Genome researchPub Date : 2025-08-14DOI: 10.1101/gr.279997.124
Ran Zhang, Chengxiang Qiu, Galina Filippova, Gang Li, Jay Shendure, Jean-Philippe Vert, Xinxian Deng, William Stafford Noble, Christine Disteche
{"title":"Multicondition and multimodal temporal profile inference during mouse embryonic development","authors":"Ran Zhang, Chengxiang Qiu, Galina Filippova, Gang Li, Jay Shendure, Jean-Philippe Vert, Xinxian Deng, William Stafford Noble, Christine Disteche","doi":"10.1101/gr.279997.124","DOIUrl":"https://doi.org/10.1101/gr.279997.124","url":null,"abstract":"The emergence of single-cell time-series datasets enables modeling of changes in various types of cellular profiles over time. However, due to the disruptive nature of single-cell measurements, it is impossible to capture the full temporal trajectory of a particular cell. Furthermore, single-cell profiles can be collected at mismatched time points across different conditions (e.g., sex, batch, disease) and data modalities (e.g., scRNA-seq, scATAC-seq), which makes modeling challenging. Here we propose a joint modeling framework, Sunbear, for integrating multicondition and multimodal single-cell profiles across time. Sunbear can be used to impute single-cell temporal profile changes, align multidataset and multimodal profiles across time, and extrapolate single-cell profiles in a missing modality. We applied Sunbear to reveal sex-biased transcription during mouse embryonic development and predict dynamic relationships between epigenetic priming and transcription for cells in which multimodal profiles are unavailable. Sunbear thus enables the projection of single-cell time-series snapshots to multimodal and multicondition views of cellular trajectories.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"2 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144850667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome researchPub Date : 2025-08-14DOI: 10.1101/gr.280584.125
Han Shu, Jing Chen, Chang Xu, Jialu Hu, Yongtian Wang, Jiajie Peng, Qinghua Jiang, Xuequn Shang, Tao Wang
{"title":"Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA","authors":"Han Shu, Jing Chen, Chang Xu, Jialu Hu, Yongtian Wang, Jiajie Peng, Qinghua Jiang, Xuequn Shang, Tao Wang","doi":"10.1101/gr.280584.125","DOIUrl":"https://doi.org/10.1101/gr.280584.125","url":null,"abstract":"Spatial omics (SO) is a powerful methodology that enables the study of genes, proteins, and other molecular features within the spatial context of tissue architecture. With the growing availability of SO datasets, researchers are eager to extract biological insights from larger datasets for a more comprehensive understanding. However, existing approaches focus on batch effect correction, often neglecting complex biological patterns in tissue slices, complicating feature integration and posing challenges when combining transcriptomics with other omics layers. Here, we introduce stMSA (SpaTial Multi-Slice/omics Analysis), a deep graph contrastive learning model that incorporates graph auto-encoder techniques. stMSA is specifically designed to produce batch-corrected representations while retaining the distinct spatial patterns within each slice, considering both intra- and interbatch relationships during integration. Extensive evaluations show that stMSA outperforms state-of-the-art methods in distinguishing tissue structures across diverse slices, even when faced with varying experimental protocols and sequencing technologies. Furthermore, stMSA effectively deciphers complex developmental trajectories by integrating spatial proteomics and transcriptomics data and excels in cross-slice matching and alignment for 3D tissue reconstruction.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"292 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144850648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome researchPub Date : 2025-08-13DOI: 10.1101/gr.280282.124
Can Luo, Zimeng Jamie Zhou, Yichen Henry Liu, Xin Maizie Zhou
{"title":"FocalSV enables target region-based structural variant assembly and refinement using single-molecule long-read sequencing data","authors":"Can Luo, Zimeng Jamie Zhou, Yichen Henry Liu, Xin Maizie Zhou","doi":"10.1101/gr.280282.124","DOIUrl":"https://doi.org/10.1101/gr.280282.124","url":null,"abstract":"Structural variants (SVs) play a critical role in shaping the diversity of the human genome and their detection holds significant potential for advancing precision medicine. Despite notable progress in single-molecule long-read sequencing technologies, accurately identifying SV breakpoints and resolving their sequence remains a major challenge. Current alignment-based tools often struggle with precise breakpoint detection and sequence characterization, while whole genome assembly-based methods are computationally demanding and less practical for targeted analyses. Neither approach is ideally suited for scenarios where regions of interest are predefined and require precise SV characterization. To address this gap, we introduce FocalSV, a targeted SV detection framework that integrates both assembly- and alignment-based signals. By combining the precision of local assemblies with the efficiency of region-specific analysis, FocalSV enables more accurate SV detection. FocalSV supports user-defined target regions and can automatically identify and expand regions with potential structural variants to enable more comprehensive detection. FocalSV was evaluated on ten germline datasets and two paired normal-tumor cancer datasets, demonstrating superior performance in both precision and efficiency.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"185 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144824980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Intergenic accumulation of RNAPII maintains the potential for swift transcriptional restart upon release from quiescence","authors":"Manuela Baquero Pérez, Gertjan Laenen, Isabelle Loïodice, Mickaël Garnier, Ugo Szachnowski, Antonin Morillon, Myriam Ruault, Angela Taddei","doi":"10.1101/gr.279874.124","DOIUrl":"https://doi.org/10.1101/gr.279874.124","url":null,"abstract":"Quiescent cells (Q) are seemingly inactive, developmentally arrested cells, whose universal characteristic is the ability to promptly reenter the cell cycle upon sensing of external cues. Q cells are responsive to the environment and flexible enough to adapt to available resources. In budding yeast, quiescent nuclear features are drastically distinct from those observed in nutrient replete conditions: the nuclear volume is reduced, the telomeres relocate from the nuclear periphery to the center of the nucleus into a hypercluster, chromatin is found in a compacted, hypoacetylated state, and transcription is globally shutdown. Yet, Q cells can restart transcription within minutes of refeeding. Here, we follow the global decrease of transcription in sorted, developing Q populations, and its reactivation upon release. We find that transcription and telomere clustering dynamics in and out of quiescence are independent events. We report a genome-wide redistribution of the transcription machinery as cells progress into quiescence. Although most genes are shut down, 3% of coding genes remain active. Furthermore, RNAPII accumulates at one third of gene promoters. The corresponding genes are highly enriched among those showing a high level of transcription and high frequency of expression in individual cells, shortly after cells are refed, as monitored by single-cell RNA-seq. Our results point toward a role for quiescent-specific RNAPII distribution to ensure a rapid and robust transcriptional response upon return to growth.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"246 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144824977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome researchPub Date : 2025-08-08DOI: 10.1101/gr.280432.125
Héloïse Muller, Rosina Savisaar, Jean Peccoud, Sylvain Charlat, Clément Gilbert
{"title":"Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals","authors":"Héloïse Muller, Rosina Savisaar, Jean Peccoud, Sylvain Charlat, Clément Gilbert","doi":"10.1101/gr.280432.125","DOIUrl":"https://doi.org/10.1101/gr.280432.125","url":null,"abstract":"Horizontal transfer of transposable elements (HTT) is an important driver of genome evolution, yet the factors conditioning this phenomenon remain poorly characterized. Here, we screen 247 animal genomes from four phyla (annelids, arthropods, mollusks, chordates), spanning 19 independent transitions between aquatic and terrestrial lifestyles, to evaluate the suspected positive effects of aquatic habitat and of phylogenetic relatedness on HTT. Among the 6043 independent HTT events recovered, the vast majority (>85%) involve DNA transposons, of which Mariner-like and hAT-like elements have the highest rates of horizontal transfer and of intragenomic amplification. Using a novel approach that circumvents putative biases linked to phylogenetic inertia and taxon sampling, we find that HTT rates positively correlate with similarity in habitat type but are not significantly higher in aquatic than in terrestrial animals. However, modeling the number of HTT events as a function of divergence time in a Bayesian framework reveals a clear positive effect of phylogenetic relatedness on HTT rates in most of the animal species studied (162 out of 247). The effect is very pronounced: A typical species is expected to show 10 times more transfers with a species it diverged from 250 million years (My) ago than with a species it diverged from 650 My ago. Overall, our study underscores the pervasiveness of HTT throughout animals and the impact of evolutionary relatedness on its dynamics.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"17 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144802840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome researchPub Date : 2025-08-07DOI: 10.1101/gr.280586.125
Jordan H. Little, Guillermo Hoffmann Meyer, Aakash Grover, Alex Michael Francette, Raghavendran Partha, Karen M. Arndt, Martin Smith, Nathan Clark, Maria Chikina
{"title":"ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies","authors":"Jordan H. Little, Guillermo Hoffmann Meyer, Aakash Grover, Alex Michael Francette, Raghavendran Partha, Karen M. Arndt, Martin Smith, Nathan Clark, Maria Chikina","doi":"10.1101/gr.280586.125","DOIUrl":"https://doi.org/10.1101/gr.280586.125","url":null,"abstract":"Evolutionary rate covariation (ERC) is an established comparative genomics method that identifies sets of genes sharing patterns of sequence evolution, which suggests shared function. Whereas many functional predictions of ERC have been empirically validated, its predictive power has hitherto been limited by its inability to tackle the large numbers of species in contemporary comparative genomics data sets. This study introduces ERC2.0, an enhanced methodology for studying ERC across phylogenies with hundreds of species and tens of thousands of genes. ERC2.0 improves upon previous iterations of ERC in algorithm speed, normalizing for heteroskedasticity, and normalizing correlations via Fisher transformations. These improvements have resulted in greater statistical power to predict biological function. In exemplar yeast and mammalian data sets, we demonstrate that the predictive power of ERC2.0 is improved relative to the previous method, ERC1.0, and that further improvements are obtained by using larger yeast and mammalian phylogenies. We attribute the improvements to both the larger data sets and improved rate normalization. We demonstrate that ERC2.0 has high predictive accuracy for known annotations and can predict the functions of genes in nonmodel systems. Our findings underscore the potential for ERC2.0 to be used as a single-pass computational tool in candidate gene screening and functional predictions.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"732 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144796708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome researchPub Date : 2025-08-06DOI: 10.1101/gr.278992.124
Shachinthaka D. Dissanayaka Mudiyanselage, Phillip Wulfridge, Kavitha Sarma
{"title":"The paradox of R-loops: guardians of the genome or drivers of disease?","authors":"Shachinthaka D. Dissanayaka Mudiyanselage, Phillip Wulfridge, Kavitha Sarma","doi":"10.1101/gr.278992.124","DOIUrl":"https://doi.org/10.1101/gr.278992.124","url":null,"abstract":"R-loops, chromatin structures containing DNA–RNA hybrids with displaced single-stranded DNA, play crucial roles in various cellular processes. Their formation is influenced by factors such as DNA topology, RNA stability, and the presence of GC-rich regions. However, excessive or uncontrolled R-loop accumulation can threaten genomic stability, leading to DNA damage, particularly double-strand breaks. To preserve genome integrity, cells have developed mechanisms to regulate R-loop formation and resolution. Dysregulation of these processes is linked to several diseases, including cancer and neurodegenerative disorders. In this review, we will explore the dynamics of R-loop formation and resolution and how they are detected, their roles in DNA damage and repair, and how their dysregulation may lead to immune responses and disease pathogenesis.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"56 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144792298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression","authors":"Sudeshna Majumdar, Lakshmi Sowjanya Bammidi, Hemant C. Naik, Avinchal Manhas, Runumi Baro, Akash Kalita, Amlan Jyoti Naskar, Sundarraj Nidharshan, Girija S. Bariha, Dimple Notani, Srimonta Gayen","doi":"10.1101/gr.279822.124","DOIUrl":"https://doi.org/10.1101/gr.279822.124","url":null,"abstract":"<em>Xist</em> long noncoding RNA is the master regulator of the X-Chromosome inactivation (XCI) process. <em>Xist</em> is expressed from the inactive X and coats the inactive X to facilitate XCI. <em>Cis</em>-regulation of <em>Xist</em> expression remains poorly understood in the context of maintenance of XCI. Here, we have explored the role of the <em>Xist</em> upstream sequences (∼6 kb) lying between <em>Tsix</em> and <em>Jpx</em> in the regulation of <em>Xist</em> and XCI in mouse extra-embryonic endoderm stem cells (XEN), which represent the maintenance phase of imprinted XCI. Here, we show that the deletion of this <em>Xist</em> upstream sequence in the inactive X leads to the upregulation of <em>Xist</em> expression accompanied by the dispersal of the <em>Xist</em> cloud. Notably, we find the loss of enrichment of repressive marks such as H3K27me3, H4K20me1, and MacroH2A, except that of H2AK119ub, in dispersed <em>Xist</em> nuclei. However, X-linked genes remain silent despite <em>Xist</em> dispersal and loss of enrichment of repressive marks. Notably, we find that many autosomal genes, including cohesin <em>Rad21</em>, are dysregulated in <em>Xist</em>-upstream-deleted cells. Additionally, we demonstrate that <em>Xist</em>-upstream deletion leads to alterations of topological contacts of the <em>Xist</em> locus with its upstream positive regulator <em>Ftx</em> and across the inactive X and autosomes. Finally, we show genome-wide alterations of the occupancy of architectural proteins CTCF/RAD21, including at many loci of the inactive X such as the <em>Xist</em> upstream regions and the <em>Firre</em> locus, which is critical for maintaining inactive X conformation. Taken together, we demonstrate that the <em>Xist</em> upstream sequence imparts a multifaceted role in genome regulation beyond the XCI.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"727 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144792280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome researchPub Date : 2025-08-06DOI: 10.1101/gr.279557.124
Daffodil M. Canson, Michael T. Parsons, Gemma Moir-Meyer, Troy Dumenil, Gemma Montalban, Erica Lin, Terri P. McVeigh, Aimee L. Davidson, Shaun M. Bouckaert, Matt Trau, Darren Korbie, Amanda B. Spurdle
{"title":"The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms","authors":"Daffodil M. Canson, Michael T. Parsons, Gemma Moir-Meyer, Troy Dumenil, Gemma Montalban, Erica Lin, Terri P. McVeigh, Aimee L. Davidson, Shaun M. Bouckaert, Matt Trau, Darren Korbie, Amanda B. Spurdle","doi":"10.1101/gr.279557.124","DOIUrl":"https://doi.org/10.1101/gr.279557.124","url":null,"abstract":"<em>BRCA1</em> and <em>BRCA2</em> germline variant classification is vital for clinical management of families with hereditary breast and ovarian cancer. However, clinical classification of rare variants outside of the splice donor/acceptor ±1,2-dinucleotides remains challenging, particularly for variants that induce new or cryptic splice site usage. Here, we present SeqSplice<em>,</em> a high-throughput RNA splicing methodology utilizing barcoded minigene constructs together with a bespoke bioinformatics pipeline for identifying and quantifying the impacts for splice-altering variants. SeqSplice exhibits excellent reproducibility across cDNA input and PCR cycle differences and is able to identify and quantitate transcripts that differed by a single base. Of the 193 <em>BRCA1</em> and 72 <em>BRCA2</em> variants profiled, 89% (237/265) had no publicly available RNA splicing data. Complete or near complete impact owing to splice site gain/loss is observed for 42 variants, with 30 (71%) producing alternative transcripts owing to new or cryptic splice sites. These findings are used to update our aberration type predictor called SpliceAI-10k calculator, resulting in 94% specificity and 90% sensitivity for major alternative transcripts (>50% proportion). Comparison of SeqSplice findings for 28 variants with published data shows the value and limitations of using construct-based results for variant classification. Overall, our findings inform use of construct-derived data for clinical variant classification. We show that construct-derived results for variants showing low or no splicing impact provide reliable evidence against variant pathogenicity, whereas—for variants demonstrating splicing impact—construct design and naturally occurring alternative splicing are important considerations for assigning and weighting evidence towards pathogenicity.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"31 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144792300","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome researchPub Date : 2025-08-05DOI: 10.1101/gr.280380.124
Caden J. Martin, Elizabeth A. Oser, Prabakaran Nagarajan, Liudmila V. Popova, Benjamin D. Sunkel, Benjamin Z. Stanton, Mark R. Parthun
{"title":"Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation","authors":"Caden J. Martin, Elizabeth A. Oser, Prabakaran Nagarajan, Liudmila V. Popova, Benjamin D. Sunkel, Benjamin Z. Stanton, Mark R. Parthun","doi":"10.1101/gr.280380.124","DOIUrl":"https://doi.org/10.1101/gr.280380.124","url":null,"abstract":"A large fraction of the genome interacts with the nuclear periphery through lamina-associated domains (LADs), repressive regions which play an important role in genome organization and gene regulation across development. Despite much work, LAD structure and regulation are not fully understood, and a mounting number of studies have identified numerous genetic and epigenetic differences within LADs, demonstrating they are not a uniform group. Here, we profile lamin B1, CBX1 (also known as HP1B), H3K9me3, H3K9me2, H3K27me3, H3K14ac, H3K27ac, and H3K9ac in MEF cell lines derived from the same mouse colony, and cluster LADs based on the abundance and distribution of these features across LADs. We find that LADs fall into three groups, each enriched in a unique set of histone modifications and genomic features. Each group is defined by a different heterochromatin modification (H3K9me3, H3K9me2, or H3K27me3), suggesting that all three of these marks play important roles in regulation of LAD chromatin and potentially of lamina association. We also discover unique features of LAD borders, including a LAD border–specific enrichment of H3K14ac. These results reveal important distinctions between LADs and highlight the rich diversity and complexity in LAD structure and regulatory mechanisms.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"161 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144786796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}