Genome Biology最新文献

DAGIP: alleviating cell-free DNA sequencing biases with optimal transport

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-03-07 DOI: 10.1186/s13059-025-03511-y

Antoine Passemiers, Stefania Tuveri, Tatjana Jatsenko, Adriaan Vanderstichele, Pieter Busschaert, An Coosemans, Dirk Timmerman, Sabine Tejpar, Peter Vandenberghe, Diether Lambrechts, Daniele Raimondi, Joris Robert Vermeesch, Yves Moreau

引用次数: 0

Ultra-sensitive detection of transposon insertions across multiple families by transposable element display sequencing

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-03-06 DOI: 10.1186/s13059-025-03512-x

Pol Vendrell-Mir, Basile Leduque, Leandro Quadrana

{"title":"Ultra-sensitive detection of transposon insertions across multiple families by transposable element display sequencing","authors":"Pol Vendrell-Mir, Basile Leduque, Leandro Quadrana","doi":"10.1186/s13059-025-03512-x","DOIUrl":"https://doi.org/10.1186/s13059-025-03512-x","url":null,"abstract":"Mobilization of transposable elements (TEs) can generate large effect mutations. However, due to the difficulty of detecting new TE insertions in genomes and the typically rare occurrence of transposition, the actual rate, distribution, and population dynamics of new insertions remain largely unexplored. We present a TE display sequencing approach that leverages target amplification of TE extremities to detect non-reference TE insertions with high specificity and sensitivity, enabling the detection of insertions at frequencies as low as 1 in 250,000 within a DNA sample. Moreover, this method allows the simultaneous detection of insertions for distinct TE families, including both retrotransposons and DNA transposons, enhancing its versatility and cost-effectiveness for investigating complex “mobilomes.” When combined with nanopore sequencing, this approach enables the identification of insertions using long-read information and achieves a turnaround time from DNA extraction to insertion identification of less than 24 h, significantly reducing the time-to-answer. By analyzing a population of Arabidopsis thaliana plants undergoing a transposition burst, we demonstrate the power of the multiplex TE display sequencing to analyze “evolve and resequence” experiments. Notably, we find that 3–4% of de novo TE insertions exhibit recurrent allele frequency changes indicative of either positive or negative selection. TE display sequencing is an ultra-sensitive, specific, simple, and cost-effective approach for investigating the rate and landscape of new TE insertions across multiple families in large-scale population experiments. We provide a step-by-step experimental protocol and ready-to-use bioinformatic pipelines to facilitate its straightforward implementation.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"15 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560689","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

Genome assembly of the maize B chromosome provides insight into its epigenetic characteristics and effects on the host genome

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-03-06 DOI: 10.1186/s13059-025-03517-6

Qian Liu, Yang Liu, Congyang Yi, Zhi Gao, Zeyan Zhang, Congle Zhu, James A. Birchler, Fangpu Han

{"title":"Genome assembly of the maize B chromosome provides insight into its epigenetic characteristics and effects on the host genome","authors":"Qian Liu, Yang Liu, Congyang Yi, Zhi Gao, Zeyan Zhang, Congle Zhu, James A. Birchler, Fangpu Han","doi":"10.1186/s13059-025-03517-6","DOIUrl":"https://doi.org/10.1186/s13059-025-03517-6","url":null,"abstract":"B chromosomes contribute to the genetic variation in numerous eukaryotes. Yet their genetic and epigenetic characteristics, as well as their effects on the host genome remain poorly understood. Here, we present a comprehensive genome assembly of diploid maize B73 with two copies of B chromosomes using long-read sequencing. We annotate a total of 1124 high-confidence protein-coding genes and 119,579,190 bp repeat elements representing 88.55% of the B chromosome assembly. Using CENH3 ChIP-seq data, we accurately determined the position of the B chromosome centromere, which features a unique monomer-composed satellite array distinct from that found on the chromosome arms. Our research provides detailed genetic and epigenetic maps of the B chromosome, shedding light on its molecular landscape, including DNA sequence composition, DNA methylation patterns, histone modifications, and R-loop distributions across various chromatin regions. Consistent with the cytological morphology of the B chromosome, the less condensed euchromatin regions displayed high levels of H3K4me3, H3K9ac, gene expression, and dense R-loop distributions. DNA methylation on the B chromosome was primarily observed at CG sites. The centromeric region is notably enriched with H3K4me3 and H3K9ac histone modifications and has lower CHG methylation compared to the pericentromeric regions. Moreover, our findings reveal that B chromosome accumulation affects R-loop formation on A chromosomes, and exerts tissue-specific influences on A chromosome gene expression. The accurate assembly and detailed epigenetic maps of the maize B chromosome will help understand the drive mechanism, reveal its conflict with the host genome, and accelerate the construction of artificial chromosomes.\u0000","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"50 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560748","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

Benchmarking single-cell cross-omics imputation methods for surface protein expression

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-03-04 DOI: 10.1186/s13059-025-03514-9

Chen-Yang Li, Yong-Jia Hong, Bo Li, Xiao-Fei Zhang

{"title":"Benchmarking single-cell cross-omics imputation methods for surface protein expression","authors":"Chen-Yang Li, Yong-Jia Hong, Bo Li, Xiao-Fei Zhang","doi":"10.1186/s13059-025-03514-9","DOIUrl":"https://doi.org/10.1186/s13059-025-03514-9","url":null,"abstract":"Recent advances in single-cell multimodal omics sequencing have facilitated the simultaneous profiling of transcriptomes and surface proteomes within individual cells, offering insights into cellular functions and heterogeneity. However, the high costs and technical complexity of protocols like CITE-seq and REAP-seq constrain large-scale dataset generation. To overcome this limitation, surface protein data imputation methods have emerged to predict protein abundances from scRNA-seq data. We present a comprehensive benchmark of twelve state-of-the-art imputation methods across eleven datasets and six scenarios. Our analysis evaluates the methods’ accuracy, sensitivity to training data size, robustness across experiments, and usability in terms of running time, memory usage, popularity, and user-friendliness. With benchmark experiments in diverse scenarios and a comprehensive evaluation framework of the results, our study offers valuable insights into the performance and applicability of surface protein data imputation methods in single-cell omics research. Based on our results, Seurat v4 (PCA) and Seurat v3 (PCA) demonstrate exceptional performance, offering promising avenues for further research in single-cell omics.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"29 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143538297","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

Decoding subcellular RNA localization one molecule at a time

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-03-03 DOI: 10.1186/s13059-025-03507-8

Josep Biayna, Gabrijela Dumbović

引用次数: 0

Admixture as a source for HLA variation in Neolithic European farming communities

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-02-28 DOI: 10.1186/s13059-025-03509-6

Nicolas Antonio da Silva, Onur Özer, Magdalena Haller-Caskie, Yan-Rong Chen, Daniel Kolbe, Sabine Schade-Lindig, Joachim Wahl, Carola Berszin, Michael Francken, Irina Görner, Kerstin Schierhold, Joachim Pechtl, Gisela Grupe, Christoph Rinne, Johannes Müller, Tobias L. Lenz, Almut Nebel, Ben Krause-Kyora

{"title":"Admixture as a source for HLA variation in Neolithic European farming communities","authors":"Nicolas Antonio da Silva, Onur Özer, Magdalena Haller-Caskie, Yan-Rong Chen, Daniel Kolbe, Sabine Schade-Lindig, Joachim Wahl, Carola Berszin, Michael Francken, Irina Görner, Kerstin Schierhold, Joachim Pechtl, Gisela Grupe, Christoph Rinne, Johannes Müller, Tobias L. Lenz, Almut Nebel, Ben Krause-Kyora","doi":"10.1186/s13059-025-03509-6","DOIUrl":"https://doi.org/10.1186/s13059-025-03509-6","url":null,"abstract":"The northern European Neolithic is characterized by two major demographic events: immigration of early farmers from Anatolia at 7500 years before present, and their admixture with local western hunter-gatherers forming late farmers, from around 6200 years before present. The influence of this admixture event on variation in the immune-relevant human leukocyte antigen (HLA) region is understudied. We analyzed genome-wide data of 125 individuals from seven archeological early farmer and late farmer sites located in present-day Germany. The late farmer group studied here is associated with the Wartberg culture, from around 5500–4800 years before present. We note that late farmers resulted from sex-biased admixture from male western hunter-gatherers. In addition, we observe Y-chromosome haplogroup I as the dominant lineage in late farmers, with site-specific sub-lineages. We analyze true HLA genotypes from 135 Neolithic individuals, the majority of which were produced in this study. We observe significant shifts in HLA allele frequencies from early farmers to late farmers, likely due to admixture with western hunter-gatherers. Especially for the haplotype DQB1*04:01-DRB1*08:01, there is evidence for a western hunter-gatherer origin. The HLA diversity increased from early farmers to late farmers. However, it is considerably lower than in modern populations. Both early farmers and late farmers exhibit a relatively narrow HLA allele spectrum compared to today. This coincides with sparse traces of pathogen DNA, potentially indicating a lower pathogen pressure at the time.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"28 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143518778","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

CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-02-28 DOI: 10.1186/s13059-025-03510-z

Xue Yang, Li Cheng, Ye Xin, Jianxiang Zhang, Xinfeng Chen, Jinchao Xu, Mengli Zhang, Ruopeng Feng, Judith Hyle, Wenjie Qi, Wojciech Rosikiewicz, Beisi Xu, Chunliang Li, Peng Xu

{"title":"CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis","authors":"Xue Yang, Li Cheng, Ye Xin, Jianxiang Zhang, Xinfeng Chen, Jinchao Xu, Mengli Zhang, Ruopeng Feng, Judith Hyle, Wenjie Qi, Wojciech Rosikiewicz, Beisi Xu, Chunliang Li, Peng Xu","doi":"10.1186/s13059-025-03510-z","DOIUrl":"https://doi.org/10.1186/s13059-025-03510-z","url":null,"abstract":"CTCF is considered as the most essential transcription factor regulating chromatin architecture and gene expression. However, genome-wide impact of CTCF on erythropoiesis has not been extensively investigated. Using a state-of-the-art human erythroid progenitor cell model (HUDEP-2 and HEL cell lines), we systematically investigate the effects of acute CTCF loss by an auxin-inducible degron system on transcriptional programs, chromatin accessibility, CTCF genome occupancy, and genome architecture. By integrating multi-omics datasets, we reveal that acute CTCF loss notably disrupts genome-wide chromatin accessibility and the transcription network. We detect over thousands of decreased chromatin accessibility regions but only a few hundred increased regions after CTCF depletion in HUDEP-2 and HEL lines, suggesting the role of CTCF in maintaining proper chromatin openness in the erythroid lineage. CTCF depletion in the erythroid context notably disrupts the boundary integrity of topologically associating domains and chromatin loops but does not affect nuclear compartmentalization. We find erythroid lineage-specific genes, including some metabolism-related genes, are suppressed at immature and mature stages. Notably, we find a subset of genes whose transcriptional levels increase upon CTCF depletion, accompanied by decreased chromatin accessibility regions enriched with the GATA motif. We further decipher the molecular mechanism underlying the CTCF/GATA2 repression axis through distal non-coding chromatin regions. These results suggest a suppressive role of CTCF in gene expression during erythroid lineage specification. Our study reveals a novel role of CTCF in regulating erythroid differentiation by maintaining its proper chromatin openness and gene expression network, which extends our understanding of CTCF biology.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"4 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143518773","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

PRODE recovers essential and context-essential genes through neighborhood-informed scores

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-02-28 DOI: 10.1186/s13059-025-03501-0

Thomas Cantore, Paola Gasperini, Riccardo Bevilacqua, Yari Ciani, Sanju Sinha, Eytan Ruppin, Francesca Demichelis

引用次数: 0

Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-02-26 DOI: 10.1186/s13059-025-03488-8

Henri Schmidt, Minsi Zhang, Dimitar Chakarov, Vineet Bansal, Haralambos Mourelatos, Francisco J. Sánchez-Rivera, Scott W. Lowe, Andrea Ventura, Christina S. Leslie, Yuri Pritykin

引用次数: 0

Cross-species imputation and comparison of single-cell transcriptomic profiles

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-02-26 DOI: 10.1186/s13059-025-03493-x

Ran Zhang, Mu Yang, Jacob Schreiber, Diana R. O’Day, James M. A. Turner, Jay Shendure, William Stafford Noble, Christine M. Disteche, Xinxian Deng

{"title":"Cross-species imputation and comparison of single-cell transcriptomic profiles","authors":"Ran Zhang, Mu Yang, Jacob Schreiber, Diana R. O’Day, James M. A. Turner, Jay Shendure, William Stafford Noble, Christine M. Disteche, Xinxian Deng","doi":"10.1186/s13059-025-03493-x","DOIUrl":"https://doi.org/10.1186/s13059-025-03493-x","url":null,"abstract":"Cross-species comparison and prediction of gene expression profiles are important to understand regulatory changes during evolution and to transfer knowledge learned from model organisms to humans. Single-cell RNA-seq (scRNA-seq) profiles enable us to capture gene expression profiles with respect to variations among individual cells; however, cross-species comparison of scRNA-seq profiles is challenging because of data sparsity, batch effects, and the lack of one-to-one cell matching across species. Moreover, single-cell profiles are challenging to obtain in certain biological contexts, limiting the scope of hypothesis generation. Here we developed Icebear, a neural network framework that decomposes single-cell measurements into factors representing cell identity, species, and batch factors. Icebear enables accurate prediction of single-cell gene expression profiles across species, thereby providing high-resolution cell type and disease profiles in under-characterized contexts. Icebear also facilitates direct cross-species comparison of single-cell expression profiles for conserved genes that are located on the X chromosome in eutherian mammals but on autosomes in chicken. This comparison, for the first time, revealed evolutionary and diverse adaptations of X-chromosome upregulation in mammals.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"14 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495231","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