatoms to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior-art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non-coding RNAs, and read densities from RNA-Seq experiments. We developed a semi-automatically updated transcriptomic module to explore both publicly available RNA-Seq experiments and users private datasets. Using gene-level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co-expression network analysis. Users can create heatmaps to visualize precomputed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum, we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260815","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}

引用次数: 0

Bone adhered soil as a source of target and environmental DNA and proteins 作为目标和环境 DNA 与蛋白质来源的骨骼附着土壤

bioRxiv - Genomics Pub Date : 2024-09-14 DOI: 10.1101/2024.09.10.611648

Toni de Dios Martinez, Biancamaria Bonucci, Remi Barbieri, Alena Kushniarevich, Eugenia D'Atanasio, Jenna M Dittmar, Craig Cessford, Anu Solnik, John E Robb, Christina Warinner, Ester Oras, Christiana L Scheib

{"title":"Bone adhered soil as a source of target and environmental DNA and proteins","authors":"Toni de Dios Martinez, Biancamaria Bonucci, Remi Barbieri, Alena Kushniarevich, Eugenia D'Atanasio, Jenna M Dittmar, Craig Cessford, Anu Solnik, John E Robb, Christina Warinner, Ester Oras, Christiana L Scheib","doi":"10.1101/2024.09.10.611648","DOIUrl":"https://doi.org/10.1101/2024.09.10.611648","url":null,"abstract":"In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, locations with favourable conditions for ancient DNA (aDNA) preservation in sediments are scarce. In this study we analysed a set of samples obtained from soil adhered to different human skeletal elements, originating from Neolithic to Medieval sites in England, and performed metagenomics and metaproteomics analysis. From them, we were able to recover aDNA sequences matching the genomes of endogenous gut and oral microbiome bacteria. We also found the presence of genetic data corresponding to animals and plants. In particular we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Furthermore, we have also been able to reconstruct a partial human genome. The genetic profile of those human sequences matches the one recovered from the original skeletal element. Our results demonstrate that material usually discarded, as it is soil adhering to human remains, can be used to get a glimpse of the environmental conditions at the time of the death of an individual, even in contexts where due to harsh environmental conditions, the skeletal remains themselves are not preserved.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260819","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}

引用次数: 0

Colora: A Snakemake Workflow for Complete Chromosome-scale De Novo Genome Assembly Colora：用于完整染色体级新基因组组装的 Snakemake 工作流程

bioRxiv - Genomics Pub Date : 2024-09-14 DOI: 10.1101/2024.09.10.612003

Lia Obinu, Timothy Booth, Heleen De Weerd, Urmi Trivedi, Andrea Porceddu

引用次数: 0

Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in Xingjiang 单倍型分辨组装揭示了新疆最古老的葡萄栽培品种（木纳格）的基因组构成

bioRxiv - Genomics Pub Date : 2024-09-14 DOI: 10.1101/2024.09.11.612401

Haixia Zhong, xiaoya Shi, Fuchun Zhang, Xu Wang, vivek yadav, Xiaoming Zhou, shuo Cao, Songlin Zhang, Chuan Zhang, Jiangxia Qiao, Zhongjie Liu, yingchun Zhang, yuting Liu, Hao Wang, hui Xue, Mengyan Zhang, Tian-Hao Zhang, Yongfeng Zhou, Xinyu Wu, Hua Xiao

{"title":"Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in Xingjiang","authors":"Haixia Zhong, xiaoya Shi, Fuchun Zhang, Xu Wang, vivek yadav, Xiaoming Zhou, shuo Cao, Songlin Zhang, Chuan Zhang, Jiangxia Qiao, Zhongjie Liu, yingchun Zhang, yuting Liu, Hao Wang, hui Xue, Mengyan Zhang, Tian-Hao Zhang, Yongfeng Zhou, Xinyu Wu, Hua Xiao","doi":"10.1101/2024.09.11.612401","DOIUrl":"https://doi.org/10.1101/2024.09.11.612401","url":null,"abstract":"Munage, an ancient grape variety that has been cultivated for thousands of years in Xinjiang, China, is recognized for its exceptional fruit traits. There are two main types of Munage: white fruit (WM) and red fruit (RM). However, the lack of a high-quality genomic resources has impeded effective breeding and restricted the potential for expanding these varieties to other growing regions. In this study, we assembled haplotype-resolved genome assemblies for WM and RM, alongside integrated whole genome resequencing (WGS) data and transcriptome data to illuminate specific mutations and associated genes in Munake and the genes associated with fruit color traits. Selective analysis between Munage clones and Eurasian grapes suggested that adaptive selection exists in Munage grapes, with genes enriched in processes including cell maturation, plant epidermal cell differentiation, and root epidermal cell differentiation. The study examined the mutations within Munage grapes and found that the genes PMAT2 on chromosome 12 and MYB123 on chromosome 13 are likely responsible for color variation in RM. These findings provide crucial genetic resources for investigating the genetics of the ancient Chinese grape variety, Munage, and will facilitate the genetic improvement in grapevine.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260814","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}

引用次数: 0

High fidelity genetic markers for sexing Cannabis sativa seedlings 用于大麻幼苗性别鉴定的高保真遗传标记

bioRxiv - Genomics Pub Date : 2024-09-14 DOI: 10.1101/2024.09.10.612257

Djivan Prentout, Salma El Aoudati, Fabienne Mathis, Gabriel Marais, Helene Henri

引用次数: 0