Genome Biology最新文献_第4页

SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data SDePER：基于空间条形码的转录组数据细胞类型解卷积的混合机器学习和回归方法

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-14 DOI: 10.1186/s13059-024-03416-2

Yunqing Liu, Ningshan Li, Ji Qi, Gang Xu, Jiayi Zhao, Nating Wang, Xiayuan Huang, Wenhao Jiang, Huanhuan Wei, Aurélien Justet, Taylor S. Adams, Robert Homer, Amei Amei, Ivan O. Rosas, Naftali Kaminski, Zuoheng Wang, Xiting Yan

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When less is more: sketching with minimizers in genomics 少即是多：在基因组学中使用最小化器绘制草图

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-14 DOI: 10.1186/s13059-024-03414-4

Malick Ndiaye, Silvia Prieto-Baños, Lucy M. Fitzgerald, Ali Yazdizadeh Kharrazi, Sergey Oreshkov, Christophe Dessimoz, Fritz J. Sedlazeck, Natasha Glover, Sina Majidian

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Drought-responsive dynamics of H3K9ac-marked 3D chromatin interactions are integrated by OsbZIP23-associated super-enhancer-like promoter regions in rice 水稻中与 OsbZIP23 相关的超级增强子样启动子区整合了 H3K9ac 标记的三维染色质相互作用的干旱响应动态变化

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-10 DOI: 10.1186/s13059-024-03408-2

Yu Chang, Jiahan Liu, Minrong Guo, Weizhi Ouyang, Jiapei Yan, Lizhong Xiong, Xingwang Li

{"title":"Drought-responsive dynamics of H3K9ac-marked 3D chromatin interactions are integrated by OsbZIP23-associated super-enhancer-like promoter regions in rice","authors":"Yu Chang, Jiahan Liu, Minrong Guo, Weizhi Ouyang, Jiapei Yan, Lizhong Xiong, Xingwang Li","doi":"10.1186/s13059-024-03408-2","DOIUrl":"https://doi.org/10.1186/s13059-024-03408-2","url":null,"abstract":"In response to drought stress (DS), plants undergo complex processes that entail significant transcriptome reprogramming. However, the intricate relationship between the dynamic alterations in the three-dimensional (3D) genome and the modulation of gene co-expression in drought responses remains a relatively unexplored area. In this study, we reconstruct high-resolution 3D genome maps based on genomic regions marked by H3K9ac, an active histone modification that dynamically responds to soil water variations in rice. We discover a genome-wide disconnection of 3D genome contact upon DS with over 10,000 chromatin loops lost, which are partially recovered in the subsequent re-watering. Loops integrating promoter–promoter interactions (PPI) contribute to gene expression in addition to basal H3K9ac modifications. Moreover, H3K9ac-marked promoter regions with high affinities in mediating PPIs, termed as super-promoter regions (SPRs), integrate spatially clustered PPIs in a super-enhancer-like manner. Interestingly, the knockout mutation of OsbZIP23, a well-defined DS-responsive transcription factor, leads to the disassociation of over 80% DS-specific PPIs and decreased expression of the corresponding genes under DS. As a case study, we show how OsbZIP23 integrates the PPI cluster formation and the co-expression of four dehydrin genes, RAB16A–D, through targeting the RAB16C SPR in a stress signaling-dependent manner. Our high-resolution 3D genome maps unveil the principles and details of dynamic genome folding in response to water supply variations and illustrate OsbZIP23 as an indispensable integrator of the yet unique 3D genome organization that is essential for gene co-expression under DS in rice.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"15 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142398276","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

Improved detection of methylation in ancient DNA 改进古 DNA 甲基化检测

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-10 DOI: 10.1186/s13059-024-03405-5

Susanna Sawyer, Pere Gelabert, Benjamin Yakir, Alejandro Llanos-Lizcano, Alessandra Sperduti, Luca Bondioli, Olivia Cheronet, Christine Neugebauer-Maresch, Maria Teschler-Nicola, Mario Novak, Ildikó Pap, Ildikó Szikossy, Tamás Hajdu, Vyacheslav Moiseyev, Andrey Gromov, Gunita Zariņa, Eran Meshorer, Liran Carmel, Ron Pinhasi

引用次数: 0

Spatiotemporal modeling reveals high-resolution invasion states in glioblastoma 时空建模揭示胶质母细胞瘤的高分辨率侵袭状态

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-10 DOI: 10.1186/s13059-024-03407-3

Varsha Thoppey Manoharan, Aly Abdelkareem, Gurveer Gill, Samuel Brown, Aaron Gillmor, Courtney Hall, Heewon Seo, Kiran Narta, Sean Grewal, Ngoc Ha Dang, Bo Young Ahn, Kata Osz, Xueqing Lun, Laura Mah, Franz Zemp, Douglas Mahoney, Donna L. Senger, Jennifer A. Chan, A. Sorana Morrissy

{"title":"Spatiotemporal modeling reveals high-resolution invasion states in glioblastoma","authors":"Varsha Thoppey Manoharan, Aly Abdelkareem, Gurveer Gill, Samuel Brown, Aaron Gillmor, Courtney Hall, Heewon Seo, Kiran Narta, Sean Grewal, Ngoc Ha Dang, Bo Young Ahn, Kata Osz, Xueqing Lun, Laura Mah, Franz Zemp, Douglas Mahoney, Donna L. Senger, Jennifer A. Chan, A. Sorana Morrissy","doi":"10.1186/s13059-024-03407-3","DOIUrl":"https://doi.org/10.1186/s13059-024-03407-3","url":null,"abstract":"Diffuse invasion of glioblastoma cells through normal brain tissue is a key contributor to tumor aggressiveness, resistance to conventional therapies, and dismal prognosis in patients. A deeper understanding of how components of the tumor microenvironment (TME) contribute to overall tumor organization and to programs of invasion may reveal opportunities for improved therapeutic strategies. Towards this goal, we apply a novel computational workflow to a spatiotemporally profiled GBM xenograft cohort, leveraging the ability to distinguish human tumor from mouse TME to overcome previous limitations in the analysis of diffuse invasion. Our analytic approach, based on unsupervised deconvolution, performs reference-free discovery of cell types and cell activities within the complete GBM ecosystem. We present a comprehensive catalogue of 15 tumor cell programs set within the spatiotemporal context of 90 mouse brain and TME cell types, cell activities, and anatomic structures. Distinct tumor programs related to invasion align with routes of perivascular, white matter, and parenchymal invasion. Furthermore, sub-modules of genes serving as program network hubs are highly prognostic in GBM patients. The compendium of programs presented here provides a basis for rational targeting of tumor and/or TME components. We anticipate that our approach will facilitate an ecosystem-level understanding of the immediate and long-term consequences of such perturbations, including the identification of compensatory programs that will inform improved combinatorial therapies.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"20 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142398214","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

Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data Transipedia.org：基于 k-mer 的大型 RNA 测序数据集探索及其在癌症数据中的应用

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-10 DOI: 10.1186/s13059-024-03413-5

Chloé Bessière, Haoliang Xue, Benoit Guibert, Anthony Boureux, Florence Rufflé, Julien Viot, Rayan Chikhi, Mikaël Salson, Camille Marchet, Thérèse Commes, Daniel Gautheret

引用次数: 0

Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing Graphasing：利用单细胞链测序对二倍体基因组组装图进行分期

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-10 DOI: 10.1186/s13059-024-03409-1

Mir Henglin, Maryam Ghareghani, William T. Harvey, David Porubsky, Sergey Koren, Evan E. Eichler, Peter Ebert, Tobias Marschall

引用次数: 0

Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation 对 SETD2、NSD1、NSD2、NSD3 和 ASH1L 的系统扰动揭示了它们对 H3K36 甲基化的不同贡献

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-10 DOI: 10.1186/s13059-024-03415-3

Gerry A. Shipman, Reinnier Padilla, Cynthia Horth, Bo Hu, Eric Bareke, Francisca N. Vitorino, Joanna M. Gongora, Benjamin A. Garcia, Chao Lu, Jacek Majewski

{"title":"Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation","authors":"Gerry A. Shipman, Reinnier Padilla, Cynthia Horth, Bo Hu, Eric Bareke, Francisca N. Vitorino, Joanna M. Gongora, Benjamin A. Garcia, Chao Lu, Jacek Majewski","doi":"10.1186/s13059-024-03415-3","DOIUrl":"https://doi.org/10.1186/s13059-024-03415-3","url":null,"abstract":"Methylation of histone 3 lysine 36 (H3K36me) has emerged as an essential epigenetic component for the faithful regulation of gene expression. Despite its importance in development and disease, how the molecular agents collectively shape the H3K36me landscape is unclear. We use mouse mesenchymal stem cells to perturb the H3K36me methyltransferases (K36MTs) and infer the activities of the five most prominent enzymes: SETD2, NSD1, NSD2, NSD3, and ASH1L. We find that H3K36me2 is the most abundant of the three methylation states and is predominantly deposited at intergenic regions by NSD1, and partly by NSD2. In contrast, H3K36me1/3 are most abundant within exons and are positively correlated with gene expression. We demonstrate that while SETD2 deposits most H3K36me3, it may also deposit H3K36me2 within transcribed genes. Additionally, loss of SETD2 results in an increase of exonic H3K36me1, suggesting other (K36MTs) prime gene bodies with lower methylation states ahead of transcription. While NSD1/2 establish broad intergenic H3K36me2 domains, NSD3 deposits H3K36me2 peaks on active promoters and enhancers. Meanwhile, the activity of ASH1L is restricted to the regulatory elements of developmentally relevant genes, and our analyses implicate PBX2 as a potential recruitment factor. Within genes, SETD2 primarily deposits H3K36me3, while the other K36MTs deposit H3K36me1/2 independently of SETD2 activity. For the deposition of H3K36me1/2, we find a hierarchy of K36MT activities where NSD1 > NSD2 > NSD3 > ASH1L. While NSD1 and NSD2 are responsible for most genome-wide propagation of H3K36me2, the activities of NSD3 and ASH1L are confined to active regulatory elements.\u0000","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"19 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142398275","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}

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Visualizing scRNA-Seq data at population scale with GloScope 利用 GloScope 在种群规模上可视化 scRNA-Seq 数据

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-08 DOI: 10.1186/s13059-024-03398-1

Hao Wang, William Torous, Boying Gong, Elizabeth Purdom

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DEMINING: A deep learning model embedded framework to distinguish RNA editing from DNA mutations in RNA sequencing data DEMINING：嵌入深度学习模型的框架，用于区分 RNA 测序数据中的 RNA 编辑和 DNA 突变

IF 12.3 1区生物学

Genome Biology Pub Date : 2024-10-08 DOI: 10.1186/s13059-024-03397-2

Zhi-Can Fu, Bao-Qing Gao, Fang Nan, Xu-Kai Ma, Li Yang

引用次数: 0