Nucleic Acids Research最新文献

{"title":"Mammalian H4K16ac regulates the spatiotemporal order of genome replication rather than gene expression.","authors":"Marta Milan,Valeria Runfola,Manthan Patel,Lucia Falbo,Roberta Noberini,Chiara Soriani,Simona Rodighiero,Tiziana Bonaldi,Vincenzo Costanzo,Madapura M Pradeepa,Paola Scaffidi","doi":"10.1093/nar/gkaf916","DOIUrl":"https://doi.org/10.1093/nar/gkaf916","url":null,"abstract":"Histone acetylation is widely assumed to directly instruct gene activation. Among acetylated residues, H4K16ac is one of the most abundant modifications, conserved across all eukaryotes. Despite its established role in X-chromosome hyperactivation in Drosophila, its function in mammalian cells has remained elusive. Here, we show that in human somatic cells, H4K16ac does not substantially affect gene expression, but instead controls the spatiotemporal program of genome replication. By combining a meta-analysis of public datasets and perturbation experiments designed to minimize confounding effects, we found that H4K16ac is neither associated with nor required for transcriptional activity. Rather, H4K16ac depletion resulted in premature replication of heterochromatic regions and widespread alterations in replication timing across the genome. These defects were driven by the aberrant activation of cryptic replication origins at long terminal repeats-repetitive elements typically marked by H4K16ac and whose sequence context resembles that of canonical origins in euchromatic regions. Our findings reveal an unexpected role for one of the most prevalent chromatin modifications and uncover a new regulatory mechanism that safeguards genome replication fidelity.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"21 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145116631","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":"Translational and clinical development of therapeutic siRNA and ASOs: current industry practices, perspectives, and recommendations.","authors":"Jesper Kammersgaard Christensen,Nicholas Colletti,Shirin Hooshfar,Rongrong Rosa Jiang,Carol Kuo,Bosse Lindmark,Annie Lumen,Amir S Youssef,Matthew Albertolle,Krishna C Aluri,Linzhi Chen,Jingxian Chen,Girish Chopda,Xien Yu Chua,Pedro Morais,Barent Dubois,Francis Frank Gibbons,Shyam Kumar Gudey,Swati Gupta,Steve Hood,Sara Humphreys,Christophe Husser,Felix Huth,Darshana Jani,Wenying Jian,Thomas Kakuda,Jeffrey Kurz,Helle Linnebjerg,Jing Liu,Sabine Lohmann,Tao Niu,Katharina Root,Sumeet Singla,Chenxiao Tang,Ravikanth Veluri,Guangnong Sunny Zhang,Steven Zhang,Vibha Jawa","doi":"10.1093/nar/gkaf778","DOIUrl":"https://doi.org/10.1093/nar/gkaf778","url":null,"abstract":"RNA-based therapies, particularly small interfering RNA (siRNA) and antisense oligonucleotides (ASOs), represent a promising modality class with the potential to target previously \"undruggable\" proteins, and with potential for precision medicine approach. The successful development of these therapeutics relies on a comprehensive understanding of several key factors, including bioconjugation, bioanalytical techniques, biotransformation, tissue distribution, computational modeling and simulation, and clinical pharmacology. Bioconjugation strategies are essential for enhancing metabolic stability, facilitating cellular uptake, and targeting specific tissues, thereby improving efficacy and minimizing dosing. Tailored bioanalytical methods are crucial for assessing pharmacokinetics (PK) and pharmacodynamics, with particular emphasis on tissue PK in cases where plasma PK does not reflect therapeutic activity. Biotransformation and tissue distribution studies are essential, although a less comprehensive package may be adequate for well-established chemistry. Given the unique properties of oligonucleotides, computational modeling plays a critical role in predicting drug behavior in target tissues, supporting dose optimization. Clinical pharmacology for oligonucleotides is less complex than for small molecules, as they are less likely to interact with common drug metabolizing enzymes or transporter proteins. This white paper, developed by the Innovation and Quality (IQ) Consortium Nucleic Acids Working Group, consolidates industry insights and recommendations to inform best practices and regulatory guidelines, ensuring the safe and efficient development of siRNA and ASO therapies.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145182726","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":"Metagenome-inspired libraries to engineer phage M13 for targeted killing of Gram-negative bacterial species.","authors":"Yanxi Yang,Dayeon Kang,Beatrice Mihalache,Shelby Vexler,Saumya Jain,Huan Peng,Nasim Annabi,Shangxin Yang,Irene A Chen","doi":"10.1093/nar/gkaf984","DOIUrl":"https://doi.org/10.1093/nar/gkaf984","url":null,"abstract":"Given concerning trends in antibiotic resistance, phages have been increasingly explored as promising antimicrobial agents. However, a major problem with phage therapy is the overly high specificity of phages for their hosts, which is currently addressed by a personalized approach involving screening a bank of wild-type phages against each clinical isolate. To shorten this process, we propose that a focused library of synthetic phages could be rapidly selected for a member binding to a given clinical isolate. We created libraries of recombinant M13 phages expressing receptor-binding proteins based on the collective metagenome of inovirus phages, a diverse group whose members appear to infect nearly all bacterial phyla. Using two rounds of a pull-down selection, phage variants were identified against several Gram-negative pathogens, including a variant (M13PAB) that bound to several Pseudomonas aeruginosa strains, including clinical isolates. To confer bactericidal activity to the nonlytic phage, a last-line but nephrotoxic lipopeptide, colistin, was cross-linked to the M13PAB virions. The colistin-M13PAB phage conjugate lowered the minimal inhibitory concentration of colistin by 1-2 orders of magnitude for multiple strains of P. aeruginosa and showed a lack of hemolytic or cytotoxic activity in vitro, suggesting high potency combined with low toxicity. Thus, a metagenome-inspired library displayed on the M13 phage scaffold, when subjected to a short selection for binding to a bacterial clinical isolate, could yield a phage variant that targets the specified strain. This approach may improve the speed, consistency, and cost-effectiveness of personalized phage therapy.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"20 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145182727","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":"Disrupted transcriptional networks regulated by CHD1L during neurodevelopment underlie the mirrored neuroanatomical and growth phenotypes of the 1q21.1 copy number variant.","authors":"Marianne Victoria Lemée, Maria Nicla Loviglio, Tao Ye, Peggy Tilly, Céline Keime, Chantal Weber, Anastasiya Petrova, Pernelle Klein, Bastien Morlet, Olivia Wendling, Hugues Jacobs, Mylène Tharreau, David Geneviève, Juliette D Godin, Christophe Romier, Delphine Duteil, Christelle Golzio","doi":"10.1093/nar/gkaf934","DOIUrl":"10.1093/nar/gkaf934","url":null,"abstract":"<p><p>Distal 1q21.1 deletions and duplications are associated with variable phenotypes including autism, head circumference and height defects. To elucidate which gene(s) are responsible for the 1q21.1 duplication/deletion-associated phenotypes, we performed gene manipulation in zebrafish and mice. We modeled 1q21.1 duplication by overexpressing the eight human protein-coding genes in zebrafish. We found that only overexpression of CHD1L led to macrocephaly and increased larval body length, whereas chd1l deletion caused opposite phenotypes. These mirrored phenotypes were also observed in mouse embryos. Transcriptomic, cistromic, and chromatin accessibility analyses of CHD1L knock-out hiPSC-derived neuronal progenitor cells revealed that CHD1L regulates the expression levels and chromatin accessibility of genes involved in neuronal differentiation and synaptogenesis, including autism genes. Moreover, we found that CHD1L favors telencephalon development during forebrain regionalization by facilitating chromatin accessibility to pioneer transcription factors, including SOX2 and OTX2, while simultaneously compacting chromatin through its interaction with the repressor NuRD complex. Overall, our data reveal a novel role for CHD1L as a master regulator of cell fate and its dosage imbalance contributes to the neuroanatomical and growth phenotypes associated with the 1q21.1 distal CNV.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 18","pages":""},"PeriodicalIF":13.1,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12456972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145131549","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}

{"title":"Click DNA ligation with deoxyribozyme.","authors":"Yangyang Chang, Yu Liang, Haodong Song, Qiang Zhang, Hong Yuan, Jiuxing Li, Zijie Zhang, Meng Liu","doi":"10.1093/nar/gkaf991","DOIUrl":"10.1093/nar/gkaf991","url":null,"abstract":"<p><p>Deoxyribozymes that ligate DNA will expand the reaction scope of DNA catalysis and are useful in the construction of DNA nanostructures. Herein, we report the first efforts to isolate a novel class of DNA ligase deoxyribozymes from a random sequence DNA pool by in vitro selection. The identified deoxyribozymes catalyze the intermolecular linear DNA-DNA ligation via the formation of unnatural triazole linkages between a 5' alkyne and a 3' azide. One remarkable click-ligating deoxyribozyme, named CLDz2, ligated DNA with an observed rate constant (kobs) up to 2.7 × 10-2 h-1 at 10 mM Mn2+ (pH 7.0, 30°C), with up to 40% yield in overnight incubations. CLDz2 is predicated to have a four-way, junction-like structure comprised of four short duplexes, three hairpin loops, and two main interhelical unpaired elements. Comprehensive nucleotide covariation experiments suggest that CLDz2 should be generally applicable for click ligation of a wide range of 3' azide DNAs. We further demonstrate a CLDz2-directed chemical ligation strategy for the synthesis of single-stranded monomeric circular DNA in high selectivity (97%), which can be used as a DNA template in rolling circle amplification.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 18","pages":""},"PeriodicalIF":13.1,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12489470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206925","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}

{"title":"New structural insights into the control of the retinoic acid receptors RAR/RXR by DNA, ligands, and transcriptional coregulators.","authors":"Izabella Tambones, Amin Sagar, Pavla Vankova, Dmitry Loginov, Coralie Carivenc, Natacha Rochel, William Bourguet, Petr Man, Pau Bernadó, Albane le Maire","doi":"10.1093/nar/gkaf967","DOIUrl":"10.1093/nar/gkaf967","url":null,"abstract":"<p><p>Retinoic acid receptors (RARs) are ligand-dependent transcription factors essential for various biological processes, including embryogenesis, differentiation, and apoptosis. RARs function as heterodimers with retinoid X receptors (RXRs) and regulate gene expression via retinoic acid response elements (RAREs). Their transcriptional activity is modulated by coregulators, with corepressors maintaining repression in the absence of ligand and coactivators enabling transcription upon ligand binding. Structural studies reveal that DNA binding induces conformational changes affecting coregulator interactions. However, the precise structural organization of RAR/RXR-coregulator complexes and the allosteric influence of DNA on receptor function remain incompletely understood. Our study presents an integrative analysis of the RAR/RXR heterodimer bound to four distinct and relevant RAREs (DR0, DR1, DR5, and IR0) in complex with either a corepressor (NCoR) or a coactivator (TIF-2) nuclear receptor interaction domain. By combining small-angle X-ray scattering, hydrogen/deuterium exchange mass spectrometry, and molecular dynamics simulations, we revealed that the heterodimer adopts distinct conformations depending on the DNA sequence, influencing interdomain distances and receptor interactions. Additionally, we uncovered the dynamic interplay between ligand, DNA, and coregulator binding. This study provides new insights into the structural features of coregulator proteins and highlights the allosteric influence of RAREs on receptor function.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 18","pages":""},"PeriodicalIF":13.1,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12489474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206928","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}

{"title":"Correction to 'Re-establishment of H3K9me2 eliminates the transcriptional inhibition of ST18 on meiotic genes and orchestrates female germ cell development'.","authors":"","doi":"10.1093/nar/gkaf979","DOIUrl":"10.1093/nar/gkaf979","url":null,"abstract":"","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 18","pages":""},"PeriodicalIF":13.1,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12476228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145182133","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}

{"title":"The early injected genomic region determines sensitivity to Type I restriction-modification defence against Autographiviridae phages.","authors":"Andrea Martinez-Cazorla,Christian Martinez-Jimenez,Patricia Elio-Lucas,Peter C Fineran,Simon Jackson,Antonio Sanchez-Amat","doi":"10.1093/nar/gkaf926","DOIUrl":"https://doi.org/10.1093/nar/gkaf926","url":null,"abstract":"Bacteriophages must evade bacterial defences to establish successful infections. Type I restriction-modification (RM) systems recognize specific DNA motifs and degrade unmethylated foreign DNA, restricting phage replication. In this study, we detected that Marinomonas mediterranea MMB-2 uses a Type I RM system (Mme2I) to protect against several new phages in the Murciavirus genus within the Autographiviridae family. Whole-genome sequencing and methylation analysis revealed a DNA sequence motif methylated in M. mediterranea MMB-2, which is also present in the phages. Phages lacking the motif within the leading, first injected, region of their genomes, either natural isolates or escape mutants of sensitive phages, successfully infect M. mediterranea MMB-2, despite the presence of the recognition motif elsewhere in their genomes. These results highlight the importance of considering RM motif locations when predicting avoidance of restriction sites as escape mechanisms from RM systems. Additionally, our findings indicate an important role for RM systems in specifically influencing the organization of the leading injected regions of phage genomes, which are highly variable and often encode diverse anti-defence systems.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"24 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145116677","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":"Comprehensive profiling of activity and specificity of RNA-guided transposons reveals opportunities to engineer improved variants.","authors":"Seong Guk Park,Jung-Un Park,Esteban Dodero-Rojas,John A Bryant,Geetha Sankaranarayanan,Elizabeth H Kellogg","doi":"10.1093/nar/gkaf917","DOIUrl":"https://doi.org/10.1093/nar/gkaf917","url":null,"abstract":"Recently discovered CRISPR-associated transposons (CASTs) are natural RNA-guided DNA transposition systems capable of single-step genomic integration of large DNA cargo. Wild-type CASTs exhibit low integration activity in heterologous systems; therefore, engineering efforts are required to develop therapeutically relevant tools. Here we developed a high-throughput dual genetic screen capable of accurately quantifying the relative activity and specificity of a large pool of CAST variants. Under the conditions of our screen, we discovered that the wild-type V-K CAST system can consistently achieve between 88% and 95% on-site targeting specificity. We used site-saturation mutagenesis of the conserved core transposition machinery (TnsB, TnsC, and TniQ) to reveal novel mechanistic insights into the function of these transposon proteins. Furthermore, we found that different components have varying trade-offs between activity and specificity, a critical aspect overlooked in conventional screening pipelines. These findings provide clear engineering principles for further optimization of CASTs. Finally, we identified several mutations that, together, enhance CAST activity up to four-fold while minimally impacting targeting specificity. These methods are a powerful tool to characterize the sequence-function landscape across multiple functional parameters while also providing a robust platform for developing enhanced genome-editing tools.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"61 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145116682","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":"Correction to 'Small molecules inhibitors of the heterogeneous ribonuclear protein A18 (hnRNP A18): a regulator of protein translation and an immune checkpoint'.","authors":"","doi":"10.1093/nar/gkaf1043","DOIUrl":"10.1093/nar/gkaf1043","url":null,"abstract":"","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 18","pages":""},"PeriodicalIF":13.1,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12507512/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145252053","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}