Genome Biology最新文献_第9页

Marsilea: an intuitive generalized paradigm for composable visualizations Marsilea：一个用于组合可视化的直观的通用范例

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-01-06 DOI: 10.1186/s13059-024-03469-3

Yimin Zheng, Zhihang Zheng, André F. Rendeiro, Edwin Cheung

引用次数: 0

Resolving the source of branch length variation in the Y chromosome phylogeny 解决Y染色体系统发育中分支长度变异的来源

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-01-06 DOI: 10.1186/s13059-024-03468-4

Yaniv Swiel, Janet Kelso, Stéphane Peyrégne

{"title":"Resolving the source of branch length variation in the Y chromosome phylogeny","authors":"Yaniv Swiel, Janet Kelso, Stéphane Peyrégne","doi":"10.1186/s13059-024-03468-4","DOIUrl":"https://doi.org/10.1186/s13059-024-03468-4","url":null,"abstract":"Genetic variation in the non-recombining part of the human Y chromosome has provided important insight into the paternal history of human populations. However, a significant and yet unexplained branch length variation of Y chromosome lineages has been observed, notably amongst those that are highly diverged from the human reference Y chromosome. Understanding the origin of this variation, which has previously been attributed to changes in generation time, mutation rate, or efficacy of selection, is important for accurately reconstructing human evolutionary and demographic history. Here, we analyze Y chromosomes from present-day and ancient modern humans, as well as Neandertals, and show that branch length variation amongst human Y chromosomes cannot solely be explained by differences in demographic or biological processes. Instead, reference bias results in mutations being missed on Y chromosomes that are highly diverged from the reference used for alignment. We show that masking fast-evolving, highly divergent regions of the human Y chromosome mitigates the effect of this bias and enables more accurate determination of branch lengths in the Y chromosome phylogeny. We show that our approach allows us to estimate the age of ancient samples from Y chromosome sequence data and provide updated estimates for the time to the most recent common ancestor using the portion of the Y chromosome where the effect of reference bias is minimized.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"12 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142929158","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

SMORE: spatial motifs reveal patterns in cellular architecture of complex tissues SMORE：空间图案揭示了复杂组织的细胞结构模式

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-01-03 DOI: 10.1186/s13059-024-03467-5

Zainalabedin Samadi, Kai Hao, Amjad Askary

引用次数: 0

Spatiotemporal dynamics of early oogenesis in pigs 猪早期卵发生的时空动态

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-01-02 DOI: 10.1186/s13059-024-03464-8

Wei Ge, Yi-Lin Niu, Yu-Kang Li, Li Li, Han Wang, Wen-Wen Li, Tian Qiao, Yan-Ni Feng, Yu-Qing Feng, Jing Liu, Jun-Jie Wang, Xiao-Feng Sun, Shun-Feng Cheng, Lan Li, Wei Shen

{"title":"Spatiotemporal dynamics of early oogenesis in pigs","authors":"Wei Ge, Yi-Lin Niu, Yu-Kang Li, Li Li, Han Wang, Wen-Wen Li, Tian Qiao, Yan-Ni Feng, Yu-Qing Feng, Jing Liu, Jun-Jie Wang, Xiao-Feng Sun, Shun-Feng Cheng, Lan Li, Wei Shen","doi":"10.1186/s13059-024-03464-8","DOIUrl":"https://doi.org/10.1186/s13059-024-03464-8","url":null,"abstract":"In humans and other mammals, the process of oogenesis initiates asynchronously in specific ovarian regions, leading to the localization of dormant and growing follicles in the cortex and medulla, respectively; however, the current understanding of this process remains insufficient. Here, we integrate single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) to comprehend spatial–temporal gene expression profiles and explore the spatial organization of ovarian microenvironments during early oogenesis in pigs. Projection of the germ cell clusters at different stages of oogenesis into the spatial atlas unveils a “cortical to medullary (C-M)” distribution of germ cells in the developing porcine ovaries. Cross-species analysis between pigs and humans unveils a conserved C-M distribution pattern of germ cells during oogenesis, highlighting the utility of pigs as valuable models for studying human oogenesis in a spatial context. RNA velocity analysis with ST identifies the molecular characteristics and spatial dynamics of granulosa cell lineages originating from the cortical and medullary regions in pig ovaries. Spatial co-occurrence analysis and intercellular communication analysis unveils a distinct cell–cell communication pattern between germ cells and somatic cells in the cortex and medulla regions. Notably, in vitro culture of ovarian tissues verifies that intercellular NOTCH signaling and extracellular matrix (ECM) proteins played crucial roles in initiating meiotic and oogenic programs, highlighting an underappreciated role of ovarian microenvironments in orchestrating germ cell fates. Overall, our work provides insight into the spatial characteristics of early oogenesis and the regulatory role of ovarian microenvironments in germ cell fate within a spatial context.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"83 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911551","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

SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells SiCLAT：活细胞中染色质环和活性转录的同时成像

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-01-02 DOI: 10.1186/s13059-024-03463-9

Xin Wan, Jie Kong, Xiaodi Hu, Lulu Liu, Yuanping Yang, Hu Li, Gaoao Liu, Xingchen Niu, Fengling Chen, Dan Zhang, Dahai Zhu, Yong Zhang

引用次数: 0

Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis 启动子捕获Hi-C在拟南芥中鉴定启动子相关环和喷泉结构

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-12-31 DOI: 10.1186/s13059-024-03465-7

Dingyue Wang, Suxin Xiao, Jiayue Shu, Lingxiao Luo, Minqi Yang, Myriam Calonje, Hang He, Baoxing Song, Yue Zhou

{"title":"Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis","authors":"Dingyue Wang, Suxin Xiao, Jiayue Shu, Lingxiao Luo, Minqi Yang, Myriam Calonje, Hang He, Baoxing Song, Yue Zhou","doi":"10.1186/s13059-024-03465-7","DOIUrl":"https://doi.org/10.1186/s13059-024-03465-7","url":null,"abstract":"Promoters serve as key elements in the regulation of gene transcription. In mammals, loop interactions between promoters and enhancers increase the complexity of the promoter-based regulatory networks. However, the identification of enhancer-promoter or promoter-related loops in Arabidopsis remains incomplete. Here, we use promoter capture Hi-C to identify promoter-related loops in Arabidopsis, which shows that gene body, proximal promoter, and intergenic regions can interact with promoters, potentially functioning as distal regulatory elements or enhancers. We find that promoter-related loops mainly repress gene transcription and are associated with ordered chromatin structures, such as topologically associating domains and fountains-chromatin structures not previously identified in Arabidopsis. Cohesin binds to the center of fountains and is involved in their formation. Moreover, fountain strength is positively correlated with the number of promoter-related loops, and the maintenance of these loops is linked to H3K4me3. In atxr3 mutants, which lack the major H3K4me3 methyltransferases in Arabidopsis, the number of promoter-related loops at fountains is reduced, leading to upregulation of fountain-regulated genes. We identify promoter-related loops associated with ordered chromatin structures and reveal the molecular mechanisms involved in fountain formation and maintenance.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"26 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904777","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

Molecular dependencies and genomic consequences of a global DNA damage tolerance defect 全球DNA损伤耐受缺陷的分子依赖性和基因组后果

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-12-31 DOI: 10.1186/s13059-024-03451-z

Daniel de Groot, Aldo Spanjaard, Ronak Shah, Maaike Kreft, Ben Morris, Cor Lieftink, Joyce J. I. Catsman, Shirley Ormel, Matilda Ayidah, Bas Pilzecker, Olimpia Alessandra Buoninfante, Paul C. M. van den Berk, Roderick L. Beijersbergen, Heinz Jacobs

{"title":"Molecular dependencies and genomic consequences of a global DNA damage tolerance defect","authors":"Daniel de Groot, Aldo Spanjaard, Ronak Shah, Maaike Kreft, Ben Morris, Cor Lieftink, Joyce J. I. Catsman, Shirley Ormel, Matilda Ayidah, Bas Pilzecker, Olimpia Alessandra Buoninfante, Paul C. M. van den Berk, Roderick L. Beijersbergen, Heinz Jacobs","doi":"10.1186/s13059-024-03451-z","DOIUrl":"https://doi.org/10.1186/s13059-024-03451-z","url":null,"abstract":"DNA damage tolerance (DDT) enables replication to continue in the presence of fork stalling lesions. In mammalian cells, DDT is regulated by two independent pathways, controlled by the polymerase REV1 and ubiquitinated PCNA, respectively. To determine the molecular and genomic impact of a global DDT defect, we studied PcnaK164R/−;Rev1−/− compound mutants in mouse cells. Double-mutant cells display increased replication stress, hypersensitivity to genotoxic agents, replication speed, and repriming. A whole-genome CRISPR-Cas9 screen revealed a strict reliance of double-mutant cells on the CST complex, where CST promotes fork stability. Whole-genome sequencing indicated that this double-mutant DDT defect favors the generation of large, replication-stress inducible deletions of 0.4–4.0 kbp, defined as type 3 deletions. Junction break sites of these deletions reveal microhomology preferences of 1–2 base pairs, differing from the smaller type 1 and type 2 deletions. These differential characteristics suggest the existence of molecularly distinct deletion pathways. Type 3 deletions are abundant in human tumors, can dominate the deletion landscape, and are associated with DNA damage response status and treatment modality. Our data highlight the essential contribution of the DDT system to genome maintenance and type 3 deletions as mutational signature of replication stress. The unique characteristics of type 3 deletions implicate the existence of a novel deletion pathway in mice and humans that is counteracted by DDT. ","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"35 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142905021","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

vmrseq: probabilistic modeling of single-cell methylation heterogeneity Vmrseq：单细胞甲基化异质性的概率建模

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-12-30 DOI: 10.1186/s13059-024-03457-7

Ning Shen, Keegan Korthauer

引用次数: 0

Chromatin-based memory as a self-stabilizing influence on cell identity 基于染色质的记忆对细胞身份的自稳定影响

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-12-30 DOI: 10.1186/s13059-024-03461-x

Charles C. Bell, Geoffrey J. Faulkner, Omer Gilan

引用次数: 0

Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations 一种检测细胞间相关性的空间染色质可及性模式的方法