Genome Biology最新文献

Cancer gene identification from RNA variant allelic frequencies using RVdriver 利用RVdriver从RNA变异等位基因频率中鉴定癌症基因

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-13 DOI: 10.1186/s13059-025-03557-y

James R. M. Black, Thomas P. Jones, Carlos Martínez-Ruiz, Maria Litovchenko, Clare Puttick, Charles Swanton, Nicholas McGranahan

引用次数: 0

cuteFC: regenotyping structural variants through an accurate and efficient force-calling method cuteFC：通过准确高效的力调用方法对结构变异进行基因分型

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-13 DOI: 10.1186/s13059-025-03642-2

Tao Jiang, Shuqi Cao, Yadong Liu, Zhendong Zhang, Bo Liu, Ruibang Luo, Guohua Wang, Yadong Wang

引用次数: 0

Engineering novel CRISPRi repressors for highly efficient mammalian gene regulation 用于高效哺乳动物基因调控的新型CRISPRi工程阻遏物

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-12 DOI: 10.1186/s13059-025-03640-4

Andrew Kristof, Krithika Karunakaran, Christopher Allen, Paula Mizote, Sophie Briggs, Zixin Jian, Patrick Nash, John Blazeck

{"title":"Engineering novel CRISPRi repressors for highly efficient mammalian gene regulation","authors":"Andrew Kristof, Krithika Karunakaran, Christopher Allen, Paula Mizote, Sophie Briggs, Zixin Jian, Patrick Nash, John Blazeck","doi":"10.1186/s13059-025-03640-4","DOIUrl":"https://doi.org/10.1186/s13059-025-03640-4","url":null,"abstract":"CRISPR interference (CRISPRi), the repurposing of the RNA-guided endonuclease dCas9 as a programmable transcriptional repressor, allows highly specific repression (knockdown) of gene expression. CRISPRi platforms can often have incomplete knockdown, performance variability across cell lines and gene targets, and inconsistencies dependent on the guide RNA sequence employed. Here, we explore the combination of novel repressor domains with strong Krüppel-associated box (KRAB) repressors, screening > 100 bipartite and tripartite fusion proteins for their ability to reduce gene expression as CRISPRi effectors. We show that these novel repressor fusions have reduced dependence on guide RNA sequences, better slow cell growth when used to knock down expression of essential genes, and function in either fusion or scaffold modalities. Furthermore, we isolate and characterize a particularly effective CRISPRi platform, dCas9-ZIM3(KRAB)-MeCP2(t), which shows improved gene repression of endogenous targets both at the transcript and protein level across several cell lines and when deployed in genome-wide screens. We posit that these novel repressor fusions can enhance the reproducibility and utility of CRISPRi in mammalian cells.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"92 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144269172","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

MINGLE: a mutual information-based interpretable framework for automatic cell type annotation in single-cell chromatin accessibility data MINGLE：用于单细胞染色质可及性数据中自动细胞类型注释的基于相互信息的可解释框架

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-11 DOI: 10.1186/s13059-025-03603-9

Siyu Li, Yifan Huang, Shengquan Chen

引用次数: 0

Plasmids, prophages, and defense systems are depleted from plant microbiota genomes 质粒、噬菌体和防御系统从植物微生物群基因组中被耗尽

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-11 DOI: 10.1186/s13059-025-03641-3

Avi Bograd, Yaara Oppenheimer-Shaanan, Asaf Levy

引用次数: 0

Evolutionary dynamics of predicted G-quadruplexes in human and other great apes 人类和其他类人猿预测的g -四肢动物的进化动力学

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-11 DOI: 10.1186/s13059-025-03635-1

Saswat K. Mohanty, Francesca Chiaromonte, Kateryna D. Makova

{"title":"Evolutionary dynamics of predicted G-quadruplexes in human and other great apes","authors":"Saswat K. Mohanty, Francesca Chiaromonte, Kateryna D. Makova","doi":"10.1186/s13059-025-03635-1","DOIUrl":"https://doi.org/10.1186/s13059-025-03635-1","url":null,"abstract":"G-quadruplexes (G4s) are non-canonical DNA structures that can form at approximately 1% of the human genome. They facilitate genomic instability by increasing point mutations and structural variation. Numerous G4s participate in telomere maintenance and regulating transcription and replication, and evolve under purifying selection. Despite these important functions, G4s have remained under-studied in human and ape genomes due to incomplete assemblies. Here, we conduct a comprehensive analysis of predicted G4s (pG4s) in the recently released, telomere-to-telomere (T2T) genomes of human, bonobo, chimpanzee, gorilla, Bornean orangutan, and Sumatran orangutan. We annotate 41,232–174,442 new pG4s in these T2T compared to previous ape genome assemblies (5%–21% increase). Analyzing inter-species whole-genome alignments, we identify pG4s shared across apes (approximately one-third of all pG4s) and thousands of species-specific pG4s. pG4s accumulate and diverge at rates consistent with divergence times between species, following molecular clock. pG4s shared across apes are enriched and hypomethylated at regulatory regions—enhancers, promoters, UTRs, and origins of replication—suggesting their conserved formation and functions. Species-specific pG4s (constituting 11–27% of all pG4s) are located in regulatory regions, potentially contributing to adaptations, and in repeats, likely driving genome expansions. Our findings illuminate the evolutionary dynamics of G4s, conservation of their role in gene regulation, and their contributions to ape genome evolution. Our study highlights the utility of high-resolution T2T genomes in revealing elusive yet likely functionally relevant genomic features previously hidden by incomplete assemblies.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"11 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144260592","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

TORC: Target-Oriented Reference Construction for supervised cell-type identification in scRNA-seq TORC：基于靶标导向的参考构建在scRNA-seq中进行监督细胞类型鉴定

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-10 DOI: 10.1186/s13059-025-03614-6

Xin Wei, Wenjing Ma, Zhijin Wu, Hao Wu

引用次数: 0

A dynamic histone-based chromatin regulatory toolkit underpins genome and developmental evolution in an invertebrate clade 一个动态的基于组蛋白的染色质调控工具包支持基因组和无脊椎动物进化的发育

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-10 DOI: 10.1186/s13059-025-03626-2

Francisco M. Martín-Zamora, Joby Cole, Rory D. Donnellan, Kero Guynes, Allan M. Carrillo-Baltodano, Mark J. Dickman, Paul J. Hurd, José M. Martín-Durán

{"title":"A dynamic histone-based chromatin regulatory toolkit underpins genome and developmental evolution in an invertebrate clade","authors":"Francisco M. Martín-Zamora, Joby Cole, Rory D. Donnellan, Kero Guynes, Allan M. Carrillo-Baltodano, Mark J. Dickman, Paul J. Hurd, José M. Martín-Durán","doi":"10.1186/s13059-025-03626-2","DOIUrl":"https://doi.org/10.1186/s13059-025-03626-2","url":null,"abstract":"The dynamic addition and removal of posttranslational modifications on eukaryotic histones define regulatory regions that play a central role in genome and chromatin biology. However, our understanding of these regulatory mechanisms in animals is primarily based on a few model systems, preventing a general understanding of how histone-based regulation directs and promotes phenotypic variation during animal embryogenesis. Here, we apply a comprehensive multi-omics approach to dissect the histone-based regulatory complement in Annelida, one of the largest invertebrate clades. Annelids exhibit a conserved histone repertoire organized in clusters of dynamically regulated, hyperaccessible chromatin. However, unlike other animals with reduced genomes, the worm Dimorphilus gyrociliatus shows a dramatically streamlined histone repertoire, revealing that genome compaction has lineage-specific effects on histone-based regulation. Notably, the annelid Owenia fusiformis has two H2A.X variants that co-occur in other animals, sometimes associate with fast cell divisions, and represent a unique case of widespread parallel evolution of a histone variant in Eukarya. Histone-modifying enzyme complements are largely conserved among annelids. Yet, temporal differences in the expression of a reduced set of histone modifiers correlate with distinct ontogenetic traits and variation in the adult landscapes of histone posttranslational modifications, as revealed by quantitative mass spectrometry in O. fusiformis and Capitella teleta. Our analysis of histone-based epigenetics within a non-model phylum informs the evolution of histone-based regulation, presenting a framework to explore how this fundamental genome regulatory layer generally contributes to developmental and morphological diversification in annelids and animals.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"586 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144252316","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

spaMGCN: a graph convolutional network with autoencoder for spatial domain identification using multi-scale adaptation 基于自编码器的多尺度空间域识别图卷积网络

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-10 DOI: 10.1186/s13059-025-03637-z

Tianjiao Zhang, Hongfei Zhang, Zhongqian Zhao, Saihong Shao, Yucai Jiang, Xiang Zhang, Guohua Wang

引用次数: 0

Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors SEU-TCA对单细胞和空间转录组学的整合揭示了早期心脏祖细胞的空间起源

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-10 DOI: 10.1186/s13059-025-03633-3

Jingjing He, Yi Yang, Rui Jiang, Yanying Zheng, Xianfa Yang, Xu Jiang, Xin Xue, Zhongzhou Yang, Naihe Jing, Hailong Cao, Zhuojuan Luo, Ke Wei, Peng Xie, Chengqi Lin

引用次数: 0