Genome Biology最新文献

The genomic portrait of the Picene culture provides new insights into the Italic Iron Age and the legacy of the Roman Empire in Central Italy 皮切尼文化的基因组画像为了解意大利铁器时代和罗马帝国在意大利中部的遗产提供了新的视角

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-11-21 DOI: 10.1186/s13059-024-03430-4

Francesco Ravasini, Helja Kabral, Anu Solnik, Luciana de Gennaro, Francesco Montinaro, Ruoyun Hui, Chiara Delpino, Stefano Finocchi, Pierluigi Giroldini, Oscar Mei, Michael Allen Beck De Lotto, Elisabetta Cilli, Mogge Hajiesmaeil, Letizia Pistacchia, Flavia Risi, Chiara Giacometti, Christiana Lyn Scheib, Kristiina Tambets, Mait Metspalu, Fulvio Cruciani, Eugenia D’Atanasio, Beniamino Trombetta

{"title":"The genomic portrait of the Picene culture provides new insights into the Italic Iron Age and the legacy of the Roman Empire in Central Italy","authors":"Francesco Ravasini, Helja Kabral, Anu Solnik, Luciana de Gennaro, Francesco Montinaro, Ruoyun Hui, Chiara Delpino, Stefano Finocchi, Pierluigi Giroldini, Oscar Mei, Michael Allen Beck De Lotto, Elisabetta Cilli, Mogge Hajiesmaeil, Letizia Pistacchia, Flavia Risi, Chiara Giacometti, Christiana Lyn Scheib, Kristiina Tambets, Mait Metspalu, Fulvio Cruciani, Eugenia D’Atanasio, Beniamino Trombetta","doi":"10.1186/s13059-024-03430-4","DOIUrl":"https://doi.org/10.1186/s13059-024-03430-4","url":null,"abstract":"The Italic Iron Age is characterized by the presence of various ethnic groups partially examined from a genomic perspective. To explore the evolution of Iron Age Italic populations and the genetic impact of Romanization, we focus on the Picenes, one of the most fascinating pre-Roman civilizations, who flourished on the Middle Adriatic side of Central Italy between the 9th and the 3rd century BCE, until the Roman colonization. More than 50 samples are reported, spanning more than 1000 years of history from the Iron Age to Late Antiquity. Despite cultural diversity, our analysis reveals no major differences between the Picenes and other coeval populations, suggesting a shared genetic history of the Central Italian Iron Age ethnic groups. Nevertheless, a slight genetic differentiation between populations along the Adriatic and Tyrrhenian coasts can be observed, possibly due to different population dynamics in the two sides of Italy and/or genetic contacts across the Adriatic Sea. Additionally, we identify several individuals with ancestries deviating from their general population. Lastly, in our Late Antiquity site, we observe a drastic change in the genetic landscape of the Middle Adriatic region, indicating a relevant influx from the Near East, possibly as a consequence of Romanization. Our findings, consistently with archeological hypotheses, suggest genetic interactions across the Adriatic Sea during the Bronze/Iron Age and a high level of individual mobility typical of cosmopolitan societies. Finally, we highlight the role of the Roman Empire in shaping genetic and phenotypic changes that greatly impact the Italian peninsula.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"81 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142678276","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

scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes scStateDynamics：通过模拟单细胞水平的表达变化，解读药物反应性肿瘤细胞的状态动态

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-11-21 DOI: 10.1186/s13059-024-03436-y

Wenbo Guo, Xinqi Li, Dongfang Wang, Nan Yan, Qifan Hu, Fan Yang, Xuegong Zhang, Jianhua Yao, Jin Gu

引用次数: 0

Considerations in the search for epistasis 寻找外显子的注意事项

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-11-19 DOI: 10.1186/s13059-024-03427-z

Marleen Balvert, Johnathan Cooper-Knock, Julian Stamp, Ross P. Byrne, Soufiane Mourragui, Juami van Gils, Stefania Benonisdottir, Johannes Schlüter, Kevin Kenna, Sanne Abeln, Alfredo Iacoangeli, Joséphine T. Daub, Brian L. Browning, Gizem Taş, Jiajing Hu, Yan Wang, Elham Alhathli, Calum Harvey, Luna Pianesi, Sara C. Schulte, Jorge González-Domínguez, Erik Garrisson, Michael P. Snyder, Alexander Schönhuth, Letitia M. F. Sng, Natalie A. Twine

引用次数: 0

Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape. 中心粒富集的逆转录因子的转录及其 RNA 的局部保留是 CENP-A 染色质景观的重要特征。

IF 10.1 1区生物学

Genome Biology Pub Date : 2024-11-18 DOI: 10.1186/s13059-024-03433-1

B J Chabot, R Sun, A Amjad, S J Hoyt, L Ouyang, C Courret, R Drennan, L Leo, A M Larracuente, L J Core, R J O'Neill, B G Mellone

{"title":"Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape.","authors":"B J Chabot, R Sun, A Amjad, S J Hoyt, L Ouyang, C Courret, R Drennan, L Leo, A M Larracuente, L J Core, R J O'Neill, B G Mellone","doi":"10.1186/s13059-024-03433-1","DOIUrl":"10.1186/s13059-024-03433-1","url":null,"abstract":"Background: Centromeres depend on chromatin containing the conserved histone H3 variant CENP-A for function and inheritance, while the role of centromeric DNA repeats remains unclear. Retroelements are prevalent at centromeres across taxa and represent a potential mechanism for promoting transcription to aid in CENP-A incorporation or for generating RNA transcripts to maintain centromere integrity.Results: In this study, we probe into the transcription and RNA localization of the centromere-enriched retroelement G2/Jockey-3 (hereafter referred to as Jockey-3) in Drosophila melanogaster, currently the only in vivo model with assembled centromeres. We find that Jockey-3 is a major component of the centromeric transcriptome and produces RNAs that localize to centromeres in metaphase. Leveraging the polymorphism of Jockey-3 and a de novo centromere system, we show that these RNAs remain associated with their cognate DNA sequences in cis, suggesting they are unlikely to perform a sequence-specific function at all centromeres. We show that Jockey-3 transcription is positively correlated with the presence of CENP-A and that recent Jockey-3 transposition events have occurred preferentially at CENP-A-containing chromatin.Conclusions: We propose that Jockey-3 preferentially inserts at the centromere to ensure its own selfish propagation, while contributing to transcription across these regions. Given the conservation of retroelements as centromere components through evolution, our findings may offer a basis for understanding similar associations in other species.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"25 1","pages":"295"},"PeriodicalIF":10.1,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142667596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

VI-VS: calibrated identification of feature dependencies in single-cell multiomics VI-VS：校准识别单细胞多组学中的特征依赖性

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-11-15 DOI: 10.1186/s13059-024-03419-z

Pierre Boyeau, Stephen Bates, Can Ergen, Michael I. Jordan, Nir Yosef

引用次数: 0

IAMSAM: image-based analysis of molecular signatures using the Segment Anything Model IAMSAM：基于图像的分子特征分析，使用分段 Anything 模型

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-11-11 DOI: 10.1186/s13059-024-03380-x

Dongjoo Lee, Jeongbin Park, Seungho Cook, Seongjin Yoo, Daeseung Lee, Hongyoon Choi

引用次数: 0

Adenine base editors induce off-target structure variations in mouse embryos and primary human T cells 腺嘌呤碱基编辑器在小鼠胚胎和原代人类 T 细胞中诱发脱靶结构变异

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-11-11 DOI: 10.1186/s13059-024-03434-0

Leilei Wu, Shutan Jiang, Meisong Shi, Tanglong Yuan, Yaqin Li, Pinzheng Huang, Yingqi Li, Erwei Zuo, Changyang Zhou, Yidi Sun

{"title":"Adenine base editors induce off-target structure variations in mouse embryos and primary human T cells","authors":"Leilei Wu, Shutan Jiang, Meisong Shi, Tanglong Yuan, Yaqin Li, Pinzheng Huang, Yingqi Li, Erwei Zuo, Changyang Zhou, Yidi Sun","doi":"10.1186/s13059-024-03434-0","DOIUrl":"https://doi.org/10.1186/s13059-024-03434-0","url":null,"abstract":"The safety of CRISPR-based gene editing methods is of the utmost priority in clinical applications. Previous studies have reported that Cas9 cleavage induced frequent aneuploidy in primary human T cells, but whether cleavage-mediated editing of base editors would generate off-target structure variations remains unknown. Here, we investigate the potential off-target structural variations associated with CRISPR/Cas9, ABE, and CBE editing in mouse embryos and primary human T cells by whole-genome sequencing and single-cell RNA-seq analyses. The results show that both Cas9 and ABE generate off-target structural variations (SVs) in mouse embryos, while CBE induces rare SVs. In addition, off-target large deletions are detected in 32.74% of primary human T cells transfected with Cas9 and 9.17% of cells transfected with ABE. Moreover, Cas9-induced aneuploid cells activate the P53 and apoptosis pathways, whereas ABE-associated aneuploid cells significantly upregulate cell cycle-related genes and are arrested in the G0 phase. A percentage of 16.59% and 4.29% aneuploid cells are still observable at 3 weeks post transfection of Cas9 or ABE. These off-target phenomena in ABE are universal as observed in other cell types such as B cells and Huh7. Furthermore, the off-target SVs are significantly reduced in cells treated with high-fidelity ABE (ABE-V106W). This study shows both CRISPR/Cas9 and ABE induce off-target SVs in mouse embryos and primary human T cells, raising an urgent need for the development of high-fidelity gene editing tools.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"2 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142598474","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

SpottedPy quantifies relationships between spatial transcriptomic hotspots and uncovers environmental cues of epithelial-mesenchymal plasticity in breast cancer SpottedPy 量化空间转录组热点之间的关系，揭示乳腺癌上皮-间质可塑性的环境线索

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-11-11 DOI: 10.1186/s13059-024-03428-y

Eloise Withnell, Maria Secrier

引用次数: 0

scDOT: optimal transport for mapping senescent cells in spatial transcriptomics scDOT：空间转录组学中绘制衰老细胞图谱的最佳传输方式

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-11-08 DOI: 10.1186/s13059-024-03426-0

Nam D. Nguyen, Lorena Rosas, Timur Khaliullin, Peiran Jiang, Euxhen Hasanaj, Jose A. Ovando-Ricardez, Marta Bueno, Irfan Rahman, Gloria S. Pryhuber, Dongmei Li, Qin Ma, Toren Finkel, Melanie Königshoff, Oliver Eickelberg, Mauricio Rojas, Ana L. Mora, Jose Lugo-Martinez, Ziv Bar-Joseph

引用次数: 0

GraphPCA: a fast and interpretable dimension reduction algorithm for spatial transcriptomics data GraphPCA：用于空间转录组学数据的快速、可解释的降维算法

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-11-07 DOI: 10.1186/s13059-024-03429-x

Jiyuan Yang, Lu Wang, Lin Liu, Xiaoqi Zheng

引用次数: 0