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Chem-CRISPR/dCas9FCPF: a platform for chemically induced epigenome editing. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-24 Mukaddes Altinbay,Jianhui Wang,Jie Chen,Daniel Schäfer,Maximilian Sprang,Biljana Blagojevic,Stefan Wölfl,Miguel A Andrade-Navarro,Ivan Dikic,Stefan Knapp,Xinlai Cheng
Epigenetic aberration is one of the major driving factors in human cancer, often leading to acquired resistance to chemotherapies. Various small molecule epigenetic modulators have been reported. Nonetheless, outcomes from animal models and clinical trials have underscored the substantial setbacks attributed to pronounced on- and off-target toxicities. To address these challenges, CRISPR/dCas9 technology
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Evolving Escherichia coli to use a tRNA with a non-canonical fold as an adaptor of the genetic code. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-24 Martin P Edelmann,Sietse Couperus,Emilio Rodríguez-Robles,Julie Rivollier,Tania M Roberts,Sven Panke,Philippe Marlière
All known bacterial tRNAs adopt the canonical cloverleaf 2D and L-shaped 3D structures. We aimed to explore whether alternative tRNA structures could be introduced in bacterial translation. To this end, we crafted a vitamin-based genetic system to evolve Escherichia coli toward activity of structurally non-canonical tRNAs. The system reliably couples (escape frequency <10-12) growth with the activities
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Switch-like phosphorylation of WRN integrates end-resection with RAD51 metabolism at collapsed replication forks Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-24 Valentina Palermo, Eva Malacaria, Maurizio Semproni, Serena Camerini, Marialuisa Casella, Benedetta Perdichizzi, Pasquale Valenzisi, Massimo Sanchez, Federica Marini, Achille Pellicioli, Annapaola Franchitto, Pietro Pichierri
Replication-dependent DNA double-strand breaks are harmful lesions preferentially repaired by homologous recombination (HR), a process that requires processing of DNA ends to allow RAD51-mediated strand invasion. End resection and subsequent repair are two intertwined processes, but the mechanism underlying their execution is still poorly appreciated. The WRN helicase is one of the crucial factors
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The transition state for coupled folding and binding of a disordered DNA binding domain resembles the unbound state Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-24 Mikhail Kuravsky, Conor Kelly, Christina Redfield, Sarah L Shammas
The basic zippers (bZIPs) are one of two large eukaryotic families of transcription factors whose DNA binding domains are disordered in isolation but fold into stable α-helices upon target DNA binding. Here, we systematically disrupt pre-existing helical propensity within the DNA binding region of the homodimeric bZIP domain of cAMP-response element binding protein (CREB) using Ala-Gly scanning and
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Kinetic mechanism and determinants of EF-P recruitment to translating ribosomes Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-24 Vitalii Mudryi, Jan Ole Frister, Bee-Zen Peng, Ingo Wohlgemuth, Frank Peske, Marina V Rodnina
EF-P is a translation factor that facilitates the formation of peptide bonds between consecutive prolines. Using FRET between EF-P and ribosomal protein bL33, we studied dynamics and specificity of EF-P binding to the ribosome. Our findings reveal that EF-P rapidly scans for a free E site and can bind to any ribosome containing a P-site tRNA, regardless of the ribosome's functional state. The interaction
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Amphiphilic shuttle peptide delivers base editor ribonucleoprotein to correct the CFTR R553X mutation in well-differentiated airway epithelial cells Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-24 Katarina Kulhankova, Anna X Cheng, Soumba Traore, Maud Auger, Mia Pelletier, Maxime Hervault, Kevin D Wells, Jonathan A Green, Addison Byrne, Benjamin Nelson, Mariana Sponchiado, Chandra Boosani, Caleb S Heffner, Kathy J Snow, Stephen A Murray, Raul A Villacreses, Michael V Rector, Nicholas D Gansemer, David A Stoltz, Chantal Allamargot, Frédéric Couture, Colin Hemez, Stéphanie Hallée, Xavier Barbeau
Base editing could correct nonsense mutations that cause cystic fibrosis (CF), but clinical development is limited by the lack of delivery methods that efficiently breach the barriers presented by airway epithelia. Here, we present a novel amphiphilic shuttle peptide based on the previously reported S10 peptide that substantially improved base editor ribonucleoprotein (RNP) delivery. Studies of the
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Structural and mechanistic insights into a mesophilic prokaryotic Argonaute Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-24 Xin Tao, Hui Ding, Shaowen Wu, Fei Wang, Hu Xu, Jie Li, Chao Zhai, Shunshun Li, Kai Chen, Shan Wu, Yang Liu, Lixin Ma
Argonaute (Ago) proteins are programmable nucleases found in all domains of life, playing a crucial role in biological processes like DNA/RNA interference and gene regulation. Mesophilic prokaryotic Agos (pAgos) have gained increasing research interest due to their broad range of potential applications, yet their molecular mechanisms remain poorly understood. Here, we present seven cryo-electron microscopy
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scMMO-atlas: a single cell multimodal omics atlas and portal for exploring fine cell heterogeneity and cell dynamics Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-24 Wenwen Cheng, Changhui Yin, Shiya Yu, Xi Chen, Ni Hong, Wenfei Jin
Single-cell multimodal sequencing parallelly captures multiple modalities of the same cell, providing unparalleled insights into cell heterogeneity and cell dynamics. For example, joint profiling of chromatin accessibility and transcriptome from the same single cell (scATAC + RNA) identified new cell subsets within the well-defined clusters. However, lack of single-cell multimodal omics (scMMO) database
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p53-dependent crosstalk between DNA replication integrity and redox metabolism mediated through a NRF2-PARP1 axis Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-24 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
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
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Phage defence loci of Streptococcus thermophilus—tip of the anti-phage iceberg? Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-24 Philip Kelleher, Guillermo Ortiz Charneco, Zoe Kampff, Natalia Diaz-Garrido, Francesca Bottacini, Brian McDonnell, Gabriele A Lugli, Marco Ventura, Alexey Fomenkov, Pascal Quénée, Saulius Kulakauskas, Paul de Waal, Noël N M E van Peij, Christian Cambillau, Richard John Roberts, Douwe van Sinderen, Jennifer Mahony
Bacteria possess (bacterio)phage defence systems to ensure their survival. The thermophilic lactic acid bacterium, Streptococcus thermophilus, which is used in dairy fermentations, harbours multiple CRISPR-Cas and restriction and modification (R/M) systems to protect itself against phage attack, with limited reports on other types of phage-resistance. Here, we describe the systematic identification
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FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-24 Tongshan Zuo, Chen Shen, Zhen Xie, Guanhong Xu, Fangdi Wei, Jing Yang, Xiaolei Zhu, Qin Hu, Zheng Zhao, Ben Zhong Tang, Yao Cen
CRISPR/Cas12a system, renowned for its precise recognition and efficient nucleic acid cleavage capabilities, has demonstrated remarkable performance in molecular diagnostics and biosensing. However, the reported Cas12a activity regulation methods often involved intricate CRISPR RNA (crRNA) structural adjustments or costly chemical modifications, which limited their applications. Here, we demonstrated
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3,N4-Etheno-5-methylcytosine blocks TET1-3 oxidation but is repaired by ALKBH2, 3 and FTO Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-24 Jian Ma, Rui Qi, Emily M Harcourt, Yi-Tzai Chen, Giovannia M Barbosa, Zhiyuan Peng, Samuel Howarth, Sarah Delaney, Deyu Li
5-Methyldeoxycytidine (5mC) is a major epigenetic marker that regulates cellular functions in mammals. Endogenous lipid peroxidation can convert 5mC into 3,N4-etheno-5-methylcytosine (ϵ5mC). ϵ5mC is structurally similar to the mutagenic analog 3,N4-ethenocytosine (ϵC), which is repaired by AlkB family enzymes in the direct reversal repair (DRR) pathway and excised by DNA glycosylases in the base excision
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High-throughput single telomere analysis using DNA microarray and fluorescent in situ hybridization Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-18 Yun-Ling Zheng, Xingjia Wu, Madeline Williams, Simon Verhulst, Jue Lin, Yusuke Takahashi, Jian-Xing Ma, Ying Wang
The human telomere system is highly dynamic. Both short and long leucocyte average telomere lengths (aTL) are associated with an increased risk of cancer and early death, illustrating the complex relationship between TL and human health and the importance of assessing TL distributions with single TL analysis. A DNA microarray and telomere fluorescent in situ hybridization (DNA-array-FISH) approach
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DciA secures bidirectional replication initiation in Vibrio cholerae Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-18 Amelie Besombes, Yazid Adam, Christophe Possoz, Ivan Junier, Francois-Xavier Barre, Jean-Luc Ferat
Replication is initiated bidirectionally in the three domains of life by the assembly of two replication forks at an origin of replication. This is made possible by the recruitment of two replicative helicases to a nucleoprotein platform built at the origin of replication with the initiator protein. The reason why replication is initiated bidirectionally has never been experimentally addressed due
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Polyubiquitinated PCNA triggers SLX4-mediated break-induced replication in alternative lengthening of telomeres (ALT) cancer cells Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-18 Sangin Kim, Su Hyung Park, Nalae Kang, Jae Sun Ra, Kyungjae Myung, Kyoo-young Lee
Replication stresses are the major source of break-induced replication (BIR). Here, we show that in alternative lengthening of telomeres (ALT) cells, replication stress-induced polyubiquitinated proliferating cell nuclear antigen (PCNA) (polyUb-PCNA) triggers BIR at telomeres and the common fragile site (CFS). Consistently, depleting RAD18, a PCNA ubiquitinating enzyme, reduces the occurrence of ALT-associated
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Correction to 'Advancing quantitative PCR with color cycle multiplex amplification'. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-18
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Transcription start site scanning requires the fungi-specific hydrophobic loop of Tfb3 Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-17 Chun Yang, Pratik Basnet, Samah Sharmin, Hui Shen, Craig D Kaplan, Kenji Murakami
RNA polymerase II (pol II) initiates transcription from transcription start sites (TSSs) located ∼30–35 bp downstream of the TATA box in metazoans, whereas in the yeast Saccharomyces cerevisiae, pol II scans further downstream TSSs located ∼40–120 bp downstream of the TATA box. Previously, we found that removal of the kinase module TFIIK (Kin28–Ccl1–Tfb3) from TFIIH shifts the TSS in a yeast in vitro
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How to scan naked DNA using promiscuous recognition and no clamping: a model for pioneer transcription factors Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-17 Rama Reddy Goluguri, Catherine Ghosh, Joshua Quintong, Mourad Sadqi, Victor Muñoz
Most DNA scanning proteins uniquely recognize their cognate sequence motif and slide on DNA assisted by some sort of clamping interface. The pioneer transcription factors that control cell fate in eukaryotes must forgo both elements to gain access to DNA in naked and chromatin forms; thus, whether or how these factors scan naked DNA is unknown. Here, we use single-molecule techniques to investigate
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4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-17 Lianrong Pu, Ron Shamir
Microbial communities usually harbor a mix of bacteria, archaea, plasmids, viruses and microeukaryotes. Within these communities, viruses, plasmids, and microeukaryotes coexist in relatively low abundance, yet they engage in intricate interactions with bacteria. Moreover, viruses and plasmids, as mobile genetic elements, play important roles in horizontal gene transfer and the development of antibiotic
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Crystal structure and nucleic acid binding mode of CPV NSP9: implications for viroplasm in Reovirales Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-17 Yeda Wang, Hangtian Guo, Yuhao Lu, Wanbin Yang, Tinghan Li, Xiaoyun Ji
Cytoplasmic polyhedrosis viruses (CPVs), like other members of the order Reovirales, produce viroplasms, hubs of viral assembly that shield them from host immunity. Our study investigates the potential role of NSP9, a nucleic acid-binding non-structural protein encoded by CPVs, in viroplasm biogenesis. We determined the crystal structure of the NSP9 core (NSP9ΔC), which shows a dimeric organization
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G-quadruplexes in an SVA retrotransposon cause aberrant TAF1 gene expression in X-linked dystonia parkinsonism Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-17 Giulia Nicoletto, Marianna Terreri, Ilaria Maurizio, Emanuela Ruggiero, Filippo M Cernilogar, Christine A Vaine, Maria Vittoria Cottini, Irina Shcherbakova, Ellen B Penney, Irene Gallina, David Monchaud, D Cristopher Bragg, Gunnar Schotta, Sara N Richter
G-quadruplexes (G4s) are non-canonical nucleic acid structures that form in guanine (G)-rich genomic regions. X-linked dystonia parkinsonism (XDP) is an inherited neurodegenerative disease in which a SINE–VNTR–Alu (SVA) retrotransposon, characterised by amplification of a G-rich repeat, is inserted into the coding sequence of TAF1, a key partner of RNA polymerase II. XDP SVA alters TAF1 expression
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A deep learning-based method enables the automatic and accurate assembly of chromosome-level genomes Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-17 Zijie Jiang, Zhixiang Peng, Zhaoyuan Wei, Jiahe Sun, Yongjiang Luo, Lingzi Bie, Guoqing Zhang, Yi Wang
The application of high-throughput chromosome conformation capture (Hi-C) technology enables the construction of chromosome-level assemblies. However, the correction of errors and the anchoring of sequences to chromosomes in the assembly remain significant challenges. In this study, we developed a deep learning-based method, AutoHiC, to address the challenges in chromosome-level genome assembly by
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Reconstruction of a robust bacterial replication module Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-14 Tao Wang, Fan He, Ting He, Chen Lin, Xin Guan, Zhongjun Qin, Xiaoli Xue
Chromosomal DNA replication is a fundamental process of life, involving the assembly of complex machinery and dynamic regulation. In this study, we reconstructed a bacterial replication module (pRC) by artificially clustering 23 genes involved in DNA replication and sequentially deleting these genes from their naturally scattered loci on the chromosome of Escherichia coli. The integration of pRC into
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Mei5–Sae3 stabilizes Dmc1 nucleating clusters for efficient Dmc1 assembly on RPA-coated single-stranded DNA Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-14 Chin-Dian Wei, Hao-Yen Chang, Chia-Hua Lu, Chih-Chun Chang, Asako Furukohri, Stephen Mwaniki, Akira Shinohara, Peter Chi, Hung-Wen Li
Interhomolog recombination in meiosis requires a meiosis-specific recombinase, Dmc1. In Saccharomyces cerevisiae, the Mei5–Sae3 complex facilitates the loading of Dmc1 onto the replication protein A (RPA)-coated single-stranded DNA (ssDNA) to form nucleoprotein filaments. In vivo, Dmc1 and Mei5–Sae3 are interdependent in their colocalization on the chromosomes. However, the mechanistic role of Mei5–Sae3
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IRescue: uncertainty-aware quantification of transposable elements expression at single cell level Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-14 Benedetto Polimeni, Federica Marasca, Valeria Ranzani, Beatrice Bodega
Transposable elements (TEs) are mobile DNA repeats known to shape the evolution of eukaryotic genomes. In complex organisms, they exhibit tissue-specific transcription. However, understanding their role in cellular diversity across most tissues remains a challenge, when employing single-cell RNA sequencing (scRNA-seq), due to their widespread presence and genetic similarity. To address this, we present
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Using nucleolytic toxins as restriction enzymes enables new RNA applications Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-14 Ulli Rothweiler, Sigurd Eidem Gundesø, Emma Wu Mikalsen, Steingrim Svenning, Mahavir Singh, Francis Combes, Frida J Pettersson, Antonia Mangold, Yvonne Piotrowski, Felix Schwab, Olav Lanes, Bernd Ketelsen Striberny
Over the past five decades, DNA restriction enzymes have revolutionized biotechnology. While these enzymes are widely used in DNA research and DNA engineering, the emerging field of RNA and mRNA therapeutics requires sequence-specific RNA endoribonucleases. Here, we describe EcoToxN1, a member of the type III toxin-antitoxin family of sequence-specific RNA endoribonucleases, and its use in RNA and
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Advancing microRNA target site prediction with transformer and base-pairing patterns Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-14 Yue Bi, Fuyi Li, Cong Wang, Tong Pan, Chen Davidovich, Geoffrey I Webb, Jiangning Song
MicroRNAs (miRNAs) are short non-coding RNAs involved in various cellular processes, playing a crucial role in gene regulation. Identifying miRNA targets remains a central challenge and is pivotal for elucidating the complex gene regulatory networks. Traditional computational approaches have predominantly focused on identifying miRNA targets through perfect Watson–Crick base pairings within the seed
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DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-14 Anowarul Kabir, Manish Bhattarai, Selma Peterson, Yonatan Najman-Licht, Kim Ø Rasmussen, Amarda Shehu, Alan R Bishop, Boian Alexandrov, Anny Usheva
It was previously shown that DNA breathing, thermodynamic stability, as well as transcriptional activity and transcription factor (TF) bindings are functionally correlated. To ascertain the precise relationship between TF binding and DNA breathing, we developed the multi-modal deep learning model EPBDxDNABERT-2, which is based on the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA dynamics model
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Accelerated discovery and miniaturization of novel single-stranded cytidine deaminases Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-14 Jiacheng Deng, Xueyuan Li, Hao Yu, Lin Yang, Ziru Wang, Wenfeng Yi, Ying Liu, Wenyu Xiao, Hongyong Xiang, Zicong Xie, Dongmei Lv, Hongsheng Ouyang, Daxin Pang, Hongming Yuan
Cytidine base editors (CBEs) hold significant potential in genetic disease treatment and in breeding superior traits into animals. However, their large protein sizes limit their delivery by adeno-associated virus (AAV), given its packing capacity of <4.7 kb. To overcome this, we employed a web-based fast generic discovery (WFG) strategy, identifying several small ssDNA deaminases (Sdds) and constructing
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DrugMAP 2.0: molecular atlas and pharma-information of all drugs Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-14 Fengcheng Li, Minjie Mou, Xiaoyi Li, Weize Xu, Jiayi Yin, Yang Zhang, Feng Zhu
The escalating costs and high failure rates have decelerated the pace of drug development, which amplifies the research interests in developing combinatorial/repurposed drugs and understanding off-target adverse drug reaction (ADR). In other words, it is demanded to delineate the molecular atlas and pharma-information for the combinatorial/repurposed drugs and off-target interactions. However, such
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Striving for clarity in language about gene expression Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-14 Ana S G Cunningham, Myriam Gorospe
What do we mean when we say ‘gene expression’? In the decades following Crick's 1958 central dogma of molecular biology, whereby genetic information flows from DNA (genes) to RNA (transcripts) to protein (products), we have learned a great deal about DNA, RNA, proteins, and the ensuing phenotypic changes. With the advent of high-throughput technologies (1990s), molecular biologists and computer scientists
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CRISETR: an efficient technology for multiplexed refactoring of biosynthetic gene clusters. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-13 Fuqiang He,Xinpeng Liu,Min Tang,Haiyi Wang,Yun Wu,Shufang Liang
The efficient refactoring of natural product biosynthetic gene clusters (BGCs) for activating silent BGCs is a central challenge for the discovery of new bioactive natural products. Herein, we have developed a simple and robust CRISETR (CRISPR/Cas9 and RecET-mediated Refactoring) technique, combining clustered regulatory interspaced short palindromic repeats (CRISPR)/Cas9 and RecET, for the multiplexed
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RTP801 interacts with the tRNA ligase complex and dysregulates its RNA ligase activity in Alzheimer’s disease Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-13 Genís Campoy-Campos, Julia Solana-Balaguer, Anna Guisado-Corcoll, Almudena Chicote-González, Pol Garcia-Segura, Leticia Pérez-Sisqués, Adrian Gabriel Torres, Mercè Canal, Laura Molina-Porcel, Joaquín Fernández-Irigoyen, Enrique Santamaria, Lluís Ribas de Pouplana, Jordi Alberch, Eulàlia Martí, Albert Giralt, Esther Pérez-Navarro, Cristina Malagelada
RTP801/REDD1 is a stress-responsive protein overexpressed in neurodegenerative diseases such as Alzheimer’s disease (AD) that contributes to cognitive deficits and neuroinflammation. Here, we found that RTP801 interacts with HSPC117, DDX1 and CGI-99, three members of the tRNA ligase complex (tRNA-LC), which ligates the excised exons of intron-containing tRNAs and the mRNA exons of the transcription
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PerturbDB for unraveling gene functions and regulatory networks Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-13 Bing Yang, Man Zhang, Yanmei Shi, Bing-Qi Zheng, Chuanping Shi, Daning Lu, Zhi-Zhi Yang, Yi-Ming Dong, Liwen Zhu, Xingyu Ma, Jingyuan Zhang, Jiehua He, Yin Zhang, Kaishun Hu, Haoming Lin, Jian-You Liao, Dong Yin
Perturb-Seq combines CRISPR (clustered regularly interspaced short palindromic repeats)-based genetic screens with single-cell RNA sequencing readouts for high-content phenotypic screens. Despite the rapid accumulation of Perturb-Seq datasets, there remains a lack of a user-friendly platform for their efficient reuse. Here, we developed PerturbDB (http://research.gzsys.org.cn/perturbdb), a platform
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Correction to 'Efficient circularization of protein-encoding RNAs via a novel cis-splicing system'. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-12
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Synergistic effect of split DNA activators of Cas12a with exon-unwinding and induced targeting effect. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-11 Shen Huang,Yongliang Lou,Laibao Zheng
CRISPR-Cas12a, an RNA-guided nuclease, has been repurposed for genome editing and molecular diagnostics due to its capability of cis-cleavage on target DNA and trans-cleavage on non-target single-strand DNA (ssDNA). However, the mechanisms underlying the activation of trans-cleavage activity of Cas12a, particularly in the context of split DNA activators, remain poorly understood. We elucidate the synergistic
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HIV-1 usurps mixed-charge domain-dependent CPSF6 phase separation for higher-order capsid binding, nuclear entry and viral DNA integration. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-11 Sooin Jang,Gregory J Bedwell,Satya P Singh,Hyun Jae Yu,Bjarki Arnarson,Parmit K Singh,Rajalingam Radhakrishnan,AidanDarian W Douglas,Zachary M Ingram,Christian Freniere,Onno Akkermans,Stefan G Sarafianos,Zandrea Ambrose,Yong Xiong,Praju V Anekal,Paula Montero Llopis,Vineet N KewalRamani,Ashwanth C Francis,Alan N Engelman
HIV-1 integration favors nuclear speckle (NS)-proximal chromatin and viral infection induces the formation of capsid-dependent CPSF6 condensates that colocalize with nuclear speckles (NSs). Although CPSF6 displays liquid-liquid phase separation (LLPS) activity in vitro, the contributions of its different intrinsically disordered regions, which includes a central prion-like domain (PrLD) with capsid
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DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-11 Kristen Marco,Lander Marc,Kilz Lea-Marie,Gleue Lukas,Jörg Marko,Bregeon Damien,Hamdane Djemel,Marchand Virginie,Motorin Yuri,Friedland Kristina,Helm Mark
Due to its high modification content tRNAs are notoriously hard to quantify by reverse transcription and RNAseq. Bypassing numerous biases resulting from concatenation of enzymatic treatments, we here report a hybrid approach that harnesses the advantages of hybridization-based and deep sequencing-based approaches. The method renders obsolete any RNAseq related workarounds and correction factors that
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CRISPR screening uncovers nucleolar RPL22 as a heterochromatin destabilizer and senescence driver. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-11 Hong-Yu Li,Min Wang,Xiaoyu Jiang,Yaobin Jing,Zeming Wu,Yifang He,Kaowen Yan,Shuhui Sun,Shuai Ma,Zhejun Ji,Si Wang,Juan Carlos Izpisua Belmonte,Jing Qu,Weiqi Zhang,Taotao Wei,Guang-Hui Liu
Dysfunction of the ribosome manifests during cellular senescence and contributes to tissue aging, functional decline, and development of aging-related disorders in ways that have remained enigmatic. Here, we conducted a comprehensive CRISPR-based loss-of-function (LOF) screen of ribosome-associated genes (RAGs) in human mesenchymal progenitor cells (hMPCs). Through this approach, we identified ribosomal
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A single rare σ70 variant establishes a unique gene expression pattern in the E. coli pathobiont LF82. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-11 Melissa Arroyo-Mendoza,Alexandra Proctor,Abraham Correa-Medina,Sarah DeWolf,Meghan Wymore Brand,Virginia Rosas,Hernan Lorenzi,Michael J Wannemuehler,Gregory J Phillips,Deborah M Hinton
LF82, an adherent-invasive Escherichia coli (AIEC) pathobiont, is associated with Crohn's disease, an inflammatory bowel disease of unknown etiology. Although AIEC phenotypes differ from those of 'commensal' or pathogenic E. coli, work has failed to identify genetic features accounting for these differences. We have investigated a natural, but rare, single nucleotide polymorphism (SNP) in LF82 present
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MBNL splicing factors regulate the microtranscriptome of skeletal muscles. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-11 Agnieszka Piasecka,Michał W Szcześniak,Michał Sekrecki,Arkadiusz Kajdasz,Łukasz J Sznajder,Anna Baud,Krzysztof Sobczak
Muscleblind like splicing regulators (MBNLs) govern various RNA-processing steps, including alternative splicing, polyadenylation, RNA stability and mRNA intracellular localization. In myotonic dystrophy type 1 (DM1), the most common muscular dystrophy in adults, MBNLs are sequestered on toxic RNA containing expanded CUG repeats, which leads to disruption of MBNL-regulated processes and disease features
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Making target sites in large structured RNAs accessible to RNA-cleaving DNAzymes through hybridization with synthetic DNA oligonucleotides Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-09 Connor Nurmi, Jimmy Gu, Amal Mathai, John D Brennan, Yingfu Li
The 10–23 DNAzyme is one of the most active DNA-based enzymes, and in theory, can be designed to target any purine-pyrimidine junction within an RNA sequence for cleavage. However, purine-pyrimidine junctions within a large, structured RNA (lsRNA) molecule of biological origin are not always accessible to 10–23, negating its general utility as an RNA-cutting molecular scissor. Herein, we report a generalizable
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DFF-ChIP: a method to detect and quantify complex interactions between RNA polymerase II, transcription factors, and chromatin Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-09 Benjamin M Spector, Juan F Santana, Miles A Pufall, David H Price
Recently, we introduced a chromatin immunoprecipitation (ChIP) technique utilizing the human DNA Fragmentation Factor (DFF) to digest the DNA prior to immunoprecipitation (DFF-ChIP) that provides the precise location of transcription complexes and their interactions with neighboring nucleosomes. Here we expand the technique to new targets and provide useful information concerning purification of DFF
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Trinucleotide cap analogs with triphosphate chain modifications: synthesis, properties, and evaluation as mRNA capping reagents Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-09 Marcin Warminski, Anais Depaix, Kamil Ziemkiewicz, Tomasz Spiewla, Joanna Zuberek, Karolina Drazkowska, Hanna Kedzierska, Agnieszka Popielec, Marek R Baranowski, Marta Sklucka, Marcelina Bednarczyk, Miroslaw Smietanski, Karol Wolosewicz, Bartosz Majewski, Remigiusz A Serwa, Dominika Nowis, Jakub Golab, Joanna Kowalska, Jacek Jemielity
The recent COVID-19 pandemics have demonstrated the great therapeutic potential of in vitro transcribed (IVT) mRNAs, but improvements in their biochemical properties, such as cellular stability, reactogenicity and translational activity, are critical for further practical applications in gene replacement therapy and anticancer immunotherapy. One of the strategies to overcome these limitations is the
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Mapping the structural landscape of the yeast Ty3 retrotransposon RNA genome. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-09 Angelika Andrzejewska-Romanowska,Julita Gumna,Ewa Tykwińska,Katarzyna Pachulska-Wieczorek
Long terminal repeat (LTR)-retrotransposons are significant contributors to the evolution and diversity of eukaryotic genomes. Their RNA genomes (gRNA) serve as a template for protein synthesis and reverse transcription to a DNA copy, which can integrate into the host genome. Here, we used the SHAPE-MaP strategy to explore Ty3 retrotransposon gRNA structure in yeast and under cell-free conditions.
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Synthesis of 2′-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-05 Kohei Nomura, Seongjin An, Yoshiaki Kobayashi, Jiro Kondo, Ting Shi, Hirotaka Murase, Kosuke Nakamoto, Yasuaki Kimura, Naoko Abe, Kumiko Ui-Tei, Hiroshi Abe
In this study, we report the synthesis of 2′-formamidonucleoside phosphoramidite derivatives and their incorporation into siRNA strands to reduce seed-based off-target effects of small interfering RNAs (siRNAs). Formamido derivatives of all four nucleosides (A, G, C and U) were synthesized in 5–11 steps from commercial compounds. Introducing these derivatives into double-stranded RNA slightly reduced
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Engineered Cas9 variants bypass Keap1-mediated degradation in human cells and enhance epigenome editing efficiency Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-05 Jianfeng Chen, Siyuan Su, Adrian Pickar-Oliver, Anna M Chiarella, Quentin Hahn, Dennis Goldfarb, Erica W Cloer, George W Small, Smaran Sivashankar, Dale A Ramsden, Michael B Major, Nathaniel A Hathaway, Charles A Gersbach, Pengda Liu
As a potent and convenient genome-editing tool, Cas9 has been widely used in biomedical research and evaluated in treating human diseases. Numerous engineered variants of Cas9, dCas9 and other related prokaryotic endonucleases have been identified. However, as these bacterial enzymes are not naturally present in mammalian cells, whether and how bacterial Cas9 proteins are recognized and regulated by
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Mechanism of activation of contact-dependent growth inhibition tRNase toxin by the amino acid biogenesis factor CysK in the bacterial competition system. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-04 Zhaohang Feng,Yuka Yashiro,Kozo Tomita
Contact-dependent growth inhibition (CDI) is a bacterial competition mechanism, wherein the C-terminal toxin domain of CdiA protein (CdiA-CT) is transferred from one bacterium to another, impeding the growth of the toxin recipient. In uropathogenic Escherichia coli 536, CdiA-CT (CdiA-CTEC536) is a tRNA anticodon endonuclease that requires a cysteine biogenesis factor, CysK, for its activity. However
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LAP2alpha facilitates myogenic gene expression by preventing nucleoplasmic lamin A/C from spreading to active chromatin regions. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-04 Simona Ferraioli,Fatih Sarigol,Celine Prakash,Daria Filipczak,Roland Foisner,Nana Naetar
A-type lamins form a filamentous meshwork beneath the nuclear membrane that anchors large heterochromatic genomic regions at the nuclear periphery. A-type lamins also exist as a dynamic, non-filamentous pool in the nuclear interior, where they interact with lamin-associated polypeptide 2 alpha (LAP2α). Both proteins associate with largely overlapping euchromatic genomic regions in the nucleoplasm,
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Elucidating microRNA-34a organisation within human Argonaute-2 by dynamic nuclear polarisation-enhanced magic angle spinning NMR. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-04 Rubin Dasgupta,Walter Becker,Katja Petzold
Understanding mRNA regulation by microRNA (miR) relies on the structural understanding of the RNA-induced silencing complex (RISC). Here, we elucidate the structural organisation of miR-34a, which is de-regulated in various cancers, in human Argonaute-2 (hAgo2), the effector protein in RISC. This analysis employs guanosine-specific isotopic labelling and dynamic nuclear polarisation (DNP)-enhanced
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Eukaryotic initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-03 Ana Quintas, Robert F Harvey, Emilie Horvilleur, Gavin D Garland, Tobias Schmidt, Lajos Kalmar, Veronica Dezi, Alberto Marini, Alexander M Fulton, Tuija A A Pöyry, Cameron H Cole, Martin Turner, Ritwick Sawarkar, Michael A Chapman, Martin Bushell, Anne E Willis
RNA binding proteins drive proliferation and tumorigenesis by regulating the translation and stability of specific subsets of messenger RNAs (mRNAs). We have investigated the role of eukaryotic initiation factor 4B (eIF4B) in this process and identify 10-fold more RNA binding sites for eIF4B in tumour cells from patients with diffuse large B-cell lymphoma compared to control B cells and, using individual-nucleotide
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PROTAC-DB 3.0: an updated database of PROTACs with extended pharmacokinetic parameters Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-03 Jingxuan Ge, Shimeng Li, Gaoqi Weng, Huating Wang, Meijing Fang, Huiyong Sun, Yafeng Deng, Chang- Yu Hsieh, Dan Li, Tingjun Hou
Proteolysis-targeting chimera (PROTAC) is an emerging therapeutic technology that leverages the ubiquitin-proteasome system to target protein degradation. Due to its event-driven mechanistic characteristics, PROTAC has the potential to regulate traditionally non-druggable targets. Recently, AI-aided drug design has accelerated the development of PROTAC drugs. However, the rational design of PROTACs
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Structural basis of DNA recognition by BEN domain proteins reveals a role for oligomerization in unmethylated DNA selection by BANP Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-03 Jiahao Ren, Junmeng Wang, Yanpeng Ren, Yuyang Zhang, Pengshuai Wei, Meng Wang, Yimeng Zhang, Meng Li, Chuyan Yuan, Haipeng Gong, Junyi Jiang, Zhanxin Wang
The BEN domain is a newly discovered type of DNA-binding domain that exists in a variety of species. There are nine BEN domain-containing proteins in humans, and most have been shown to have chromatin-related functions. NACC1 preferentially binds to CATG motif-containing sequences and functions primarily as a transcriptional coregulator. BANP and BEND3 preferentially bind DNA bearing unmethylated CpG
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Correction to 'Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch'. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-01
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Correction to 'Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R'. Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-01
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The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAArg and tRNALys isoacceptors in the P site Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-01 Kathryn Turnbull, Helge Paternoga, Esther von der Weth, Artyom A Egorov, Agnieszka A Pochopien, Yujie Zhang, Lilit Nersisyan, Tõnu Margus, Marcus J O Johansson, Vicent Pelechano, Daniel N Wilson, Vasili Hauryliuk
The efficiency of translation termination is determined by the nature of the stop codon as well as its context. In eukaryotes, recognition of the A-site stop codon and release of the polypeptide are mediated by release factors eRF1 and eRF3, respectively. Translation termination is modulated by other factors which either directly interact with release factors or bind to the E-site and modulate the
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Machine learning unravels inherent structural patterns in Escherichia coli Hi-C matrices and predicts chromosome dynamics Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-01 Palash Bera, Jagannath Mondal
High dimensional nature of the chromosomal conformation contact map (‘Hi-C Map’), even for microscopically small bacterial cell, poses challenges for extracting meaningful information related to its complex organization. Here we first demonstrate that an artificial deep neural network-based machine-learnt (ML) low-dimensional representation of a recently reported Hi-C interaction map of archetypal
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Structural basis for the concerted antiphage activity in the SIR2–HerA system Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-01 Fumeng Liao, Guimei Yu, Chendi Zhang, Zhikun Liu, Xuzichao Li, Qiuqiu He, Hang Yin, Xiang Liu, Zhuang Li, Heng Zhang
Recently, a novel two-gene bacterial defense system against phages, encoding a SIR2 NADase and a HerA ATPase/helicase, has been identified. However, the molecular mechanism of the bacterial SIR2–HerA immune system remains unclear. Here, we determine the cryo-EM structures of SIR2, HerA and their complex from Paenibacillus sp. 453MF in different functional states. The SIR2 proteins oligomerize into
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PARP1-TRIM44-MRN loop dictates the response to PARP inhibitors Nucleic Acids Res. (IF 16.6) Pub Date : 2024-09-01 Yonghyeon Kim, Sunwoo Min, Soyeon Kim, Seo Yun Lee, Yeon-Ji Park, Yungyeong Heo, Soon Sang Park, Tae Jun Park, Jae-Ho Lee, Ho Chul Kang, Jae-Hoon Ji, Hyeseong Cho
PARP inhibitors (PARPi) show selective efficacy in tumors with homologous recombination repair (HRR)-defects but the activation mechanism of HRR pathway in PARPi-treated cells remains enigmatic. To unveil it, we searched for the mediator bridging PARP1 to ATM pathways by screening 211 human ubiquitin-related proteins. We discovered TRIM44 as a crucial mediator that recruits the MRN complex to damaged