Nucleic Acids Research最新文献

CellPie: a scalable spatial transcriptomics factor discovery method via joint non-negative matrix factorization

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-01 DOI: 10.1093/nar/gkaf251

Sokratia Georgaka, William Geraint Morgans, Qian Zhao, Diego Sanchez Martinez, Amin Ali, Mohamed Ghafoor, Syed-Murtuza Baker, Robert G Bristow, Mudassar Iqbal, Magnus Rattray

引用次数: 0

Long-read whole-genome sequencing-based concurrent haplotyping and aneuploidy profiling of single cells

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-01 DOI: 10.1093/nar/gkaf247

Yan Zhao, Olga Tsuiko, Tatjana Jatsenko, Greet Peeters, Erika Souche, Mathilde Geysens, Eftychia Dimitriadou, Arne Vanhie, Karen Peeraer, Sophie Debrock, Hilde Van Esch, Joris Robert Vermeesch

{"title":"Long-read whole-genome sequencing-based concurrent haplotyping and aneuploidy profiling of single cells","authors":"Yan Zhao, Olga Tsuiko, Tatjana Jatsenko, Greet Peeters, Erika Souche, Mathilde Geysens, Eftychia Dimitriadou, Arne Vanhie, Karen Peeraer, Sophie Debrock, Hilde Van Esch, Joris Robert Vermeesch","doi":"10.1093/nar/gkaf247","DOIUrl":"https://doi.org/10.1093/nar/gkaf247","url":null,"abstract":"Long-read whole-genome sequencing (lrWGS) enhances haplotyping by providing more phasing information per read compared to short-read sequencing. However, its use for single-cell haplotype phasing remains underexplored. This proof-of-concept study examines lrWGS data from single cells for small variant (single nucleotide variant (SNV) and indel) and structural variation (SV) calling, as well as haplotyping, using the Genome in a Bottle (GIAB) Ashkenazi trio. lrWGS was performed on single-cell (1 cell) and multi-cell (10 cells) samples from the offspring. Chromosome-length haplotypes were obtained by leveraging both long reads and pedigree information. These haplotypes were further refined by replacing them with matched parental haplotypes. In single-cell and multi-cell samples, 92% and 98% of heterozygous SNVs, and 74% and 78% of heterozygous indels were accurately haplotyped. Applied to human embryos for preimplantation genetic testing (PGT), lrWGS demonstrated 100% consistency with array-based methods for detecting monogenic disorders, without requiring phasing references. Aneuploidies were accurately detected, with insights into the mechanistic origins of chromosomal abnormalities inferred from the parental unique allele fractions (UAFs). We show that lrWGS-based concurrent haplotyping and aneuploidy profiling of single cells provides an alternative to current PGT methods, with applications potential in areas such as cell-based prenatal diagnosis and animal and plant breeding.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"15 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143744937","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

Fungal chromatin remodeler Isw1 modulates translation via regulating tRNA transcription

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-01 DOI: 10.1093/nar/gkaf225

Jing Wang, Yueqi Zhang, Jingrui Wang, Liuqin Wang, Binshan Li, Shuang Liu, Xuepeng Sun, Zhonghua Ma

{"title":"Fungal chromatin remodeler Isw1 modulates translation via regulating tRNA transcription","authors":"Jing Wang, Yueqi Zhang, Jingrui Wang, Liuqin Wang, Binshan Li, Shuang Liu, Xuepeng Sun, Zhonghua Ma","doi":"10.1093/nar/gkaf225","DOIUrl":"https://doi.org/10.1093/nar/gkaf225","url":null,"abstract":"Chromatin dynamics are essential for regulating DNA processes in response to environmental stimuli. Although ISWI-family enzymes are known to remodel chromatin by sliding nucleosomes in budding yeast, their functional roles and outputs in eukaryotes remain largely unknown. In this study, we investigated chromatin accessibility in the phytopathogenic fungus Fusarium graminearum treated with and without putrescine, a compound that rapidly induces the biosynthesis of the mycotoxin deoxynivalenol (DON). Putrescine globally alters chromatin accessibility, with the ATP-dependent chromatin remodeler FgIsw1 emerging as a key regulator. Unexpectedly, deletion of FgIsw1 did not affect the transcription of DON biosynthesis genes (Tri) but significantly disrupted transfer RNA (tRNA) transcription, leading to a dramatic decline in translation of DON biosynthesis enzymes. Mechanistically, FgIsw1 maintains nucleosome phasing in tRNA chromatin regions, ensuring efficient tRNA transcription. As a result, ΔFgIsw1 was unable to produce DON and lost its virulence on the host plant. These results highlight a novel role of chromatin remodelers in regulating protein translation through the control of tRNA transcription.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"75 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143744931","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

N4-acetylcytidine coordinates with NP1 and CPSF5 to facilitate alternative RNA processing during the replication of minute virus of canines

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-01 DOI: 10.1093/nar/gkaf229

Xueyan Zhang, Shuangkang Qin, Fang Huang, Haizhou Liu, Jun Wang, Zhen Chen, Haojie Hao, Shuang Ding, Lishi Liu, Baocheng Yu, Yi Liu, Haibin Liu, Wuxiang Guan

{"title":"N4-acetylcytidine coordinates with NP1 and CPSF5 to facilitate alternative RNA processing during the replication of minute virus of canines","authors":"Xueyan Zhang, Shuangkang Qin, Fang Huang, Haizhou Liu, Jun Wang, Zhen Chen, Haojie Hao, Shuang Ding, Lishi Liu, Baocheng Yu, Yi Liu, Haibin Liu, Wuxiang Guan","doi":"10.1093/nar/gkaf229","DOIUrl":"https://doi.org/10.1093/nar/gkaf229","url":null,"abstract":"RNA modifications play crucial roles in RNA metabolism, structure, and functions. N4-acetylcytidine (ac4C) modifications have been shown to enhance stability and translation efficiency of messenger RNAs and viral RNAs. However, the relationship between ac4C and alternative RNA processing remains unexplored. Here, N-acetyltransferase 10 (NAT10) and its catalyzed ac4C modifications on minute virus of canines (MVC) were shown to regulate viral DNA replication and RNA processing, including both the alternative RNA splicing and polyadenylation. Through acRIP-seq and RedaC:T-seq, functional ac4C-modified residue 3311 was identified and characterized, which affected MVC RNA processing rather than altered the viral RNA stability. Ac4C modification at nt 3311 was revealed to participate in NP1-mediated viral RNA processing without influencing RNA affinity of NP1. Meanwhile, CPSF5 was identified to interact with NP1 and mediate viral RNA processing in an ac4C-dependent manner. Further in vitro assays showed that NP1 recruited CPSF5 to MVC RNAs, and the ac4C modification promoted specific binding of CPSF5 to the target region, which ensured precise alternative MVC RNA processing. This study not only reveals the functions of NAT10 and ac4C but also elucidates the mechanisms by which RNA modifications orchestrate MVC proteins and host factors for efficient viral replication and alternative RNA processing.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"34 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143744943","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

Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-03-24 DOI: 10.1093/nar/gkaf152

Goro Nishide, Keesiang Lim, Akiko Kobayashi, Yujia Qiu, Masaharu Hazawa, Toshio Ando, Yuki Okada, Richard W Wong

{"title":"Spatiotemporal dynamics of protamine–DNA condensation revealed by high-speed atomic force microscopy","authors":"Goro Nishide, Keesiang Lim, Akiko Kobayashi, Yujia Qiu, Masaharu Hazawa, Toshio Ando, Yuki Okada, Richard W Wong","doi":"10.1093/nar/gkaf152","DOIUrl":"https://doi.org/10.1093/nar/gkaf152","url":null,"abstract":"Protamines (PRMs) play a crucial role in sperm chromatin condensation, replacing histones to form nucleo–PRM structures, specifically PRM–DNA complexes. Despite their importance in reproduction, the detailed mechanisms underlying PRM-mediated DNA condensation have remained elusive. In this study, we employed high-speed atomic force microscopy (HS-AFM) to directly visualize the real-time binding dynamics of PRM to DNA under physiological conditions. Our HS-AFM observations reveal that PRM insertion initiating the formation of DNA coils. Further, we observed a heterogeneous spatial distribution of PRM-induced DNA looping. With continuous PRM addition, DNA progresses through a series of folding transitions, forming coiled-like structures that evolve into clockwise spirals, rod-shaped intermediates, and ultimately toroid-like nanostructures. Based on these real-time observations, we propose the CARD (Coil-Assembly-Rod-Doughnut) model to describe the stepwise process of toroid formation during DNA condensation. Our findings underscore the versatility of HS-AFM in capturing the spatiotemporal dynamics of PRM–DNA interactions and provide critical insights into the molecular mechanisms driving PRM-induced chromatin compaction. This study advances our understanding of sperm chromatin architecture and offers a framework for future research into chromatin organization, reproductive biology, and nucleic acid therapeutics.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"25 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677570","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 dynamic structural unit of phase-separated heterochromatin protein 1α as revealed by integrative structural analyses

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-03-24 DOI: 10.1093/nar/gkaf154

Ayako Furukawa, Kento Yonezawa, Tatsuki Negami, Yuriko Yoshimura, Aki Hayashi, Jun-ichi Nakayama, Naruhiko Adachi, Toshiya Senda, Kentaro Shimizu, Tohru Terada, Nobutaka Shimizu, Yoshifumi Nishimura

{"title":"A dynamic structural unit of phase-separated heterochromatin protein 1α as revealed by integrative structural analyses","authors":"Ayako Furukawa, Kento Yonezawa, Tatsuki Negami, Yuriko Yoshimura, Aki Hayashi, Jun-ichi Nakayama, Naruhiko Adachi, Toshiya Senda, Kentaro Shimizu, Tohru Terada, Nobutaka Shimizu, Yoshifumi Nishimura","doi":"10.1093/nar/gkaf154","DOIUrl":"https://doi.org/10.1093/nar/gkaf154","url":null,"abstract":"The heterochromatin protein HP1α consists of an N-terminal disordered tail (N-tail), chromodomain (CD), hinge region (HR), and C-terminal chromo shadow domain (CSD). While CD binds to the lysine9-trimethylated histone H3 (H3K9me3) tail in nucleosomes, CSD forms a dimer bridging two nucleosomes with H3K9me3. Phosphorylation of serine residues in the N-tail enhances both H3K9me3 binding and liquid–liquid phase separation (LLPS) by HP1α. We have used integrative structural methods, including nuclear magnetic resonance, small-angle X-ray scattering (SAXS), and multi-angle-light scattering combined with size-exclusion chromatography, and coarse-grained molecular dynamics simulation with SAXS, to probe the HP1α dimer and its CSD deletion monomer. We show that dynamic intra- and intermolecular interactions between the N-tails and basic segments in CD and HR depend on N-tail phosphorylation. While the phosphorylated HP1α dimer undergoes LLPS via the formation of aggregated multimers, the N-tail phosphorylated mutant without CSD still undergoes LLPS, but its structural unit is a dynamic intermolecular dimer formed via the phosphorylated N-tail and a basic segment at the CD end. Furthermore, we reveal that mutation of this basic segment in HP1α affects the size of heterochromatin foci in cultured mammalian cells, suggesting that this interaction plays an important role in heterochromatin formation in vivo.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"57 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677571","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

Correction to 'Fam170a deficiency causes male infertility by impairing histone-to-protamine exchange during mouse spermiogenesis'.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-03-20 DOI: 10.1093/nar/gkaf237

引用次数: 0

Integrative structural analysis of NF45-NF90 heterodimers reveals architectural rearrangements and oligomerization on binding dsRNA.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-03-20 DOI: 10.1093/nar/gkaf204

Sophie Winterbourne, Uma Jayachandran, Juan Zou, Juri Rappsilber, Sander Granneman, Atlanta G Cook

{"title":"Integrative structural analysis of NF45-NF90 heterodimers reveals architectural rearrangements and oligomerization on binding dsRNA.","authors":"Sophie Winterbourne, Uma Jayachandran, Juan Zou, Juri Rappsilber, Sander Granneman, Atlanta G Cook","doi":"10.1093/nar/gkaf204","DOIUrl":"10.1093/nar/gkaf204","url":null,"abstract":"Complexes of nuclear factors 45 and 90 (NF45-NF90) play a multitude of roles in co- and post-transcriptional RNA processing, including regulating adenosine-to-inosine editing, cassette exon and back splicing, and splicing fidelity. NF45-NF90 complexes recognize double-stranded RNA (dsRNA) and, in human cells, primarily interact with Alu inverted repeats (AluIRs) that are commonly inserted into introns and other non-coding RNA regions. Intronic AluIRs of ∼300 bp can regulate splicing outcomes, such as generation of circular RNAs. We examined domain reorganization of NF45-NF90 domains on dsRNAs exceeding 50 bp to gain insight into its RNA recognition properties on longer dsRNAs. Using a combination of phylogenetic analysis, solution methods (including small angle X-ray scattering and quantitative cross-linking mass spectrometry), machine learning, and negative stain electron microscopy, we generated a model of NF45-NF90 complex formation on dsRNA. Our data reveal that different interactions of NF45-NF90 complexes allow these proteins to coat long stretches of dsRNA. This property of the NF45-NF90 complex has important implications for how long, nuclear dsRNAs are recognized in the nucleus and how this might promote (co)-regulation of specific RNA splicing and editing events that shape the mammalian transcriptome.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 6","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11952958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143743432","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

Template-independent enzymatic functionalization of DNA oligonucleotides with environment-sensitive nucleotide probes using terminal deoxynucleotidyl transferase.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-03-20 DOI: 10.1093/nar/gkaf108

Pulak Ghosh, Apeksha A Phadte, Bindu Bhojappa, Saravanan Palani, Seergazhi G Srivatsan

{"title":"Template-independent enzymatic functionalization of DNA oligonucleotides with environment-sensitive nucleotide probes using terminal deoxynucleotidyl transferase.","authors":"Pulak Ghosh, Apeksha A Phadte, Bindu Bhojappa, Saravanan Palani, Seergazhi G Srivatsan","doi":"10.1093/nar/gkaf108","DOIUrl":"10.1093/nar/gkaf108","url":null,"abstract":"Given the emerging use of terminal deoxynucleotidyl transferase (TdT) in biotechnology and its clinical potential as a cancer marker and target, the development of a versatile probe system to study its processivity, substrate properties, and inhibition is highly desired. Here, we demonstrate a multilayered application of a series of environment-sensitive fluorescent 2'-deoxynucleotide probes that harness the activity of TdT in accessing site-specifically functionalized DNA oligonucleotides and devising a real-time fluorescence platform to monitor the enzyme activity and identify potential inhibitors. The nucleotides constructed by coupling heterocycles of progressively increasing chemical modifications (selenophene, benzothiophene, benzofuran, and fluorobenzofuran) at the C5 position of 2'-deoxyuridine serve as suitable substrates for TdT, albeit differences in incorporation efficiency. A battery of experiments provided valuable insights into the scope of this functionalization method. It revealed how a fine balance between steric hindrance and stacking interaction between the heterocycle moiety and primer 3'-end nucleobase in the active site modulates the recognition and processing of nucleotides based on their size. Remarkably, the excellent responsiveness of benzofuran-modified dUTP enabled the design of fluorescence assays to estimate TdT activity, and detect nucleotide and non-nucleotide inhibitors. The findings obtained using our probes should significantly advance TdT-based functionalization, diagnostic, and therapeutic strategies.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 6","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143773022","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

A mediator-free sonogenetic switch for therapeutic protein expression in mammalian cells.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-03-20 DOI: 10.1093/nar/gkaf191

Jinbo Huang, Shuai Xue, Ana Palma Teixeira, Martin Fussenegger

{"title":"A mediator-free sonogenetic switch for therapeutic protein expression in mammalian cells.","authors":"Jinbo Huang, Shuai Xue, Ana Palma Teixeira, Martin Fussenegger","doi":"10.1093/nar/gkaf191","DOIUrl":"10.1093/nar/gkaf191","url":null,"abstract":"An ultrasound-responsive transgene circuit can provide non-invasive, spatiotemporally precise remote control of gene expression and cellular behavior in synthetic biology applications. However, current ultrasound-based systems often rely on nanoparticles or harness ultrasound's thermal effects, posing risks of tissue damage and cellular stress that limit their therapeutic potential. Here, we present Spatiotemporal Ultrasound-induced Protein Expression Regulator (SUPER), a novel gene switch enabling mediator-free, non-invasive and direct regulation of protein expression via ultrasound in mammalian cells. SUPER leverages the mammalian reactive oxygen species (ROS) sensing system, featuring KEAP1 (Kelch-like ECH-associated protein 1), NRF2 (nuclear factor erythroid 2-related factor 2), and antioxidant response element (ARE) as its core components. We demonstrate that low-intensity (1.5 W/cm2, ∼45 kHz), brief (40 s) ultrasound exposure generates non-toxic levels of ROS, activating the KEAP1/NRF2 pathway in engineered cells and leading to the controlled expression of target gene(s) via a synthetic ARE promoter. The system exhibits robust expression dynamics, excellent reversibility, and functionality in various cell types, including human mesenchymal stem cell-derived lines (hMSC-TERT). In a proof-of-concept study, ultrasound stimulation of subcutaneously implanted microencapsulated engineered cells stably expressing the sonogenetic circuit in a type 1 diabetic mouse model triggered sufficient insulin production to restore normoglycemia. Our work highlights ultrasound's potential as a precise and non-invasive tool for advancing cell and gene therapies in personalized medicine.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 6","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11925730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143670480","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