Genome research最新文献_第2页

Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes 揭示甲基化依赖性基因对不同基因组调控元件功能的影响

IF 7 2区生物学

Genome research Pub Date : 2025-07-14 DOI: 10.1101/gr.279957.124

Rachel M. Petersen, Christopher M. Vockley, Amanda J. Lea

{"title":"Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes","authors":"Rachel M. Petersen, Christopher M. Vockley, Amanda J. Lea","doi":"10.1101/gr.279957.124","DOIUrl":"https://doi.org/10.1101/gr.279957.124","url":null,"abstract":"A major goal in evolutionary biology and biomedicine is to understand the complex interactions between genetic variants, the epigenome, and gene expression. However, the causal relationships between these factors remain poorly understood. mSTARR-seq, a methylation-sensitive massively parallel reporter assay, is capable of identifying methylation-dependent regulatory activity at many thousands of genomic regions simultaneously and allows for the testing of causal relationships between DNA methylation and gene expression on a region-by-region basis. Here, we develop a multiplexed mSTARR-seq protocol to assay naturally occurring human genetic variation from 25 individuals from 10 localities in Europe and Africa. We identify 6957 regulatory elements in either the unmethylated or methylated state, and this set was enriched for enhancer and promoter chromatin annotations, as expected. The expression of 58% of these regulatory elements is modulated by methylation, which is generally associated with decreased transcription. Within our set of regulatory elements, we use allele-specific expression analyses to identify 8020 sites with genetic effects on gene regulation; further, we find that 42.3% of these genetic effects vary in direction or magnitude between methylated and unmethylated states. Sites exhibiting methylation-dependent genetic effects are enriched for GWAS and EWAS annotations, implicating them in human disease. Compared with data sets that assay DNA from a single European ancestry individual, our multiplexed assay is able to uncover more genetic effects and methylation-dependent genetic effects, highlighting the importance of including diverse genomes in assays that aim to understand gene regulatory processes.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"45 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144622378","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}

引用次数: 0

A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq 利用捕获的STARR-seq技术绘制人类原代神经祖细胞的增强子区域图

IF 7 2区生物学

Genome research Pub Date : 2025-07-11 DOI: 10.1101/gr.279584.124

Sophia C. Gaynor-Gillett, Lijun Cheng, Manman Shi, Jason Liu, Gaoyuan Wang, Megan Spector, Qiuyu Guo, Le Qi, Mary Flaherty, Martha Wall, Ahyeon Hwang, Mengting Gu, Zhanlin Chen, Yuhang Chen, PsychENCODE Consortium, Jennifer R. Moran, Jing Zhang, Donghoon Lee, Mark Gerstein, Daniel Geschwind, Kevin P. White

{"title":"A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq","authors":"Sophia C. Gaynor-Gillett, Lijun Cheng, Manman Shi, Jason Liu, Gaoyuan Wang, Megan Spector, Qiuyu Guo, Le Qi, Mary Flaherty, Martha Wall, Ahyeon Hwang, Mengting Gu, Zhanlin Chen, Yuhang Chen, PsychENCODE Consortium, Jennifer R. Moran, Jing Zhang, Donghoon Lee, Mark Gerstein, Daniel Geschwind, Kevin P. White","doi":"10.1101/gr.279584.124","DOIUrl":"https://doi.org/10.1101/gr.279584.124","url":null,"abstract":"Genome-wide association studies (GWASs) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. Here, we perform capture STARR-sequencing of over 70,000 candidate regions to identify active enhancers in primary human neural progenitor cells (phNPCs). We select candidate regions by integrating data from NPCs, prefrontal cortex, developmental timepoints, and GWASs. Over 8000 regions demonstrate enhancer activity in the phNPCs, and we link these regions to over 2200 predicted target genes. These genes are involved in neuronal and psychiatric disease-associated pathways, including neuronal system, nervous system development, and developmental delay. We functionally validate a subset of these enhancers using mutation STARR-sequencing and CRISPR deletions, demonstrating the effects of genetic variation on enhancer activity and enhancer deletion on gene expression. Overall, we identify thousands of highly active enhancers and functionally validated a subset of these enhancers, improving our understanding of regulatory networks underlying brain function and disease.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"12 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144611024","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}

引用次数: 0

De novo gene birth and the conundrum of ORFan genes in bacteria 细菌中新生基因的诞生和ORFan基因的难题

IF 7 2区生物学

Genome research Pub Date : 2025-07-10 DOI: 10.1101/gr.280157.124

Md. Hassan uz-Zaman, Howard Ochman

引用次数: 0

Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth 具有丰富Chi重组热点的羔羊样噬菌体反映了重组依赖性生长的多种病毒策略

IF 7 2区生物学

Genome research Pub Date : 2025-07-10 DOI: 10.1101/gr.280248.124

Clarence Zheng, Sherwood R. Casjens, Alan R. Davidson, Susan K. Amundsen, Gerald R. Smith

{"title":"Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth","authors":"Clarence Zheng, Sherwood R. Casjens, Alan R. Davidson, Susan K. Amundsen, Gerald R. Smith","doi":"10.1101/gr.280248.124","DOIUrl":"https://doi.org/10.1101/gr.280248.124","url":null,"abstract":"Many phages encode recombination-mediating enzymes, but characterization of their roles in phage lifecycles is limited, and their impact on phage replication is controversial. To address these issues, we have searched for phages whose growth is impacted by the major recombination-promoting helicase-nuclease of Escherichia coli, the RecBCD enzyme. Although no phages inhibited by RecBCD are identified, growth of a newly isolated phage, named LLS, is enhanced by RecBCD. LLS's genome sequence reveals it is related to bacteriophage λ but encodes no recombination-promoting (Rec) proteins or associated RecBCD inhibitor. However, it contains an unexpectedly high number of Chi sites, activators of RecBCD-dependent recombination. Through analysis of 325 genomes of phages related to λ (lambdoid phages), we have found 71 other phage genomes that encode no Rec proteins but mostly possess large numbers of Chi sites. Conversely, phages encoding Rec proteins and a RecBCD inhibitor (collectively a Rec module) mostly lack Chi sites. Lambdoid phages of both diverse enteric bacteria and a pseudomonad have these properties. For this study, we thoroughly analyze the Rec modules of 246 lambdoid phage genomes. These analyses reveal a remarkable heterogeneity of Rec module protein types, both in sequence and in function, and allow us to identify phages that do not contain Rec modules. We conclude that phages lacking their own recombination systems have compensated by becoming enriched in Chi sites, enabling them to use the host's RecBCD to fulfill the requirement for recombination to efficiently replicate. This study highlights the importance of recombination for phage survival and the diversity of strategies to achieve it.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"688 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144593970","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}

引用次数: 0

Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq 利用SpectralSeq整合来自单个细胞的高光谱成像和转录组学

IF 7 2区生物学

Genome research Pub Date : 2025-07-08 DOI: 10.1101/gr.280014.124

Yike Xie, Abbas Habibalahi, Ayad G. Anwer, Kanu Wahi, Jacqueline Bailey, Francis Lin, Catherine Gatt, Emma M.V. Johansson, Tatyana Chtanova, Jeff Holst, Ewa Goldys, Fabio Zanini

{"title":"Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq","authors":"Yike Xie, Abbas Habibalahi, Ayad G. Anwer, Kanu Wahi, Jacqueline Bailey, Francis Lin, Catherine Gatt, Emma M.V. Johansson, Tatyana Chtanova, Jeff Holst, Ewa Goldys, Fabio Zanini","doi":"10.1101/gr.280014.124","DOIUrl":"https://doi.org/10.1101/gr.280014.124","url":null,"abstract":"Microscopy and omics are complementary approaches to probe cellular molecular states in health and disease, combining granularity with scalability. However, integrating both imaging- and sequencing-based assays on the same cell has proven challenging. This study demonstrates a new approach called SpectralSeq that combines hyperspectral autofluorescence imaging with transcriptomics on the same cell. SpectralSeq is applied to Michigan Cancer Foundation-7 (MCF-7) breast cancer cells and identifies a subpopulation of cells exhibiting bright autofluorescence rings at the plasma membrane in optical channel 13 (λex = 431 nm, λem = 594 nm). Correlating the presence of a ring with the gene expression in the same cell indicates that ringed cells show higher expression of apoptosis-related genes and lower expression of ATP production genes. Furthermore, correlation of cell morphology with gene expression reveals downregulation of multiple spliceosome members in larger MCF-7 cells. Multiple genes exhibit consistent expression across cell sizes but varied exon usage. Finally, correlation between gene expression and fluorescence within the spectral range of nicotinamide adenine dinucleotide hydrogen (NADH) provides insights into the metabolic states of MCF-7 cells. Overall, SpectralSeq links optical spectrum with internal molecular states, offering a single streamlined workflow for single-cell resolution studies integrating spectral, morphological, and transcriptomic analyses.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"27 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144586556","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}

引用次数: 0

Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy 动态屏障调节内聚定位和基因组折叠在固定占用

IF 7 2区生物学

Genome research Pub Date : 2025-07-08 DOI: 10.1101/gr.280108.124

Hadi Rahmaninejad, Yao Xiao, Maxime M.C. Tortora, Geoffrey Fudenberg

{"title":"Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy","authors":"Hadi Rahmaninejad, Yao Xiao, Maxime M.C. Tortora, Geoffrey Fudenberg","doi":"10.1101/gr.280108.124","DOIUrl":"https://doi.org/10.1101/gr.280108.124","url":null,"abstract":"In mammalian interphase cells, genomes are folded by cohesin loop extrusion limited by directional CTCF barriers. This process enriches cohesin at barriers, isolates neighboring topologically associating domains, and elevates contact frequency between convergent CTCF barriers across the genome. However, recent in vivo measurements present a puzzle: reported CTCF residence times on chromatin are in the range of a few minutes, whereas cohesin lifetimes are much longer. Can the observed features of genome folding result from relatively transient barriers? To address this question, we develop a dynamic barrier model, where CTCF sites switch between bound and unbound states. Using this model, we investigate how barrier dynamics would impact observables for a range of experimental genomic and imaging data sets, including ChIP-seq, Hi-C, and microscopy. We find the interplay of CTCF and cohesin binding timescales influence the strength of each of these features, leaving a signature of barrier dynamics even in the population-averaged snapshots offered by genomic data sets. First, in addition to barrier occupancy, barrier bound times are crucial for instructing features of genome folding. Second, the ratio of boundary to extruder lifetime greatly alters simulated ChIP-seq and simulated Hi-C. Third, large-scale changes in chromosome morphology observed experimentally after increasing extruder lifetime require dynamic barriers. By integrating multiple sources of experimental data, our biophysical model argues that CTCF barrier bound times effectively approach those of cohesin extruder lifetimes. Together, we demonstrate how models that are informed by biophysically measured protein dynamics broaden our understanding of genome folding.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"21 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144586557","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}

引用次数: 0

Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated 单细胞RNA测序分析中使用的批量校正方法往往校准不良

IF 7 2区生物学

Genome research Pub Date : 2025-07-07 DOI: 10.1101/gr.279886.124

Sindri Emmanúel Antonsson, Páll Melsted

{"title":"Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated","authors":"Sindri Emmanúel Antonsson, Páll Melsted","doi":"10.1101/gr.279886.124","DOIUrl":"https://doi.org/10.1101/gr.279886.124","url":null,"abstract":"As the number of experiments that employ single-cell RNA sequencing (scRNA-seq) grows, it opens up the possibility of combining results across experiments or processing cells from the same experiment assayed in separate sequencing runs. The gain in the number of cells that can be compared comes at the cost of batch effects that may be present. Several methods have been proposed to combat this for scRNA-seq data sets. We compare eight widely used methods used for batch correction of scRNA-seq data sets. We present a novel approach to measure the degree to which the methods alter the data in the process of batch correction, both at the fine scale, comparing distances between cells, as well as measuring effects observed across clusters of cells. We demonstrate that many of the published methods are poorly calibrated in the sense that the process of correction creates measurable artifacts in the data. In particular, MNN, SCVI, and LIGER perform poorly in our tests, often altering the data considerably. Batch correction with Combat, ComBat-seq, BBKNN, and Seurat introduces artifacts that could be detected in our setup. However, we find that Harmony is the only method that consistently performs well in all the testing methodology we present. Therefore, Harmony is the only method we recommend using when performing batch correction of scRNA-seq data.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"21 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144578401","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}

引用次数: 0

QuadST identifies cell-cell interaction-changed genes in spatially resolved transcriptomics data QuadST在空间解析转录组学数据中识别细胞-细胞相互作用改变的基因

IF 7 2区生物学

Genome research Pub Date : 2025-06-23 DOI: 10.1101/gr.279859.124

Xiaoyu Song, Yuqing Shang, Michelle Ehrlich, Panos Roussos, Guo-Cheng Yuan, Pei Wang

引用次数: 0

Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes Wnt信号激活诱导CTCF结合并在靶基因的顺式调控元件上形成环

IF 7 2区生物学

Genome research Pub Date : 2025-06-23 DOI: 10.1101/gr.279684.124

Anna Nordin, Chaitali Chakraborty, Mattias Jonasson, Orgena Dano, Gianluca Zambanini, Pierfrancesco Pagella, Silvia Remeseiro, Claudio Cantu

{"title":"Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes","authors":"Anna Nordin, Chaitali Chakraborty, Mattias Jonasson, Orgena Dano, Gianluca Zambanini, Pierfrancesco Pagella, Silvia Remeseiro, Claudio Cantu","doi":"10.1101/gr.279684.124","DOIUrl":"https://doi.org/10.1101/gr.279684.124","url":null,"abstract":"Wnt signaling plays a pivotal role during development and homeostasis. Upon pathway activation, CTNNB1 (also known as beta-catenin) drives the expression of target genes from regulatory regions bound by TCF/LEF transcription factors. Gene regulation, however, entails the interplay between sequence information and 3D genome structure, yet the impact of Wnt signaling on genome structure has been poorly explored. Here we investigate how Wnt signaling influences CTCF and cohesin, key regulators of 3D genome organization. We identify a series of novel CTCF binding sites that emerge upon Wnt stimulation: CTCF redistributions under Wnt (RUW). RUW sites are characterized by CTCF, cohesin and TCF/LEF occupancy and are dependent on beta-catenin. Beta-catenin and CTCF colocalize upon pathway activation, and disruption of selected binding sites perturbs target gene regulation. Moreover, Wnt signaling reorganizes the 3D genome as evidenced by genome-wide alterations in CTCF-bound loops. This work reveals a previously unexplored role for CTCF in the regulation of Wnt signaling.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"243 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144371139","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}

引用次数: 0

Multi-tissue single-nucleus RNA-seq reveals cell type-specific regulatory patterns of alternative polyadenylation in pigs 多组织单核RNA-seq揭示了猪选择性聚腺苷酸化的细胞类型特异性调控模式

IF 7 2区生物学

Genome research Pub Date : 2025-06-16 DOI: 10.1101/gr.280095.124

Qiuhan Wen, Zhen Wang, Qi Bao, Tianli Ding, Haihan Zhang, Jianbo Li, Zhuang Liu, Jieping Huang, Guoqiang Yi

{"title":"Multi-tissue single-nucleus RNA-seq reveals cell type-specific regulatory patterns of alternative polyadenylation in pigs","authors":"Qiuhan Wen, Zhen Wang, Qi Bao, Tianli Ding, Haihan Zhang, Jianbo Li, Zhuang Liu, Jieping Huang, Guoqiang Yi","doi":"10.1101/gr.280095.124","DOIUrl":"https://doi.org/10.1101/gr.280095.124","url":null,"abstract":"As an important post-transcriptional modification mechanism, alternative polyadenylation (APA) plays a crucial role in gene regulation and phenotypic diversity. While extensive studies have explored the global APA landscape using bulk RNA-seq data, in-depth analyses of APA events at the single-cell level remain limited - particularly in farm animals. In this study, we constructed a comprehensive APA atlas for 261 cell types across 19 porcine tissues based on single-nucleus RNA sequencing (snRNA-seq) data. This analysis revealed tissue- and cell type-specific patterns of APA. We found that many genes displayed a clear correlation between the average length of 3' untranslated regions (3'UTRs) and expression levels in various cell types, with most showing a negative correlation. Early cell types within the developmental lineage, such as spermatogonia and satellite cells, displayed longer 3'UTRs, especially for spermatogenesis, where 3'UTR lengths showed significant decreasing trends along the differentiation trajectory. Notably, we identified that variable 3'UTR lengths in the CD47 and GPD1 genes might be critical regulators during spermatogenesis and myogenesis, respectively, potentially through modulation of RNA-binding protein and miRNA binding sites. Furthermore, the SNP rs323354626, located in the 3'UTR of the CD47 gene, significantly impacts gene splicing and is strongly associated with reproductive phenotypes. Additionally, we observed that neuronal cells generally possess longer 3'UTRs – a pattern conserved across humans, mice, fruit flies, and pigs. Together, these findings enrich the single-cell atlas of pigs by adding a layer of post-transcriptional regulation to the existing gene expression data, highlighting the significant role of cell type-specific 3'UTR lengths in cell commitment and complex trait regulation.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"21 1","pages":"gr.280095.124"},"PeriodicalIF":7.0,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144304922","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}

引用次数: 0