{"title":"MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species","authors":"Funyun Liu, Bingcheng Cai, Shanshan Lian, Xinyao Chang, Dongsheng Chen, Zhongqi Pu, Lisui Bao, Jing Wang, Jia Lv, Hongkun Zheng, Zhenmin Bao, Lingling Zhang, Shi Wang, Yuli Li","doi":"10.1093/nar/gkae1026","DOIUrl":"https://doi.org/10.1093/nar/gkae1026","url":null,"abstract":"Mollusca represents the second-largest animal phylum but remains less explored genomically. The increase in high-quality genomes and diverse functional genomic data holds great promise for advancing our understanding of molluscan biology and evolution. To address the opportunities and challenges facing the molluscan research community in managing vast multi-omics resources, we developed MolluscDB 2.0 (http://mgbase.qnlm.ac), which integrates extensive functional genomic data and offers user-friendly tools for multilevel integrative and comparative analyses. MolluscDB 2.0 covers 1450 species across all eight molluscan classes and compiles ∼4200 datasets, making it the most comprehensive multi-omics resource for molluscs to date. MolluscDB 2.0 expands the layers of multi-omics data, including genomes, bulk transcriptomes, single-cell transcriptomes, proteomes, epigenomes and metagenomes. MolluscDB 2.0 also more than doubles the number of functional modules and analytical tools, updating 14 original modules and introducing 20 new, specialized modules. Overall, MolluscDB 2.0 provides highly valuable, open-access multi-omics platform for the molluscan research community, expediting scientific discoveries and deepening our understanding of molluscan biology and evolution.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"18 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142600997","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}
Xiaoxuan Song, Ziting Chen, Wenjun Sun, Hao Yang, Lijuan Guo, Yilin Zhao, Yanan Li, Zhiyun Ren, Jin Shi, Cong Liu, Peixiang Ma, Xingxu Huang, Quanjiang Ji, Bo Sun
{"title":"CRISPR-AsCas12f1 couples out-of-protospacer DNA unwinding with exonuclease activity in the sequential target cleavage.","authors":"Xiaoxuan Song, Ziting Chen, Wenjun Sun, Hao Yang, Lijuan Guo, Yilin Zhao, Yanan Li, Zhiyun Ren, Jin Shi, Cong Liu, Peixiang Ma, Xingxu Huang, Quanjiang Ji, Bo Sun","doi":"10.1093/nar/gkae989","DOIUrl":"https://doi.org/10.1093/nar/gkae989","url":null,"abstract":"<p><p>Type V-F CRISPR-Cas12f is a group of hypercompact RNA-guided nucleases that present a versatile in vivo delivery platform for gene therapy. Upon target recognition, Acidibacillus sulfuroxidans Cas12f (AsCas12f1) distinctively engenders three DNA break sites, two of which are located outside the protospacer. Combining ensemble and single-molecule approaches, we elucidate the molecular details underlying AsCas12f1-mediated DNA cleavages. We find that following the protospacer DNA unwinding and non-target strand (NTS) DNA nicking, AsCas12f1 surprisingly carries out bidirectional exonucleolytic cleavage from the nick. Subsequently, DNA unwinding is extended to the out-of-protospacer region, and AsCas12f1 gradually digests the unwound DNA beyond the protospacer. Eventually, the single endonucleolytic target-strand DNA cleavage at 3 nt downstream of the protospacer readily dissociates the ternary AsCas12f1-sgRNA-DNA complex from the protospacer adjacent motif-distal end, leaving a staggered double-strand DNA break. The coupling between the unwinding and cleavage of both protospacer and out-of-protospacer DNA is promoted by Mg2+. Kinetic analysis on the engineered AsCas12f1-v5.1 variant identifies the only accelerated step of the protospacer NTS DNA trimming within the sequential DNA cleavage. Our findings provide a dynamic view of AsCas12f1 catalyzing DNA unwinding-coupled nucleolytic cleavage and help with practical improvements of Cas12f-based genome editing tools.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624732","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}
Lindsey M Pale, Jude B Khatib, Alexandra Nusawardhana, Joshua Straka, Claudia M Nicolae, George-Lucian Moldovan
{"title":"CRISPR knockout genome-wide screens identify the HELQ-RAD52 axis in regulating the repair of cisplatin-induced single-stranded DNA gaps","authors":"Lindsey M Pale, Jude B Khatib, Alexandra Nusawardhana, Joshua Straka, Claudia M Nicolae, George-Lucian Moldovan","doi":"10.1093/nar/gkae998","DOIUrl":"https://doi.org/10.1093/nar/gkae998","url":null,"abstract":"Treatment with genotoxic agents, such as platinum compounds, is still the mainstay therapeutical approach for the majority of cancers. Our understanding of the mechanisms of action of these drugs is, however, imperfect and continuously evolving. Recent advances highlighted single-stranded DNA (ssDNA) gap accumulation as a potential determinant underlying cisplatin chemosensitivity, at least in some genetic backgrounds, such as BRCA mutations. Cisplatin-induced ssDNA gaps form upon restart of DNA synthesis downstream of cisplatin-induced lesions through repriming catalyzed by the PRIMPOL enzyme. Here, we show that PRIMPOL overexpression in otherwise wild-type cells results in accumulation of cisplatin-induced ssDNA gaps without sensitizing cells to cisplatin, suggesting that ssDNA gap accumulation does not confer cisplatin sensitivity in BRCA-proficient cells. To understand how ssDNA gaps may cause cellular sensitivity, we employed CRISPR-mediated genome-wide genetic screening to identify factors which enable the cytotoxicity of cisplatin-induced ssDNA gaps. We found that the helicase HELQ specifically suppresses cisplatin sensitivity in PRIMPOL-overexpressing cells, and this is associated with reduced ssDNA accumulation. We moreover identify RAD52 as a mediator of this pathway. RAD52 promotes ssDNA gap accumulation through a BRCA-mediated mechanism. Our work identified the HELQ-RAD52-BRCA axis as a regulator of ssDNA gap processing and cisplatin sensitization.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"8 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142600992","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}
Michelle S Glossop, Irina Chelysheva, Ruth F Ketley, Adele Alagia, Monika Gullerova
{"title":"TIRR regulates mRNA export and association with P-bodies in response to DNA damage.","authors":"Michelle S Glossop, Irina Chelysheva, Ruth F Ketley, Adele Alagia, Monika Gullerova","doi":"10.1093/nar/gkae688","DOIUrl":"10.1093/nar/gkae688","url":null,"abstract":"<p><p>To ensure the integrity of our genetic code, a coordinated network of signalling and repair proteins, known as the DNA damage response (DDR), detects and repairs DNA insults, the most toxic being double-strand breaks (DSBs). Tudor interacting repair regulator (TIRR) is a key factor in DSB repair, acting through its interaction with p53 binding protein 1 (53BP1). TIRR is also an RNA binding protein, yet its role in RNA regulation during the DDR remains elusive. Here, we show that TIRR selectively binds to a subset of messenger RNAs (mRNAs) in response to DNA damage. Upon DNA damage, TIRR interacts with the nuclear export protein Exportin-1 through a nuclear export signal. Furthermore, TIRR plays a crucial role in the modulation of RNA processing bodies (PBs). TIRR itself and TIRR-bound RNA co-localize with PBs, and TIRR depletion results in nuclear RNA retention and impaired PB formation. We also suggest a potential link between TIRR-regulated RNA export and efficient DDR. This work reveals intricate involvement of TIRR in orchestrating mRNA nuclear export and storage within PBs, emphasizing its significance in the regulation of RNA-mediated DDR.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":"12633-12649"},"PeriodicalIF":16.6,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11551748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141907303","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}
Gamal Ahmed Elfar, Obed Aning, Tsz Wai Ngai, Pearlyn Yeo, Joel Wai Kit Chan, Shang Hong Sim, Leonard Goh, Ju Yuan, Cheryl Zi Jin Phua, Joanna Zhen Zhen Yeo, Shi Ya Mak, Brian Kim Poh Goh, Pierce Kah-Hoe Chow, Wai Leong Tam, Ying Swan Ho, Chit Fang Cheok
{"title":"p53-dependent crosstalk between DNA replication integrity and redox metabolism mediated through a NRF2-PARP1 axis.","authors":"Gamal Ahmed Elfar, Obed Aning, Tsz Wai Ngai, Pearlyn Yeo, Joel Wai Kit Chan, Shang Hong Sim, Leonard Goh, Ju Yuan, Cheryl Zi Jin Phua, Joanna Zhen Zhen Yeo, Shi Ya Mak, Brian Kim Poh Goh, Pierce Kah-Hoe Chow, Wai Leong Tam, Ying Swan Ho, Chit Fang Cheok","doi":"10.1093/nar/gkae811","DOIUrl":"10.1093/nar/gkae811","url":null,"abstract":"<p><p>Mechanisms underlying p53-mediated protection of the replicating genome remain elusive, despite the quintessential role of p53 in maintaining genomic stability. Here, we uncover an unexpected function of p53 in curbing replication stress by limiting PARP1 activity and preventing the unscheduled degradation of deprotected stalled forks. We searched for p53-dependent factors and elucidated RRM2B as a prime factor. Deficiency in p53/RRM2B results in the activation of an NRF2 antioxidant transcriptional program, with a concomitant elevation in basal PARylation in cells. Dissecting the consequences of p53/RRM2B loss revealed a crosstalk between redox metabolism and genome integrity that is negotiated through a hitherto undescribed NRF2-PARP1 axis, and pinpoint G6PD as a primary oxidative stress-induced NRF2 target and activator of basal PARylation. This study elucidates how loss of p53 could be destabilizing for the replicating genome and, importantly, describes an unanticipated crosstalk between redox metabolism, PARP1 and p53 tumor suppressor pathway that is broadly relevant in cancers and can be leveraged therapeutically.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":"12351-12377"},"PeriodicalIF":16.6,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11551750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308250","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":"Pathological R-loops in bacteria from engineered expression of endogenous antisense RNAs whose synthesis is ordinarily terminated by Rho.","authors":"Apuratha Pandiyan, Jillella Mallikarjun, Himanshi Maheshwari, Jayaraman Gowrishankar","doi":"10.1093/nar/gkae839","DOIUrl":"10.1093/nar/gkae839","url":null,"abstract":"<p><p>In many bacteria, the essential factors Rho and NusG mediate termination of synthesis of nascent transcripts (including antisense RNAs) that are not being simultaneously translated. It has been proposed that in Rho's absence toxic RNA-DNA hybrids (R-loops) may be generated from nascent untranslated transcripts, and genome-wide mapping studies in Escherichia coli have identified putative loci of R-loop formation from more than 100 endogenous antisense transcripts that are synthesized only in a Rho-deficient strain. Here we provide evidence that engineered expression in wild-type E. coli of several such individual antisense regions on a plasmid or the chromosome generates R-loops that, in an RNase H-modulated manner, serve to disrupt genome integrity. Rho inhibition was associated with increased prevalence of antisense R-loops also in Xanthomonas oryzae pv. oryzae and Caulobacter crescentus. Our results confirm the essential role of Rho in several bacterial genera for prevention of toxic R-loops from pervasive yet cryptic endogenous antisense transcripts. Engineered antisense R-looped regions may be useful for studies on both site-specific impediments to bacterial chromosomal replication and the mechanisms of their resolution.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":"12438-12455"},"PeriodicalIF":16.6,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11551753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142381384","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":"PWOs repress gene transcription by regulating chromatin structures in Arabidopsis","authors":"Tingting Yang, Dingyue Wang, Lingxiao Luo, Xiaochang Yin, Zhihan Song, Minqi Yang, Yue Zhou","doi":"10.1093/nar/gkae958","DOIUrl":"https://doi.org/10.1093/nar/gkae958","url":null,"abstract":"PWWP-DOMAIN INTERACTOR OF POLYCOMBS (PWO) family proteins play a vital role in regulating plant development. However, the molecular mechanisms of how PWOs regulate chromatin structure is elusive. Our data show that the PWO1 binding sites are enriched with positive modifications but exclusive with H3K27me3. Moreover, PWO1 binds to the H3K27me3-enriched compartment domain (H3K27me3-CD) boundary regions, and functions to maintain the boundary strength. Meanwhile, we found that PWOs and Polycomb repressive complex 2 (PRC2) function parallelly in maintaining H3K27me3-CDs’ structure. Loss of either PWOs or PRC2 leads to H3K27me3-CD strength reduction, B to A compartment switching as well as the H3K27me3-CD relocating away from the nuclear periphery. Additionally, PWOs and lamin-like proteins collaborate to regulate multiple chromatin structures to repress gene transcription within H3K27me3-CDs. We conclude that PWOs maintain H3K27me3-CDs’ repressive state and regulate their spatial position in the nucleus.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"69 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142599566","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}
Vincent Lombard, Bernard Henrissat, Marie-Line Garron
{"title":"CAZac: an activity descriptor for carbohydrate-active enzymes","authors":"Vincent Lombard, Bernard Henrissat, Marie-Line Garron","doi":"10.1093/nar/gkae1045","DOIUrl":"https://doi.org/10.1093/nar/gkae1045","url":null,"abstract":"The Carbohydrate-Active enZYme database (CAZy; www.cazy.org) has been providing the reference classification of carbohydrate-active enzymes (CAZymes) for &gt;30 years. Based on literature survey, the sequence-based families of CAZymes are enriched with functional data by using the International Union of Biochemistry and Molecular Biology Enzyme Commission (EC) number system. However, this system was not developed to search or compare functional information. To better harness functional information, we have developed CAZac (CAZyme activity descriptor), a multicriterion system that describes CAZymes’ mechanisms, glycosidic bond orientations, subsites and inter-residue connectivities. This new system, implemented for glycoside hydrolases, glycoside phosphorylases, transglycosidases, polysaccharide lyases and lytic polysaccharide monooxygenases allows complex searches in the CAZy database to uncover the evolution of substrate specificity and mechanisms of CAZymes across families.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"24 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142598301","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":"Synthetic translational coupling element for multiplexed signal processing and cellular control","authors":"Hyunseop Goh, Seungdo Choi, Jongmin Kim","doi":"10.1093/nar/gkae980","DOIUrl":"https://doi.org/10.1093/nar/gkae980","url":null,"abstract":"Repurposing natural systems to develop customized functions in biological systems is one of the main thrusts of synthetic biology. Translational coupling is a common phenomenon in diverse polycistronic operons for efficient allocation of limited genetic space and cellular resources. These beneficial features of translation coupling can provide exciting opportunities for creating novel synthetic biological devices. Here, we introduce a modular synthetic translational coupling element (synTCE) and integrate this design with de novo designed riboregulators, toehold switches. A systematic exploration of sequence domain variants for synTCEs led to the identification of critical design considerations for improving the system performance. Next, this design approach was seamlessly integrated into logic computations and applied to construct multi-output transcripts with well-defined stoichiometric control. This module was further applied to signaling cascades for combined signal transduction and multi-input/multi-output synthetic devices. Further, the synTCEs can precisely manipulate the N-terminal ends of output proteins, facilitating effective protein localization and cellular population control. Therefore, the synTCEs could enhance computational capability and applicability of riboregulators for reprogramming biological systems, leading to future applications in synthetic biology, metabolic engineering and biotechnology.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"245 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142598304","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":"dbPTM 2025 update: comprehensive integration of PTMs and proteomic data for advanced insights into cancer research","authors":"Chia-Ru Chung, Yun Tang, Yen-Peng Chiu, Shangfu Li, Wen-Kai Hsieh, Lantian Yao, Ying-Chih Chiang, Yuxuan Pang, Guan-Ting Chen, Kai-Chen Chou, You Sheng Paik, Phuong Lam Tran, Cheng-Pei Lin, Yu-Min Kao, Yi-Jie Chen, Wen-Chi Chang, Justin Bo-Kai Hsu, Jorng-Tzong Horng, Tzong-Yi Lee","doi":"10.1093/nar/gkae1005","DOIUrl":"https://doi.org/10.1093/nar/gkae1005","url":null,"abstract":"Post-translational modifications (PTMs) are essential for modulating protein function and influencing stability, activity and signaling processes. The dbPTM 2025 update significantly expands the database to include over 2.79 million PTM sites, of which 2.243 million are experimentally validated from 48 databases and over 80 000 research articles. This version integrates proteomic data from 13 cancer types, with a particular focus on phosphoproteomic data and kinase activity profiles, allowing the exploration of personalized phosphorylation patterns in tumor samples. Integrating kinase–substrate phosphorylations with E3 ligase–substrate interactions, dbPTM 2025 provides a detailed map of PTM regulatory networks, offering insights into cancer-specific post-translational regulations. This update also includes advanced search capabilities, enabling users to efficiently query PTM data across species, PTM types and modified residues. The platform’s new features—interactive visualization tools and streamlined data downloads—allow researchers to access and analyze PTM data easily. dbPTM 2025 also enhances functional annotations, regulatory networks and disease associations, broadening its application for cancer research and the study of disease-associated PTMs. Through these enhancements, dbPTM 2025 is a comprehensive, user-friendly resource, facilitating the study of PTMs and their roles in cancer research. The database is now freely accessible at https://biomics.lab.nycu.edu.tw/dbPTM/.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"10 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142598314","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}