Genome research最新文献_第5页

Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression 单核CUT&RUN阐明了内在和基因组学驱动的表观遗传异质性在头颈癌进展中的作用

IF 7 2区生物学

Genome research Pub Date : 2024-12-02 DOI: 10.1101/gr.279105.124

Howard Womersley, Daniel Muliaditan, Ramanuj DasGupta, Lih Feng Cheow

{"title":"Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression","authors":"Howard Womersley, Daniel Muliaditan, Ramanuj DasGupta, Lih Feng Cheow","doi":"10.1101/gr.279105.124","DOIUrl":"https://doi.org/10.1101/gr.279105.124","url":null,"abstract":"Interrogating regulatory epigenetic alterations during tumor progression at the resolution of single cells has remained an understudied area of research. Here we developed a highly sensitive single-nucleus CUT&RUN (snCUT&RUN) assay to profile histone modifications in isogenic primary, metastatic, and cisplatin-resistant head and neck squamous cell carcinoma (HNSCC) patient-derived tumor cell lines. We find that the epigenome can be involved in diverse modes to contribute towards HNSCC progression. First, we demonstrate that gene expression changes during HNSCC progression can be comodulated by alterations in both copy number and chromatin activity, driving epigenetic rewiring of cell states. Furthermore, intratumour epigenetic heterogeneity (ITeH) may predispose subclonal populations within the primary tumour to adapt to selective pressures and foster the acquisition of malignant characteristics. In conclusion, snCUT&RUN serves as a valuable addition to the existing toolkit of single-cell epigenomic assays and can be used to dissect the functionality of the epigenome during cancer progression.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"13 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142760655","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

Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging 嵌合线粒体 RNA 转录本预测线粒体遗传疾病和衰老中的线粒体基因组缺失突变

IF 7 2区生物学

Genome research Pub Date : 2024-11-27 DOI: 10.1101/gr.279072.124

Amy R Vandiver, Allen Herbst, Paul Stothard, Jonathan Wanagat

{"title":"Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging","authors":"Amy R Vandiver, Allen Herbst, Paul Stothard, Jonathan Wanagat","doi":"10.1101/gr.279072.124","DOIUrl":"https://doi.org/10.1101/gr.279072.124","url":null,"abstract":"While it is well understood that mitochondrial DNA (mtDNA) deletion mutations cause incurable diseases and contribute to aging, little is known about the transcriptional products that arise from these DNA structural variants. We hypothesized that mitochondrial genomes containing deletion mutations express chimeric mitochondrial RNAs. To test this, we analyzed human and rat RNA sequencing data to identify, quantitate, and characterize chimeric mitochondrial RNAs. We observed increased chimeric mitochondrial RNA frequency in samples from patients with mitochondrial genetic diseases and in samples from aged humans. The spectrum of chimeric mitochondrial transcripts reflected the known pattern of mtDNA deletion mutations. To test the hypothesis that mtDNA deletions induce chimeric RNA transcripts, we treated 18 mo and 34 mo rats with guanidinopropionic acid to induce high levels of skeletal muscle mtDNA deletion mutations. With mtDNA deletion induction, we demonstrate that the chimeric mitochondrial transcript frequency also increased and correlated strongly with an orthogonal DNA-based mutation assay performed on identical samples. Further, we show that the frequency of chimeric mitochondrial transcripts predicts expression of both nuclear and mitochondrial genes central to mitochondrial function, demonstrating the utility of these events as metrics of age-induced metabolic change. Mapping and quantitation of chimeric mitochondrial RNAs provides an accessible, orthogonal approach to DNA-based mutation assays, offers a potential method for identifying mitochondrial pathology in widely accessible datasets, and opens a new area of study in mitochondrial genetics and transcriptomics.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"25 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142718243","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 deconvolution framework that uses single-cell sequencing plus a small benchmark dataset for accurate analysis of cell type ratios in complex tissue samples 利用单细胞测序和小型基准数据集精确分析复杂组织样本中细胞类型比例的解卷积框架

IF 7 2区生物学

Genome research Pub Date : 2024-11-25 DOI: 10.1101/gr.278822.123

Shuai Guo, Xiaoqian Liu, Xuesen Cheng, Yujie Jiang, Shuangxi Ji, Qingnan Liang, Andrew Koval, Yumei Li, Leah A. Owen, Ivana K. Kim, Ana Aparicio, Sanghoon Lee, Anil K. Sood, Scott Kopetz, John Paul Shen, John N. Weinstein, Margaret M. DeAngelis, Rui Chen, Wenyi Wang

{"title":"A deconvolution framework that uses single-cell sequencing plus a small benchmark dataset for accurate analysis of cell type ratios in complex tissue samples","authors":"Shuai Guo, Xiaoqian Liu, Xuesen Cheng, Yujie Jiang, Shuangxi Ji, Qingnan Liang, Andrew Koval, Yumei Li, Leah A. Owen, Ivana K. Kim, Ana Aparicio, Sanghoon Lee, Anil K. Sood, Scott Kopetz, John Paul Shen, John N. Weinstein, Margaret M. DeAngelis, Rui Chen, Wenyi Wang","doi":"10.1101/gr.278822.123","DOIUrl":"https://doi.org/10.1101/gr.278822.123","url":null,"abstract":"Bulk deconvolution with single-cell/nucleus RNA-seq data is critical for understanding heterogeneity in complex biological samples, yet the technological discrepancy across sequencing platforms limits deconvolution accuracy. To address this, we utilize an experimental design to match inter-platform biological signals, hence revealing the technological discrepancy, and then develop a deconvolution framework called DeMixSC using this well-matched, i.e., benchmark, data. Built upon a novel weighted nonnegative least-squares framework, DeMixSC identifies and adjusts genes with high technological discrepancy and aligns the benchmark data with large patient cohorts of matched-tissue-type for large-scale deconvolution. Our results using two benchmark datasets of healthy retinas and ovarian cancer tissues suggest much-improved deconvolution accuracy. Leveraging tissue-specific benchmark datasets, we applied DeMixSC to a large cohort of 453 age-related macular degeneration patients and a cohort of 30 ovarian cancer patients with various responses to neoadjuvant chemotherapy. Only DeMixSC successfully unveiled biologically meaningful differences across patient groups, demonstrating its broad applicability in diverse real-world clinical scenarios. Our findings reveal the impact of technological discrepancy on deconvolution performance and underscore the importance of a well-matched dataset to resolve this challenge. The developed DeMixSC framework is generally applicable for accurately deconvolving large cohorts of disease tissues, including cancers, when a well-matched benchmark dataset is available.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"35 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142712790","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

Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay 哺乳动物宿主和嵌套基因对的全球鉴定揭示了组织特异性转录相互作用

IF 7 2区生物学

Genome research Pub Date : 2024-11-22 DOI: 10.1101/gr.279430.124

Bertille Montibus, James A. Cain, Rocio T. Martinez-Nunez, Rebecca J. Oakey

{"title":"Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay","authors":"Bertille Montibus, James A. Cain, Rocio T. Martinez-Nunez, Rebecca J. Oakey","doi":"10.1101/gr.279430.124","DOIUrl":"https://doi.org/10.1101/gr.279430.124","url":null,"abstract":"Nucleotide sequences along a gene provide instructions to transcriptional and cotranscriptional machinery allowing genome expansion into the transcriptome. Nucleotide sequence can often be shared between two genes and in some occurrences, a gene is located completely within a different gene; these are known as host/nested gene pairs. In these instances, if both genes are transcribed, overlap can result in a transcriptional crosstalk where genes regulate each other. Despite this, a comprehensive annotation of where such genes are located and their expression patterns is lacking. To address this, we provide an up-to-date catalog of host/nested gene pairs in mouse and human, showing that over a tenth of all genes contain a nested gene. We discovered that transcriptional co-occurrence is often tissue specific. This coexpression was especially prevalent within the transcriptionally permissive tissue, testis. We use this developmental system and scRNA-seq analysis to demonstrate that the coexpression of pairs can occur in single cells and transcription in the same place at the same time can enhance the transcript diversity of the host gene. In agreement, host genes are more transcript-diverse than the rest of the transcriptome. Host/nested gene configurations are common in both human and mouse, suggesting that interplay between gene pairs is a feature of the mammalian genome. This highlights the relevance of transcriptional crosstalk between genes which share nucleic acid sequence. The results and analysis are available on an Rshiny application (https://hngeneviewer.sites.er.kcl.ac.uk/hn_viewer/).","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"34 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142690668","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

Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets 食草动物分子约束的趋同性放松揭示了肝脏和肾脏功能在哺乳动物饮食中不断变化的作用

IF 7 2区生物学

Genome research Pub Date : 2024-11-22 DOI: 10.1101/gr.278930.124

Matthew D. Pollard, Wynn K. Meyer, Emily E. Puckett

{"title":"Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets","authors":"Matthew D. Pollard, Wynn K. Meyer, Emily E. Puckett","doi":"10.1101/gr.278930.124","DOIUrl":"https://doi.org/10.1101/gr.278930.124","url":null,"abstract":"Mammalia comprises a great diversity of diet types and associated adaptations. An understanding of the genomic mechanisms underlying these adaptations may offer insights for improving human health. Comparative genomic studies of diet that employ taxonomically restricted analyses or simplified diet classifications may suffer reduced power to detect molecular convergence associated with diet evolution. Here, we use a quantitative carnivory score—indicative of the amount of animal protein in the diet—for 80 mammalian species to detect significant correlations between the relative evolutionary rates of genes and changes in diet. We have identified six genes—ACADSB, CLDN16, CPB1, PNLIP, SLC13A2, and SLC14A2—that experienced significant changes in evolutionary constraint alongside changes in carnivory score, becoming less constrained in lineages evolving more herbivorous diets. We further consider the biological functions associated with diet evolution and observe that pathways related to amino acid and lipid metabolism, biological oxidation, and small molecule transport experienced reduced purifying selection as lineages became more herbivorous. Liver and kidney functions show similar patterns of constraint with dietary change. Our results indicate that these functions are important for the consumption of animal matter and become less important with the evolution of increasing herbivory. So, genes expressed in these tissues experience a relaxation of evolutionary constraint in more herbivorous lineages.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"5 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142690669","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

KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome KAS-ATAC 揭示人类基因组的全基因组单链可访问染色质景观

IF 7 2区生物学

Genome research Pub Date : 2024-11-21 DOI: 10.1101/gr.279621.124

Samuel H Kim, Georgi K. Marinov, William Greenleaf

{"title":"KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome","authors":"Samuel H Kim, Georgi K. Marinov, William Greenleaf","doi":"10.1101/gr.279621.124","DOIUrl":"https://doi.org/10.1101/gr.279621.124","url":null,"abstract":"Gene regulation in most eukaryotes involves two fundamental physical processes -- alterations in the packaging of the genome by nucleosomes, with active cis-regulatory elements (CREs) generally characterized by an open-chromatin configuration, and the activation of transcription. Mapping these physical properties and biochemical activities genome-wide -- through profiling chromatin accessibility and active transcription -- are key tools used to understand the logic and mechanisms of transcription and its regulation. However, the relationship between these two states has until now not been accessible to simultaneous measurement. To address this, we developed KAS-ATAC, a combination of the KAS-seq (Kethoxal-Assisted SsDNA sequencing and ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) methods for mapping single-stranded DNA (and thus active transcription) and chromatin accessibility, respectively, enabling the genome-wide identification of DNA fragments that are simultaneously accessible and contain ssDNA. We use KAS-ATAC to evaluate levels of active transcription over different classes of regulatory elements in the human genome, to estimate the absolute levels of transcribed accessible DNA over CREs, to map the nucleosomal configurations associated with RNA polymerase activities, and to assess transcription factor association with transcribed DNA through transcription factor binding site (TFBS) footprinting. We observe lower levels of transcription over distal enhancers compared to promoters and distinct nucleosomal configurations around transcription initiation sites associated with active transcription. Most TFs associate equally with transcribed and nontranscribed DNA but a few factors specifically do not exhibit footprints over ssDNA-containing fragments. We anticipate KAS-ATAC to continue to derive useful insights into chromatin organization and transcriptional regulation in other contexts in the future.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"27 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684311","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

The chromatin landscape of the histone-possessing Bacteriovorax bacteria 拥有组蛋白的杆菌的染色质景观

IF 7 2区生物学

Genome research Pub Date : 2024-11-21 DOI: 10.1101/gr.279418.124

Georgi K. Marinov, Benjamin Doughty, Anshul Kundaje, William J Greenleaf

{"title":"The chromatin landscape of the histone-possessing Bacteriovorax bacteria","authors":"Georgi K. Marinov, Benjamin Doughty, Anshul Kundaje, William J Greenleaf","doi":"10.1101/gr.279418.124","DOIUrl":"https://doi.org/10.1101/gr.279418.124","url":null,"abstract":"Histone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, histone proteins have recently been identified in a few bacterial clades, most notably the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared to histones in archaea and eukaryotes. However, no functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription and three-dimensional genome organization in a member of Bdellovibrionota (a Bacteriovorax strain). We find that, similar to what is observed in some archaea and in eukaryotes with compact genomes such as yeast, Bacteriovorax chromatin is characterized by preferential accessibility around promoter regions. Similar to eukaryotes, chromatin accessibility in Bacteriovorax positively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that unlike in yeast, but similar to the state of mammalian and fly promoters, Bacteriovorax promoters exhibit very strong polymerase pausing. Finally, similar to that of other bacteria without histones, the Bacteriovorax genome exists in a three-dimensional (3D) configuration organized by the parABS system along the axis defined by replication origin and termination regions. These results provide a foundation for understanding the chromatin biology of the unique Bdellovibrionota bacteria and the functional diversity in chromatin organization across the tree of life.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"61 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684319","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

Advancements in prospective single-cell lineage barcoding and their applications in research 前瞻性单细胞系条码技术的进展及其在研究中的应用

IF 7 2区生物学

Genome research Pub Date : 2024-11-21 DOI: 10.1101/gr.278944.124

Xiaoli Zhang, Yirui Huang, Yajing Yang, Qi-En Wang, Lang Li

引用次数: 0

An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing. 利用纳米孔直接 RNA 测序对基因治疗载体进行质量控制的优化方案。

IF 6.2 2区生物学

Genome research Pub Date : 2024-11-20 DOI: 10.1101/gr.279405.124

Kathleen Zeglinski, Christian Montellese, Matthew E Ritchie, Monther Alhamdoosh, Cédric Vonarburg, Rory Bowden, Monika Jordi, Quentin Gouil, Florian Aeschimann, Arthur Hsu

{"title":"An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing.","authors":"Kathleen Zeglinski, Christian Montellese, Matthew E Ritchie, Monther Alhamdoosh, Cédric Vonarburg, Rory Bowden, Monika Jordi, Quentin Gouil, Florian Aeschimann, Arthur Hsu","doi":"10.1101/gr.279405.124","DOIUrl":"10.1101/gr.279405.124","url":null,"abstract":"Despite recent advances made toward improving the efficacy of lentiviral gene therapies, a sizeable proportion of produced vector contains an incomplete and thus potentially nonfunctional RNA genome. This can undermine gene delivery by the lentivirus as well as increase manufacturing costs and must be improved to facilitate the widespread clinical implementation of lentiviral gene therapies. Here, we compare three long-read sequencing technologies for their ability to detect issues in vector design and determine nanopore direct RNA sequencing to be the most powerful. We show how this approach identifies and quantifies incomplete RNA caused by cryptic splicing and polyadenylation sites, including a potential cryptic polyadenylation site in the widely used Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE). Using artificial polyadenylation of the lentiviral RNA, we also identify multiple hairpin-associated truncations in the analyzed lentiviral vectors (LVs), which account for most of the detected RNA fragments. Finally, we show that these insights can be used for the optimization of LV design. In summary, nanopore direct RNA sequencing is a powerful tool for the quality control and optimization of LVs, which may help to improve lentivirus manufacturing and thus the development of higher quality lentiviral gene therapies.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":" ","pages":"1966-1975"},"PeriodicalIF":6.2,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications. 纳米孔链条特异性错配可实现对细菌 DNA 修饰的从头检测。

IF 6.2 2区生物学

Genome research Pub Date : 2024-11-20 DOI: 10.1101/gr.279012.124

Xudong Liu, Ying Ni, Lianwei Ye, Zhihao Guo, Lu Tan, Jun Li, Mengsu Yang, Sheng Chen, Runsheng Li

{"title":"Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications.","authors":"Xudong Liu, Ying Ni, Lianwei Ye, Zhihao Guo, Lu Tan, Jun Li, Mengsu Yang, Sheng Chen, Runsheng Li","doi":"10.1101/gr.279012.124","DOIUrl":"10.1101/gr.279012.124","url":null,"abstract":"DNA modifications in bacteria present diverse types and distributions, playing crucial functional roles. Current methods for detecting bacterial DNA modifications via nanopore sequencing typically involve comparing raw current signals to a methylation-free control. In this study, we found that bacterial DNA modification induces errors in nanopore reads. And these errors are found only in one strand but not the other, showing a strand-specific bias. Leveraging this discovery, we developed Hammerhead, a pioneering pipeline designed for de novo methylation discovery that circumvents the necessity of raw signal inference and a methylation-free control. The majority (14 out of 16) of the identified motifs can be validated by raw signal comparison methods or by identifying corresponding methyltransferases in bacteria. Additionally, we included a novel polishing strategy employing duplex reads to correct modification-induced errors in bacterial genome assemblies, achieving a reduction of over 85% in such errors. In summary, Hammerhead enables users to effectively locate bacterial DNA methylation sites from nanopore FASTQ/FASTA reads, thus holds promise as a routine pipeline for a wide range of nanopore sequencing applications, such as genome assembly, metagenomic binning, decontaminating eukaryotic genome assemblies, and functional analysis for DNA modifications.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":" ","pages":"2025-2038"},"PeriodicalIF":6.2,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365032","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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