Nucleic Acids Research最新文献_第10页

Transcriptome-scale analysis uncovers conserved residues in the hydrophobic core of the bacterial RNA chaperone Hfq required for small regulatory RNA stability.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkaf019

Josh McQuail, Miroslav Krepl, Kai Katsuya-Gaviria, Aline Tabib-Salazar, Lynn Burchell, Thorsten Bischler, Tom Gräfenhan, Paul Brear, Jiří Šponer, Ben F Luisi, Sivaramesh Wigneshweraraj

{"title":"Transcriptome-scale analysis uncovers conserved residues in the hydrophobic core of the bacterial RNA chaperone Hfq required for small regulatory RNA stability.","authors":"Josh McQuail, Miroslav Krepl, Kai Katsuya-Gaviria, Aline Tabib-Salazar, Lynn Burchell, Thorsten Bischler, Tom Gräfenhan, Paul Brear, Jiří Šponer, Ben F Luisi, Sivaramesh Wigneshweraraj","doi":"10.1093/nar/gkaf019","DOIUrl":"10.1093/nar/gkaf019","url":null,"abstract":"The RNA chaperone Hfq plays crucial roles in bacterial gene expression and is a major facilitator of small regulatory RNA (sRNA) action. The toroidal architecture of the Hfq hexamer presents three well-characterized surfaces that allow it to bind sRNAs to stabilize them and engage target transcripts. Hfq-interacting sRNAs are categorized into two classes based on the surfaces they use to bind Hfq. By characterizing a systematic alanine mutant library of Hfq to identify amino acid residues that impact survival of Escherichia coli experiencing nitrogen (N) starvation, we corroborated the important role of the three RNA-binding surfaces for Hfq function. We uncovered two, previously uncharacterized, conserved residues, V22 and G34, in the hydrophobic core of Hfq, to have a profound impact on Hfq's RNA-binding activity in vivo. Transcriptome-scale analysis revealed that V22A and G34A Hfq mutants cause widespread destabilization of both sRNA classes, to the same extent as seen in bacteria devoid of Hfq. However, the alanine substitutions at these residues resulted in only modest alteration in stability and structure of Hfq. We propose that V22 and G34 have impact on Hfq function, especially critical under cellular conditions when there is an increased demand for Hfq, such as N starvation.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 3","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11770335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143047380","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

Correction to 'DNA target binding-induced pre-crRNA processing in type II and V CRISPR-Cas systems'.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkaf024

引用次数: 0

DNA target binding-induced pre-crRNA processing in type II and V CRISPR-Cas systems. II 型和 V 型 CRISPR-Cas 系统中 DNA 靶标结合诱导的前 CRRNA 处理。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkae1241

Jiyun Chen, Xiaofeng Lin, Wenwen Xiang, Ying Chen, Yueming Zhao, Linglong Huang, Liang Liu

{"title":"DNA target binding-induced pre-crRNA processing in type II and V CRISPR-Cas systems.","authors":"Jiyun Chen, Xiaofeng Lin, Wenwen Xiang, Ying Chen, Yueming Zhao, Linglong Huang, Liang Liu","doi":"10.1093/nar/gkae1241","DOIUrl":"10.1093/nar/gkae1241","url":null,"abstract":"Precursor (pre)-CRISPR RNA (crRNA) processing can occur in both the repeat and spacer regions, leading to the removal of specific segments from the repeat and spacer sequences, thereby facilitating crRNA maturation. The processing of pre-crRNA repeat by Cas effector and ribonuclease has been observed in CRISPR-Cas9 and CRISPR-Cas12a systems. However, no evidence of pre-crRNA spacer cleavage by any enzyme has been reported in these systems. In this study, we demonstrate that DNA target binding triggers efficient cleavage of pre-crRNA spacers by type II and V Cas effectors such as Cas12a, Cas12b, Cas12i, Cas12j and Cas9. We show that the pre-crRNA spacer cleavage catalyzed by Cas12a and Cas9 has distinct characteristics. Activation of the cleavage activity in Cas12a is induced by both single-stranded DNA (ssDNA) and double-stranded DNA target binding, whereas only ssDNA target binding triggers cleavage in Cas9 toward the pre-crRNA spacer. We present a series of structures elucidating the underlying mechanisms governing conformational activation in both Cas12a and Cas9. Furthermore, leveraging the trans-cutting activity of the pre-crRNA spacer, we develop a one-step DNA detection method characterized by its simplicity, high sensitivity, and excellent specificity.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11797020/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142829398","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

methylGrapher: genome-graph-based processing of DNA methylation data from whole genome bisulfite sequencing.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkaf028

Wenjin Zhang, Juan F Macias-Velasco, Xiaoyu Zhuo, Edward A Belter, Chad Tomlinson, John Garza, Nina Tekkey, Daofeng Li, Ting Wang

{"title":"methylGrapher: genome-graph-based processing of DNA methylation data from whole genome bisulfite sequencing.","authors":"Wenjin Zhang, Juan F Macias-Velasco, Xiaoyu Zhuo, Edward A Belter, Chad Tomlinson, John Garza, Nina Tekkey, Daofeng Li, Ting Wang","doi":"10.1093/nar/gkaf028","DOIUrl":"10.1093/nar/gkaf028","url":null,"abstract":"Genome graphs, including the recently released draft human pangenome graph, can represent the breadth of genetic diversity and thus transcend the limits of traditional linear reference genomes. However, there are no genome-graph-compatible tools for analyzing whole genome bisulfite sequencing (WGBS) data. To close this gap, we introduce methylGrapher, a tool tailored for accurate DNA methylation analysis by mapping WGBS data to a genome graph. Notably, methylGrapher can reconstruct methylation patterns along haplotype paths precisely and efficiently. To demonstrate the utility of methylGrapher, we analyzed the WGBS data derived from five individuals whose genomes were included in the first Human Pangenome draft as well as WGBS data from ENCODE (EN-TEx). Along with standard performance benchmarking, we show that methylGrapher fully recapitulates DNA methylation patterns defined by classic linear genome analysis approaches. Importantly, methylGrapher captures a substantial number of CpG sites that are missed by linear methods, and improves overall genome coverage while reducing alignment reference bias. Thus, methylGrapher is a first step toward unlocking the full potential of Human Pangenome graphs in genomic DNA methylation analysis.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 3","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11770346/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143047377","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

Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkaf043

Robert C Monsen, T Michael Sabo, Robert Gray, Jesse B Hopkins, Jonathan B Chaires

{"title":"Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering.","authors":"Robert C Monsen, T Michael Sabo, Robert Gray, Jesse B Hopkins, Jonathan B Chaires","doi":"10.1093/nar/gkaf043","DOIUrl":"10.1093/nar/gkaf043","url":null,"abstract":"Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in the folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 24.3 to 12.6 Å. The collapse is monophasic and is complete in <600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, showing that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 3","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143067111","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

Large serine integrases utilise scavenged phage proteins as directionality cofactors.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkaf050

Abdulrazak Alsaleh, Alexandria Holland, Heewhan Shin, Tania Pena Reyes, Aron Baksh, Oluwateniola T Taiwo-Aiyerin, Ying Pigli, Phoebe A Rice, Femi J Olorunniji

{"title":"Large serine integrases utilise scavenged phage proteins as directionality cofactors.","authors":"Abdulrazak Alsaleh, Alexandria Holland, Heewhan Shin, Tania Pena Reyes, Aron Baksh, Oluwateniola T Taiwo-Aiyerin, Ying Pigli, Phoebe A Rice, Femi J Olorunniji","doi":"10.1093/nar/gkaf050","DOIUrl":"10.1093/nar/gkaf050","url":null,"abstract":"Recombination directionality factors (RDFs) for large serine integrases (LSIs) are cofactor proteins that control the directionality of recombination to favour excision over insertion. Although RDFs are predicted to bind their cognate LSIs in similar ways, there is no overall common structural theme across LSI RDFs, leading to the suggestion that some of them may be moonlighting proteins with other primary functions. To test this hypothesis, we searched for characterized proteins with structures similar to the predicted structures of known RDFs. Our search shows that the RDFs for two LSIs, TG1 integrase and Bxb1 integrase, show high similarities to a single-stranded DNA binding (SSB) protein and an editing exonuclease, respectively. We present experimental data to show that Bxb1 RDF is probably an exonuclease and TG1 RDF is a functional SSB protein. We used mutational analysis to validate the integrase-RDF interface predicted by AlphaFold2 multimer for TG1 integrase and its RDF, and establish that control of recombination directionality is mediated via protein-protein interaction at the junction of recombinase's second DNA binding domain and the base of the coiled-coil domain.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 3","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11795197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143190052","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

RNA G-quadruplex structure-based PROTACs for targeted DHX36 protein degradation and gene activity modulation in mammalian cells.

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkaf039

Kun Zhang,Qichang Nie,Maolin Li,Xiaona Chen,Liting Zhong,Tianle Dai,Xiaofan Guo,Haizhou Zhao,Terrence Chi-Kong Lau,Huating Wang,Shuo-Bin Chen,Chun Kit Kwok

{"title":"RNA G-quadruplex structure-based PROTACs for targeted DHX36 protein degradation and gene activity modulation in mammalian cells.","authors":"Kun Zhang,Qichang Nie,Maolin Li,Xiaona Chen,Liting Zhong,Tianle Dai,Xiaofan Guo,Haizhou Zhao,Terrence Chi-Kong Lau,Huating Wang,Shuo-Bin Chen,Chun Kit Kwok","doi":"10.1093/nar/gkaf039","DOIUrl":"https://doi.org/10.1093/nar/gkaf039","url":null,"abstract":"RNA G-quadruplexes (rG4s) are non-canonical secondary nucleic acid structures found in the transcriptome. They play crucial roles in gene regulation by interacting with G4-binding proteins (G4BPs) in cells. rG4-G4BP complexes have been associated with human diseases, making them important targets for drug development. Generating innovative tools to disrupt rG4-G4BP interactions will provide a unique opportunity to explore new biological mechanisms and potentially treat related diseases. Here, we have rationally designed and developed a series of rG4-based proteolytic targeting chimeras (rG4-PROTACs) aimed at degrading G4BPs, such as DHX36, a specific G4BP that regulates gene expression by binding to and unraveling rG4 structures in messenger RNAs (mRNAs). Our comprehensive data and systematic analysis reveals that rG4-PROTACs predominantly and selectively degrade DHX36 through a proteosome-dependent mechanism, which promotes the formation of the rG4 structure in mRNA, leading to the translation inhibition of rG4-containing transcripts. Notably, rG4-PROTACs inhibit rG4-mediated APP protein expression, and impact the proliferative capacity of skeletal muscle stem cells by negatively regulating Gnai2 protein expression. In summary, rG4-PROTACs provide a new avenue to understand rG4-G4BP interactions and the biological implications of dysregulated G4BPs, promoting the development of PROTACs technology based on the non-canonical structure of nucleic acids.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062062","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

Dual DNA replication modes: varying fork speeds and initiation rates within the spatial replication program in Xenopus.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkaf007

Diletta Ciardo, Olivier Haccard, Francesco de Carli, Olivier Hyrien, Arach Goldar, Kathrin Marheineke

{"title":"Dual DNA replication modes: varying fork speeds and initiation rates within the spatial replication program in Xenopus.","authors":"Diletta Ciardo, Olivier Haccard, Francesco de Carli, Olivier Hyrien, Arach Goldar, Kathrin Marheineke","doi":"10.1093/nar/gkaf007","DOIUrl":"10.1093/nar/gkaf007","url":null,"abstract":"Large vertebrate genomes duplicate by activating tens of thousands of DNA replication origins, irregularly spaced along the genome. The spatial and temporal regulation of the replication process is not yet fully understood. To investigate the DNA replication dynamics, we developed a methodology called RepliCorr, which uses the spatial correlation between replication patterns observed on stretched single-molecule DNA obtained by either DNA combing or high-throughput optical mapping. The analysis revealed two independent spatiotemporal processes that regulate the replication dynamics in the Xenopus model system. These mechanisms are referred to as a fast and a slow replication mode, differing by their opposite replication fork speed and rate of origin firing. We found that Polo-like kinase 1 (Plk1) depletion abolished the spatial separation of these two replication modes. In contrast, neither replication checkpoint inhibition nor Rap1-interacting factor (Rif1) depletion affected the distribution of these replication patterns. These results suggest that Plk1 plays an essential role in the local coordination of the spatial replication program and the initiation-elongation coupling along the chromosomes in Xenopus, ensuring the timely completion of the S phase.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 3","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11781033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143067106","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

Hypoxia increases methylated histones to prevent histone clipping and heterochromatin redistribution during Raf-induced senescence. 在raf诱导的衰老过程中，缺氧增加甲基化组蛋白以防止组蛋白剪切和异染色质重新分布。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkae1210

Soojeong Chang, Ramhee Moon, Dowoon Nam, Sang-Won Lee, Insoo Yoon, Dong-Sung Lee, Seunghyuk Choi, Eunok Paek, Daehee Hwang, Junho K Hur, Youhyun Nam, Rakwoo Chang, Hyunsung Park

{"title":"Hypoxia increases methylated histones to prevent histone clipping and heterochromatin redistribution during Raf-induced senescence.","authors":"Soojeong Chang, Ramhee Moon, Dowoon Nam, Sang-Won Lee, Insoo Yoon, Dong-Sung Lee, Seunghyuk Choi, Eunok Paek, Daehee Hwang, Junho K Hur, Youhyun Nam, Rakwoo Chang, Hyunsung Park","doi":"10.1093/nar/gkae1210","DOIUrl":"10.1093/nar/gkae1210","url":null,"abstract":"Hypoxia enhances histone methylation by inhibiting oxygen- and α-ketoglutarate-dependent demethylases, resulting in increased methylated histones. This study reveals how hypoxia-induced methylation affects histone clipping and the reorganization of heterochromatin into senescence-associated heterochromatin foci (SAHF) during oncogene-induced senescence (OIS) in IMR90 human fibroblasts. Notably, using top-down proteomics, we discovered specific cleavage sites targeted by Cathepsin L (CTSL) in H3, H2B and H4 during Raf activation, identifying novel sites in H2B and H4. Hypoxia counteracts CTSL-mediated histone clipping by promoting methylation without affecting CTSL's activity. This increase in methylation under hypoxia protects against clipping, reshaping the epigenetic landscape and influencing chromatin accessibility, as shown by ATAC-seq analysis. These insights underscore the pivotal role of hypoxia-induced histone methylation in protecting chromatin from significant epigenetic shifts during cellular aging.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11797049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807102","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

Antagonistic roles by the conserved nuclear poly(A)-binding proteins PABPN1 and ZC3H14 in nuclear RNA surveillance.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkaf060

Mélodie Latour, Lauren Kwiatek, Anne-Marie Landry-Voyer, François Bachand

引用次数: 0