Genome Biology最新文献_第3页

Medieval genomes from eastern Iberia illuminate the role of Morisco mass deportations in dismantling a long-standing genetic bridge with North Africa 来自伊比利亚东部的中世纪基因组阐明了摩洛哥大规模驱逐在拆除与北非长期存在的基因桥梁中的作用

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-04-28 DOI: 10.1186/s13059-025-03570-1

Gonzalo Oteo-Garcia, Marina Silva, M. George B. Foody, Bobby Yau, Alessandro Fichera, Llorenç Alapont, Pierre Justeau, Simão Rodrigues, Rita Monteiro, Francesca Gandini, María Luisa Rovira Gomar, Albert Ribera i Lacomba, Josep Pascual Beneyto, Valeria Mattiangeli, Daniel G. Bradley, Ceiridwen J. Edwards, Maria Pala, Martin B. Richards

{"title":"Medieval genomes from eastern Iberia illuminate the role of Morisco mass deportations in dismantling a long-standing genetic bridge with North Africa","authors":"Gonzalo Oteo-Garcia, Marina Silva, M. George B. Foody, Bobby Yau, Alessandro Fichera, Llorenç Alapont, Pierre Justeau, Simão Rodrigues, Rita Monteiro, Francesca Gandini, María Luisa Rovira Gomar, Albert Ribera i Lacomba, Josep Pascual Beneyto, Valeria Mattiangeli, Daniel G. Bradley, Ceiridwen J. Edwards, Maria Pala, Martin B. Richards","doi":"10.1186/s13059-025-03570-1","DOIUrl":"https://doi.org/10.1186/s13059-025-03570-1","url":null,"abstract":"The Islamic influence on the Iberian Peninsula left an enduring cultural and linguistic legacy. However, the demographic impact is less well understood. This study aims to explore the dynamics of gene flow and population structure in eastern Iberia from the early to late medieval period through ancient DNA. Our comprehensive genomic analysis uncovers gene flow from various Mediterranean regions into Iberia before the Islamic period, supporting a pre-existing pan-Mediterranean homogenization phenomenon during the Roman Empire. North African ancestry is present but sporadic in late antiquity genomes but becomes consolidated during the Islamic period. We uncover one of the earliest dated Islamic burials in Spain, which shows high levels of consanguinity. For the first time, we also demonstrate the persistence of North African ancestry in a Christian cemetery until the seventeenth century, in addition to evidence of slave trafficking from North Africa. This study reveals the complex interaction between political events and cultural shifts that influenced the population of eastern Iberia. It highlights the existence of a slave trade, underscores the low impact of the Reconquista in the genetic landscape, and shows the lasting impact of post-medieval events, such as the Expulsion of the Moriscos in 1609 CE, on the region’s genetic and cultural landscape, through mass population displacement and replacement.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"31 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143880421","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

Rewiring of SINE-MIR enhancer topology and Esrrb modulation in expanded and naive pluripotency 扩展和初始多能性中sin - mir增强子拓扑和Esrrb调制的重新布线

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-04-28 DOI: 10.1186/s13059-025-03577-8

Nadia Omega Cipta, Yingying Zeng, Ka Wai Wong, Zi Hao Zheng, Yao Yi, Tushar Warrier, Jian Zhou Teo, Jia Hao Jackie Teo, Yee Jiun Kok, Xuezhi Bi, Reshma Taneja, Derrick Sek Tong Ong, Jian Xu, Florent Ginhoux, Hu Li, Yih-Cherng Liou, Yuin-Han Loh

{"title":"Rewiring of SINE-MIR enhancer topology and Esrrb modulation in expanded and naive pluripotency","authors":"Nadia Omega Cipta, Yingying Zeng, Ka Wai Wong, Zi Hao Zheng, Yao Yi, Tushar Warrier, Jian Zhou Teo, Jia Hao Jackie Teo, Yee Jiun Kok, Xuezhi Bi, Reshma Taneja, Derrick Sek Tong Ong, Jian Xu, Florent Ginhoux, Hu Li, Yih-Cherng Liou, Yuin-Han Loh","doi":"10.1186/s13059-025-03577-8","DOIUrl":"https://doi.org/10.1186/s13059-025-03577-8","url":null,"abstract":"The interplay between 3D genomic structure and transposable elements (TE) in regulating cell state-specific gene expression program is largely unknown. Here, we explore the utilization of TE-derived enhancers in naïve and expanded pluripotent states by integrative analysis of genome-wide Hi-C-defined enhancer interactions, H3K27ac HiChIP profiling and CRISPR-guided TE proteomics landscape. We find that short interspersed nuclear elements (SINEs) are the more involved TEs in the active chromatin and 3D genome architecture. In particular, mammalian-wide interspersed repeat (MIR), a SINE family member, is highly associated with naïve-specific genomic interactions compared to the expanded state. Primarily, in the naïve pluripotent state, MIR enhancer is co-opted by ESRRB for naïve-specific gene expression program. This ESRRB and MIR enhancer interaction is crucial for the formation of loops that build a network of enhancers and super-enhancers regulating pluripotency genes. We demonstrate that loss of a ESRRB-bound MIR enhancer impairs self-renewal. We also find that MIR is co-bound by structural protein complex, ESRRB-YY1, in the naïve pluripotent state. Altogether, our study highlights the topological regulation of ESRRB on MIR in the naïve potency state.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"17 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143880422","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

InSituCor: exploring spatially correlated genes conditional on the cell type landscape InSituCor：探索细胞类型景观条件下的空间相关基因

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-04-24 DOI: 10.1186/s13059-025-03554-1

Patrick Danaher, Dan McGuire, Lidan Wu, Michael Patrick, David Kroeppler, Haiyan Zhai, Deniz G. Olgun, Dennis Gong, Jingyi Cao, William L. Hwang, Joachim Schmid, Joseph M. Beechem

引用次数: 0

Variant effect predictor correlation with functional assays is reflective of clinical classification performance 变异效应预测因子与功能分析的相关性反映了临床分类表现

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-04-22 DOI: 10.1186/s13059-025-03575-w

Benjamin J. Livesey, Joseph A. Marsh

{"title":"Variant effect predictor correlation with functional assays is reflective of clinical classification performance","authors":"Benjamin J. Livesey, Joseph A. Marsh","doi":"10.1186/s13059-025-03575-w","DOIUrl":"https://doi.org/10.1186/s13059-025-03575-w","url":null,"abstract":"Understanding the relationship between protein sequence and function is crucial for accurate classification of missense variants. Variant effect predictors (VEPs) play a vital role in deciphering this complex relationship, yet evaluating their performance remains challenging for several reasons, including data circularity, where the same or related data is used for training and assessment. High-throughput experimental strategies like deep mutational scanning (DMS) offer a promising solution. In this study, we extend upon our previous benchmarking approach, assessing the performance of 97 VEPs using missense DMS measurements from 36 different human proteins. In addition, a new pairwise, VEP-centric approach mitigates the impact of missing predictions on overall performance comparison. We observe a strong correspondence between VEP performance in DMS-based benchmarks and clinical variant classification, especially for predictors that have not been directly trained on human clinical variants. Our results suggest that comparing VEP performance against diverse functional assays represents a reliable strategy for assessing their relative performance in clinical variant classification. However, major challenges in clinical interpretation of VEP scores persist, highlighting the need for further research to fully leverage computational predictors for genetic diagnosis. We also address practical considerations for end users in terms of choice of methodology.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"28 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857435","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

Weighted 2D-kernel density estimations provide a new probabilistic measure for epigenetic age 加权二维核密度估计为表观遗传年龄提供了一种新的概率测量方法

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-04-22 DOI: 10.1186/s13059-025-03562-1

Juan-Felipe Perez-Correa, Thomas Stiehl, Riccardo E. Marioni, Janie Corley, Simon R. Cox, Ivan G. Costa, Wolfgang Wagner

引用次数: 0

miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRs miRglmm：异构体水平计数的广义线性混合模型改善了对mirna水平差异表达的估计，并揭示了异构体之间可变的差异表达

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-04-22 DOI: 10.1186/s13059-025-03549-y

Andrea M. Baran, Arun H. Patil, Ernesto Aparicio-Puerta, Seong-Hwan Jun, Marc K. Halushka, Matthew N. McCall

引用次数: 0

Zero-shot evaluation reveals limitations of single-cell foundation models 零射击评估揭示了单细胞基础模型的局限性

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-04-18 DOI: 10.1186/s13059-025-03574-x

Kasia Z. Kedzierska, Lorin Crawford, Ava P. Amini, Alex X. Lu

引用次数: 0

Hmgb2 improves astrocyte to neuron conversion by increasing the chromatin accessibility of genes associated with neuronal maturation in a proneuronal factor-dependent manner Hmgb2通过增加与神经元成熟相关的基因的染色质可及性，以神经元前因子依赖的方式促进星形胶质细胞向神经元的转化

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-04-17 DOI: 10.1186/s13059-025-03556-z

Priya Maddhesiya, Tjasa Lepko, Andrea Steiner-Mezzardi, Julia Schneider, Veronika Schwarz, Juliane Merl-Pham, Finja Berger, Stefanie M. Hauck, Lorenza Ronfani, Marco Bianchi, Tatiana Simon, Anthodesmi Krontira, Giacomo Masserdotti, Magdalena Götz, Jovica Ninkovic

{"title":"Hmgb2 improves astrocyte to neuron conversion by increasing the chromatin accessibility of genes associated with neuronal maturation in a proneuronal factor-dependent manner","authors":"Priya Maddhesiya, Tjasa Lepko, Andrea Steiner-Mezzardi, Julia Schneider, Veronika Schwarz, Juliane Merl-Pham, Finja Berger, Stefanie M. Hauck, Lorenza Ronfani, Marco Bianchi, Tatiana Simon, Anthodesmi Krontira, Giacomo Masserdotti, Magdalena Götz, Jovica Ninkovic","doi":"10.1186/s13059-025-03556-z","DOIUrl":"https://doi.org/10.1186/s13059-025-03556-z","url":null,"abstract":"Direct conversion of reactive glial cells to neurons is a promising avenue for neuronal replacement therapies after brain injury or neurodegeneration. The overexpression of neurogenic fate determinants in glial cells results in conversion to neurons. For repair purposes, the conversion should ideally be induced in the pathology-induced neuroinflammatory environment. However, very little is known regarding the influence of the injury-induced neuroinflammatory environment and released growth factors on the direct conversion process. We establish a new in vitro culture system of postnatal astrocytes without epidermal growth factor that reflects the direct conversion rate in the injured, neuroinflammatory environment in vivo. We demonstrate that the growth factor combination corresponding to the injured environment defines the ability of glia to be directly converted to neurons. Using this culture system, we show that chromatin structural protein high mobility group box 2 (HMGB2) regulates the direct conversion rate downstream of the growth factor combination. We further demonstrate that Hmgb2 cooperates with neurogenic fate determinants, such as Neurog2, in opening chromatin at the loci of genes regulating neuronal maturation and synapse formation. Consequently, early chromatin rearrangements occur during direct fate conversion and are necessary for full fate conversion. Our data demonstrate novel growth factor-controlled regulation of gene expression during direct fate conversion. This regulation is crucial for proper maturation of induced neurons and could be targeted to improve the repair process.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"22 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143841185","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

DNA methylation dynamics play crucial roles in shaping the distinct transcriptomic profiles for different root-type initiation in rice DNA甲基化动力学在水稻不同根型起始的转录组谱形成中起着至关重要的作用

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-04-17 DOI: 10.1186/s13059-025-03571-0

Wei Jiang, Zhou Zhou, Xiaoying Li, Yu Zhao, Shaoli Zhou

{"title":"DNA methylation dynamics play crucial roles in shaping the distinct transcriptomic profiles for different root-type initiation in rice","authors":"Wei Jiang, Zhou Zhou, Xiaoying Li, Yu Zhao, Shaoli Zhou","doi":"10.1186/s13059-025-03571-0","DOIUrl":"https://doi.org/10.1186/s13059-025-03571-0","url":null,"abstract":"Monocots possess a fibrous root system comprising an embryonic root, crown roots, and lateral roots. The distinct cellular origins highlight the diversity of the initiation mechanism. To date, the distinct initiation mechanisms have been poorly studied. In this study, we conduct a comprehensive transcriptome and DNA methylome assay of these root types during their initiation. Our findings indicate significant divergence in transcriptome regulation trajectories with apparent transcriptional activation in post-embryonic root initials (crown root and lateral root) contrasted by suppression in embryonic root generation. Additionally, CHH methylation is dynamically and differentially regulated across the initiation stages of the various root types, and is significantly associated with the short transposon element within the promoter regions of functional genes, which plays crucial roles in determining the genes’ spatiotemporal transcription. Moreover, our work reveals that the activation of DNA glycosylase 702 (DNG702) and repression of Domains Rearranged Methyltransferase 2 (DRM2) play important roles in the erasure of CHH methylation and activation of functional genes during the processes, such as a novel identified key regulatory bZip65, thus directly impacting the initiation of post-embryonic roots in rice. Our extensive analysis delineates the landscapes of spatiotemporal transcriptomes and DNA methylomes during the initiation of the three root types in rice, shedding light on the pivotal role of CHH methylation in the spatiotemporal regulation of various key genes, ensuring the successful initiation of distinct root types in rice.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"30 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143841186","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

Bayesian multi-study non-negative matrix factorization for mutational signatures 突变特征的贝叶斯多研究非负矩阵因式分解

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-04-16 DOI: 10.1186/s13059-025-03563-0

Isabella N. Grabski, Lorenzo Trippa, Giovanni Parmigiani

引用次数: 0