Junfang Song, Peter Geary, Khadisha Salemova, John Rouse, Ye Hong, Stéphane G M Rolland, Anton Gartner
{"title":"Functional dissection of the conserved C. elegans LEM-3/ANKLE1 nuclease reveals a crucial requirement for the LEM-like and GIY-YIG domains for DNA bridge processing.","authors":"Junfang Song, Peter Geary, Khadisha Salemova, John Rouse, Ye Hong, Stéphane G M Rolland, Anton Gartner","doi":"10.1093/nar/gkaf265","DOIUrl":"https://doi.org/10.1093/nar/gkaf265","url":null,"abstract":"<p><p>Faithful chromosome segregation requires the removal of all DNA bridges physically linking chromatids before the completion of cell division. While several redundant safeguard mechanisms to process these DNA bridges exist from S-phase to late anaphase, the conserved LEM-3/ANKLE1 nuclease has been proposed to be part of a 'last chance' mechanism that acts at the midbody to eliminate DNA bridges that persist until late cytokinesis. We show that LEM-3 can cleave a wide range of branched DNA substrates, including flaps, forks, nicked, and intact Holliday junctions. AlphaFold modelling data suggest that the catalytic mechanism of LEM-3/ANKLE1 is conserved, mirroring the mechanism observed in bacterial GIY-YIG nucleases. We present evidence that LEM-3 may form a homodimeric complex on the Holliday junction DNA. LEM-3 LEM-like and GIY-YIG nuclease domains are essential for LEM-3 recruitment to the midbody and its nuclease activity, while its LEM-like domain is sufficient for DNA binding. Finally, we show that preventing LEM-3 nuclear access is important to avoid toxicity, likely caused by branched DNAs cleavage during normal DNA metabolism. Our data suggest that Caenorhabditis elegans LEM-3 acts as a 'last chance catch-all' enzyme that processes DNA bridges caused by various perturbations of DNA metabolism just before cells divide.</p>","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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803931","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":"In vivo nucleotide excision repair by mycobacterial UvrD1 requires ATP hydrolysis but does not depend on cysteine disulfide-mediated dimerization and DNA unwinding.","authors":"Garrett M Warren, Stewart Shuman","doi":"10.1093/nar/gkaf269","DOIUrl":"https://doi.org/10.1093/nar/gkaf269","url":null,"abstract":"<p><p>Mycobacterial UvrD1 is an SF1-type ATPase that participates in nucleotide excision repair (NER). UvrD1 consists of N-terminal ATPase and C-terminal Tudor domains. The monomeric UvrD1 characterized originally displays vigorous DNA-dependent ATPase activity but only feeble helicase activity. A recent study demonstrated that: (i) cysteine disulfide-mediated homodimerization of UvrD1 generates a highly active helicase; and (ii) an obligate monomeric UvrD1 (by virtue of mutating the domain 2B cysteine) is active as an ATP-dependent 3'-to-5' single-stranded DNA translocase but not as a double-stranded DNA-unwinding helicase. Here we test genetically which physical and functional states of UvrD1 are relevant for its functions in DNA repair, by complementation of an NER-defective Mycobacterium smegmatis ΔuvrD1 strain with a series of biochemically-defined UvrD1 mutants. By assaying complemented strains for sensitivity to UVC, MMC, cisplatin, and psoralen-UVA, we conclude that monomeric UvrD1 ATPase activity suffices for the NER functions of UvrD1 in vivo. Decoupling ATP hydrolysis from duplex unwinding does not affect the repair activity of UvrD1, nor does interdiction of domain 2B cysteine disulfide-mediated dimerization or deletion of the Tudor domain. Our results militate against a proposed model in which UvrD1's repair function is governed by the redox state of the bacterium via its impact on UvrD1 dimerization and helicase activity.</p>","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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803932","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":"Oxidative events in a double helix system promote the formation of kinetically trapped G-quadruplexes.","authors":"Simon Aleksič, Peter Podbevšek, Janez Plavec","doi":"10.1093/nar/gkaf260","DOIUrl":"10.1093/nar/gkaf260","url":null,"abstract":"<p><p>Guanine-rich oligonucleotide sequences can adopt four-stranded G-quadruplex structures. These sequences are highly susceptible to oxidative damage due to the low redox potential of their constituent guanine nucleotides. Oxidative lesions of guanine residue exhibit perturbations in the position of hydrogen-bond donors and acceptors, which can impair the formation of G-quadruplexes. Here we studied the effect of guanine oxidation in model systems comprised of a G-rich as well as a complementary C-rich DNA strand to discern how oxidative damage can destabilize double-stranded DNA and promote G-quadruplex formation. Our data show that G-rich strands containing oxidative lesions can still adopt the G-quadruplex fold due to the presence of spare G-tracts, which rescue the damaged G-tracts via either full or partial replacement. However, most of the observed G-quadruplexes are kinetically trapped structures and the preferred equilibrium state of the two-stranded constructs is double-stranded DNA.</p>","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/PMC11969667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780783","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}
Magdalena L Russell, Assya Trofimov, Philip Bradley, Frederick A Matsen Iv
{"title":"Statistical analysis of repertoire data demonstrates the influence of microhomology in V(D)J recombination.","authors":"Magdalena L Russell, Assya Trofimov, Philip Bradley, Frederick A Matsen Iv","doi":"10.1093/nar/gkaf250","DOIUrl":"10.1093/nar/gkaf250","url":null,"abstract":"<p><p>V(D)J recombination generates the diverse B and T cell receptors essential for recognizing a wide array of antigens. This diversity arises from the combinatorial assembly of V(D)J genes and the junctional deletion and insertion of nucleotides. While previous in vitro studies have shown that microhomology-short stretches of sequence homology between gene ends-can bias the recombination process, the extent of microhomology's impact in vivo, particularly in humans, remains unknown. In this paper, we assess how germline-encoded microhomology influences trimming and ligation during V(D)J recombination using statistical inference on previously published high-throughput TCRα repertoire sequencing data. We find that microhomology increases both trimming and ligation probabilities, making it an important predictor of recombination outcomes. These effects are consistent across other receptor loci and sequence types. Further, we demonstrate that accounting for germline microhomology effects significantly alters sequence annotation probabilities and rankings, highlighting its practical importance for accurately inferring the V(D)J recombination events that generated an observed sequence. Together, these results enhance our understanding of how germline-encoded microhomologous nucleotides shape the human V(D)J recombination process.</p>","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/PMC11963759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772996","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":"Homeodomain protein PRRX1 anchors the Ku heterodimers at DNA double-strand breaks to promote nonhomologous end-joining.","authors":"Yan Wang, Fuyuan Shen, Chen Zhao, Jiali Li, Wen Wang, Yamu Li, Jia Gan, Haojian Zhang, Xuefeng Chen, Qiang Chen, Fangyu Wang, Ying Liu, Yan Zhou","doi":"10.1093/nar/gkaf200","DOIUrl":"10.1093/nar/gkaf200","url":null,"abstract":"<p><p>The DNA-dependent protein kinase (DNA-PK) complex plays a critical role in nonhomologous end-joining (NHEJ), a template-independent pathway for repairing DNA double-strand breaks (DSBs). The association of Ku70/80 with DSB ends facilitates the assembly of the DNA-PK holoenzyme. However, key mechanisms underlying the attachment and stabilization of DNA-PK at broken DNA ends remain unclear. Here, we identify PRRX1, a homeodomain-containing protein, as a mediator of chromatin localization and subsequent activation of DNA-PK. PRRX1 oligomerizes to simultaneously bind to double-strand DNA and the SAP (SAF-A/B, Acinus, and PIAS) domain of Ku70, thereby enhancing Ku anchoring at DSBs and stabilizing DNA-PK for efficient NHEJ repair. Reduced expression or pathogenic mutations of PRRX1 are associated with genomic instability and impaired NHEJ repair. Furthermore, a peptide that disrupts PRRX1 oligomerization compromises NHEJ efficiency and reduces cell survival following irradiation. These findings provide new insights into the activation of the NHEJ machinery and offer potential strategies for optimizing cancer therapies.</p>","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/PMC11925728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143670485","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}
Supuni Thalalla Gamage, Shereen Howpay Manage, Aldema Sas-Chen, Ronit Nir, Brett W Burkhart, Isita Jhulki, Courtney N Link, Manini S Penikalapati, Jane E Jones, Lakshminarayan M Iyer, L Aravind, Thomas J Santangelo, Schraga Schwartz, Jordan L Meier
{"title":"A sequence-specific RNA acetylation catalyst.","authors":"Supuni Thalalla Gamage, Shereen Howpay Manage, Aldema Sas-Chen, Ronit Nir, Brett W Burkhart, Isita Jhulki, Courtney N Link, Manini S Penikalapati, Jane E Jones, Lakshminarayan M Iyer, L Aravind, Thomas J Santangelo, Schraga Schwartz, Jordan L Meier","doi":"10.1093/nar/gkaf217","DOIUrl":"10.1093/nar/gkaf217","url":null,"abstract":"<p><p>N4-acetylcytidine (ac4C) is a ubiquitous RNA modification incorporated by cytidine acetyltransferase enzymes. Here, we report the biochemical characterization of Thermococcus kodakarensis Nat10 (TkNat10), an RNA acetyltransferase involved in archaeal thermotolerance. We demonstrate that TkNat10's catalytic activity is critical for T. kodakarensis fitness at elevated temperatures. Unlike eukaryotic homologs, TkNat10 exhibits robust stand-alone activity, modifying diverse RNA substrates in a temperature, ATP, and acetyl-CoA-dependent manner. Transcriptome-wide analysis reveals TkNat10 preferentially modifies unstructured RNAs containing a 5'-CCG-3' consensus sequence. Using a high-throughput mutagenesis approach, we define sequence and structural determinants of TkNat10 substrate recognition. We find TkNat10 can be engineered to facilitate use of propionyl-CoA, providing insight into its cofactor specificity. Finally, we demonstrate TkNat10's utility for site-specific acetylation of RNA oligonucleotides, enabling analysis of ac4C-dependent RNA-protein interactions. Our findings establish a framework for understanding archaeal RNA acetylation and a new tool for studying the functional consequences of ac4C in diverse RNA contexts.</p>","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/PMC11928934/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677118","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}
Diego Velasquez Pulgarin, Nathalie Pelo, Lin Ferrandiz, Tilen Tršelič, William A Nyberg, Gary Bowlin, Alexander Espinosa
{"title":"Light-induced expression of gRNA allows for optogenetic gene editing of T lymphocytes in vivo.","authors":"Diego Velasquez Pulgarin, Nathalie Pelo, Lin Ferrandiz, Tilen Tršelič, William A Nyberg, Gary Bowlin, Alexander Espinosa","doi":"10.1093/nar/gkaf213","DOIUrl":"10.1093/nar/gkaf213","url":null,"abstract":"<p><p>There is currently a lack of tools capable of perturbing genes in both a precise and a spatiotemporal fashion. The flexibility of CRISPR (clustered regularly interspaced short palindromic repeats), coupled with light's unparalleled spatiotemporal resolution deliverable from a controllable source, makes optogenetic CRISPR a well-suited solution for precise spatiotemporal gene perturbations. Here, we present a new optogenetic CRISPR tool (Blue Light-inducible Universal VPR-Improved Production of RGRs, BLU-VIPR) that diverges from prevailing split-Cas design strategies and instead focuses on optogenetic regulation of guide RNA (gRNA) production. We engineered BLU-VIPR around a new potent blue-light activated transcription factor (VPR-EL222) and ribozyme-flanked gRNA. The BLU-VIPR design is genetically encoded and ensures precise excision of multiple gRNAs from a single messenger RNA transcript. This simplified spatiotemporal gene perturbation and allowed for several types of optogenetic CRISPR, including indels, CRISPRa, and base editing. BLU-VIPR also worked in vivo with cells previously intractable to optogenetic gene editing, achieving optogenetic gene editing in T lymphocytes in vivo.</p>","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/PMC11925727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143670488","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}
Zhen He, Nannan Wu, Ruonan Yao, Huawei Tan, Yingying Sun, Jingxuan Chen, Lan Xue, Xiaonan Chen, Sihai Yang, Laurence D Hurst, Long Wang, Ju Huang
{"title":"RID is required for both repeat-induced point mutation and nucleation of a novel transitional heterochromatic state for euchromatic repeats.","authors":"Zhen He, Nannan Wu, Ruonan Yao, Huawei Tan, Yingying Sun, Jingxuan Chen, Lan Xue, Xiaonan Chen, Sihai Yang, Laurence D Hurst, Long Wang, Ju Huang","doi":"10.1093/nar/gkaf263","DOIUrl":"10.1093/nar/gkaf263","url":null,"abstract":"<p><p>To maintain genome integrity, repeat sequences are subject to heterochromatin inactivation and, in Neurospora, repeat-induced point mutation (RIP). The initiating factors behind both are poorly understood. We resolve the paradoxical observation that newly introduced Repeat-Linker-Repeat (R-L-R) constructs require RID alone for RIP, while genomic repeats are RIPed in the absence of RID, showing that eu- and hetero- chromatic repeats are handled differently, the latter additionally requiring DIM-2. The differences between mechanisms associated with older and newer duplicates caution against extrapolation from mechanisms inferred from model experimental systems. Additionally, while chromatin status affects RIP, we also show that RID, when tethered with LexA, acts as a nucleation center for the transition from euchromatin to heterochromatin in an HDA-1 dependent fashion. Constitutive heterochromatin by contrast is largely HDA1 independent and depends on HDA-1 paralogs. RID is thus a dual function initiator of both RIP and the transition to heterochromatin.</p>","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/PMC11969663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780703","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}
Nidhi Gupta, Indira Bag, Jyothsna Visweswaraiah, Alan Hinnebusch, Anil Thakur
{"title":"Distinct uS11/Rps14 interactions with the translation preinitiation complex differentially alter the accuracy of start codon recognition.","authors":"Nidhi Gupta, Indira Bag, Jyothsna Visweswaraiah, Alan Hinnebusch, Anil Thakur","doi":"10.1093/nar/gkaf163","DOIUrl":"10.1093/nar/gkaf163","url":null,"abstract":"<p><p>The eukaryotic 43S pre-initiation complex (PIC), containing methionyl initiator transfer RNA (Met-tRNAiMet) in a ternary complex (TC) with eIF2-GTP, scans the messenger RNA (mRNA) leader for an AUG start codon in favorable \"Kozak\" context. Recognition of AUG triggers the rearrangement of the PIC from an open scanning conformation to a closed arrested state with more tightly bound Met-tRNAiMet. Cryo-EM reconstructions of yeast PICs suggest remodeling of the interaction between 40S protein uS11/Rps14 with ribosomal RNA (rRNA) and mRNA between open and closed states; however, its importance in start codon recognition was unknown. uS11/Rps14-L137 substitutions disrupting rRNA contacts favored in the open complex increase initiation at suboptimal sites, and L137E stabilizes TC binding to PICs reconstituted in vitro with a UUG start codon, all indicating inappropriate rearrangement to the closed state at suboptimal initiation sites. Conversely, uS11/Rps14-R135 and -R136 substitutions perturbing interactions with rRNA exclusively in the closed state confer the opposite phenotypes of initiation hyperaccuracy, and for R135E, accelerated TC dissociation from reconstituted PICs. Thus, distinct interactions of uS11/Rps14 with rRNA stabilize first the open and then the closed conformation of the PIC to influence the accuracy of initiation in vivo.</p>","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/PMC11952957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143743424","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":"Conservation assessment of human splice site annotation based on a 470-genome alignment.","authors":"Ilia Minkin, Steven L Salzberg","doi":"10.1093/nar/gkaf184","DOIUrl":"10.1093/nar/gkaf184","url":null,"abstract":"<p><p>Despite many improvements over the years, the annotation of the human genome remains imperfect. The use of evolutionarily conserved sequences provides a strategy for selecting a high-confidence subset of the annotation. Using the latest whole-genome alignment, we found that splice sites from protein-coding genes in the high-quality MANE annotation are consistently conserved across >350 species. We also studied splice sites from the RefSeq, GENCODE, and CHESS databases not present in MANE. In addition, we analyzed the completeness of the alignment with respect to the human genome annotations and described a method that would allow us to fix up to 60% of the missing alignments of the protein-coding exons. We trained a logistic regression classifier to distinguish between the conservation exhibited by sites from MANE versus sites chosen randomly from neutrally evolving sequences. We found that splice sites classified by our model as well-supported have lower single nucleotide polymorphism rates and better transcriptomic evidence. We then computed a subset of transcripts using only \"well-supported\" splice sites or ones from MANE. This subset is enriched in high-confidence transcripts of the major gene catalogs that appear to be under purifying selection and are more likely to be correct and functionally relevant.</p>","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/PMC11928937/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677052","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}