Genome Biology最新文献_第3页

STASCAN deciphers fine-resolution cell distribution maps in spatial transcriptomics by deep learning STASCAN 通过深度学习解译空间转录组学中的精细分辨率细胞分布图

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-22 DOI: 10.1186/s13059-024-03421-5

Ying Wu, Jia-Yi Zhou, Bofei Yao, Guanshen Cui, Yong-Liang Zhao, Chun-Chun Gao, Ying Yang, Shihua Zhang, Yun-Gui Yang

引用次数: 0

A comprehensive study of genetic regulation and disease associations of plasma circulatory microRNAs using population-level data 利用人群水平数据对血浆循环微RNA的遗传调控和疾病相关性进行综合研究

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-21 DOI: 10.1186/s13059-024-03420-6

Rima Mustafa, Michelle M. J. Mens, Arno van Hilten, Jian Huang, Gennady Roshchupkin, Tianxiao Huan, Linda Broer, Joyce B. J. van Meurs, Paul Elliott, Daniel Levy, M. Arfan Ikram, Marina Evangelou, Abbas Dehghan, Mohsen Ghanbari

{"title":"A comprehensive study of genetic regulation and disease associations of plasma circulatory microRNAs using population-level data","authors":"Rima Mustafa, Michelle M. J. Mens, Arno van Hilten, Jian Huang, Gennady Roshchupkin, Tianxiao Huan, Linda Broer, Joyce B. J. van Meurs, Paul Elliott, Daniel Levy, M. Arfan Ikram, Marina Evangelou, Abbas Dehghan, Mohsen Ghanbari","doi":"10.1186/s13059-024-03420-6","DOIUrl":"https://doi.org/10.1186/s13059-024-03420-6","url":null,"abstract":"MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression. Perturbations in plasma miRNA levels are known to impact disease risk and have potential as disease biomarkers. Exploring the genetic regulation of miRNAs may yield new insights into their important role in governing gene expression and disease mechanisms. We present genome-wide association studies of 2083 plasma circulating miRNAs in 2178 participants of the Rotterdam Study to identify miRNA-expression quantitative trait loci (miR-eQTLs). We identify 3292 associations between 1289 SNPs and 63 miRNAs, of which 65% are replicated in two independent cohorts. We demonstrate that plasma miR-eQTLs co-localise with gene expression, protein, and metabolite-QTLs, which help in identifying miRNA-regulated pathways. We investigate consequences of alteration in circulating miRNA levels on a wide range of clinical conditions in phenome-wide association studies and Mendelian randomisation using the UK Biobank data (N = 423,419), revealing the pleiotropic and causal effects of several miRNAs on various clinical conditions. In the Mendelian randomisation analysis, we find a protective causal effect of miR-1908-5p on the risk of benign colon neoplasm and show that this effect is independent of its host gene (FADS1). This study enriches our understanding of the genetic architecture of plasma miRNAs and explores the signatures of miRNAs across a wide range of clinical conditions. The integration of population-based genomics, other omics layers, and clinical data presents opportunities to unravel potential clinical significance of miRNAs and provides tools for novel miRNA-based therapeutic target discovery.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"33 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142452047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Mapping lineage-traced cells across time points with moslin 用 moslin 绘制跨时间点的系谱追踪细胞图

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-21 DOI: 10.1186/s13059-024-03422-4

Marius Lange, Zoe Piran, Michal Klein, Bastiaan Spanjaard, Dominik Klein, Jan Philipp Junker, Fabian J. Theis, Mor Nitzan

引用次数: 0

Scalable identification of lineage-specific gene regulatory networks from metacells with NetID 利用 NetID 从元细胞中可扩展地识别特定世系的基因调控网络

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-18 DOI: 10.1186/s13059-024-03418-0

Weixu Wang, Yichen Wang, Ruiqi Lyu, Dominic Grün

引用次数: 0

MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge MHConstructor：针对 MHC 组装难题的高通量、单体型信息解决方案

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-17 DOI: 10.1186/s13059-024-03412-6

Kristen J. Wade, Rayo Suseno, Kerry Kizer, Jacqueline Williams, Juliano Boquett, Stacy Caillier, Nicholas R. Pollock, Adam Renschen, Adam Santaniello, Jorge R. Oksenberg, Paul J. Norman, Danillo G. Augusto, Jill A. Hollenbach

引用次数: 0

HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data HBI：从细胞分选的亚硫酸氢盐测序数据中结合先验估计细胞特异性甲基化数量性状位点的分层贝叶斯交互模型

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-15 DOI: 10.1186/s13059-024-03411-7

Youshu Cheng, Biao Cai, Hongyu Li, Xinyu Zhang, Gypsyamber D’Souza, Sadeep Shrestha, Andrew Edmonds, Jacquelyn Meyers, Margaret Fischl, Seble Kassaye, Kathryn Anastos, Mardge Cohen, Bradley E. Aouizerat, Ke Xu, Hongyu Zhao

引用次数: 0

Multi-omics reveals lactylation-driven regulatory mechanisms promoting tumor progression in oral squamous cell carcinoma 多组学揭示促进口腔鳞状细胞癌肿瘤进展的乳化驱动调控机制

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-15 DOI: 10.1186/s13059-024-03383-8

Fengyang Jing, Lijing Zhu, Jianyun Zhang, Xuan Zhou, Jiaying Bai, Xuefen Li, Heyu Zhang, Tiejun Li

{"title":"Multi-omics reveals lactylation-driven regulatory mechanisms promoting tumor progression in oral squamous cell carcinoma","authors":"Fengyang Jing, Lijing Zhu, Jianyun Zhang, Xuan Zhou, Jiaying Bai, Xuefen Li, Heyu Zhang, Tiejun Li","doi":"10.1186/s13059-024-03383-8","DOIUrl":"https://doi.org/10.1186/s13059-024-03383-8","url":null,"abstract":"Lactylation, a post-translational modification, is increasingly recognized for its role in cancer progression. This study investigates its prevalence and impact in oral squamous cell carcinoma (OSCC). Immunohistochemical staining of 81 OSCC cases shows lactylation levels correlate with malignancy grading. Proteomic analyses of six OSCC tissue pairs reveal 2765 lactylation sites on 1033 proteins, highlighting its extensive presence. These modifications influence metabolic processes, molecular synthesis, and transport. CAL27 cells are subjected to cleavage under targets and tagmentation assay for accessible-chromatin with high-throughput sequencing, and transcriptomic sequencing pre- and post-lactate treatment, with 217 genes upregulated due to lactylation. Chromatin immunoprecipitation-quantitative PCR and real-time fluorescence quantitative PCR confirm the regulatory role of lactylation at the K146 site of dexh-box helicase 9 (DHX9), a key factor in OSCC progression. CCK8, colony formation, scratch healing, and Transwell assays demonstrate that lactylation mitigates the inhibitory effect of DHX9 on OSCC, thereby promoting its occurrence and development. Lactylation actively modulates gene expression in OSCC, with significant effects on chromatin structure and cellular processes. This study provides a foundation for developing targeted therapies against OSCC, leveraging the role of lactylation in disease pathogenesis.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"4 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142440205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

zMAP toolset: model-based analysis of large-scale proteomic data via a variance stabilizing z-transformation zMAP工具集：通过方差稳定z变换对大规模蛋白质组数据进行基于模型的分析

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-14 DOI: 10.1186/s13059-024-03382-9

Xiuqi Gui, Jing Huang, Linjie Ruan, Yanjun Wu, Xuan Guo, Ruifang Cao, Shuhan Zhou, Fengxiang Tan, Hongwen Zhu, Mushan Li, Guoqing Zhang, Hu Zhou, Lixing Zhan, Xin Liu, Shiqi Tu, Zhen Shao

引用次数: 0

The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation 酵母核糖体图谱揭示了普遍翻译的高度多样性

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-14 DOI: 10.1186/s13059-024-03403-7

Chris Papadopoulos, Hugo Arbes, David Cornu, Nicolas Chevrollier, Sandra Blanchet, Paul Roginski, Camille Rabier, Safiya Atia, Olivier Lespinet, Olivier Namy, Anne Lopes

{"title":"The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation","authors":"Chris Papadopoulos, Hugo Arbes, David Cornu, Nicolas Chevrollier, Sandra Blanchet, Paul Roginski, Camille Rabier, Safiya Atia, Olivier Lespinet, Olivier Namy, Anne Lopes","doi":"10.1186/s13059-024-03403-7","DOIUrl":"https://doi.org/10.1186/s13059-024-03403-7","url":null,"abstract":"Pervasive translation is a widespread phenomenon that plays a critical role in the emergence of novel microproteins, but the diversity of translation patterns contributing to their generation remains unclear. Based on 54 ribosome profiling (Ribo-Seq) datasets, we investigated the yeast Ribo-Seq landscape using a representation framework that allows the comprehensive inventory and classification of the entire diversity of Ribo-Seq signals, including non-canonical ones. We show that if coding regions occupy specific areas of the Ribo-Seq landscape, noncoding regions encompass a wide diversity of Ribo-Seq signals and, conversely, populate the entire landscape. Our results show that pervasive translation can, nevertheless, be associated with high specificity, with 1055 noncoding ORFs exhibiting canonical Ribo-Seq signals. Using mass spectrometry under standard conditions or proteasome inhibition with an in-house analysis protocol, we report 239 microproteins originating from noncoding ORFs that display canonical but also non-canonical Ribo-Seq signals. Each condition yields dozens of additional microprotein candidates with comparable translation properties, suggesting a larger population of volatile microproteins that are challenging to detect. Our findings suggest that non-canonical translation signals may harbor valuable information and underscore the significance of considering them in proteogenomic studies. Finally, we show that the translation outcome of a noncoding ORF is primarily determined by the initiating codon and the codon distribution in its two alternative frames, rather than features indicative of functionality. Our results enable us to propose a topology of a species’ Ribo-Seq landscape, opening the way to comparative analyses of this translation landscape under different conditions.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"123 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142431675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

scCTS: identifying the cell type-specific marker genes from population-level single-cell RNA-seq scCTS：从群体级单细胞 RNA-seq 中识别细胞类型特异性标记基因

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-14 DOI: 10.1186/s13059-024-03410-8

Luxiao Chen, Zhenxing Guo, Tao Deng, Hao Wu

引用次数: 0