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Enhanced exon skipping and prolonged dystrophin restoration achieved by TfR1-targeted delivery of antisense oligonucleotide using FORCE conjugation in mdx mice Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-10 Cody A Desjardins, Monica Yao, John Hall, Emma O’Donnell, Reshmii Venkatesan, Sean Spring, Aiyun Wen, Nelson Hsia, Peiyi Shen, Ryan Russo, Bo Lan, Tyler Picariello, Kim Tang, Timothy Weeden, Stefano Zanotti, Romesh Subramanian, Oxana Ibraghimov-Beskrovnaya
Current therapies for Duchenne muscular dystrophy (DMD) use phosphorodiamidate morpholino oligomers (PMO) to induce exon skipping in the dystrophin pre-mRNA, enabling the translation of a shortened but functional dystrophin protein. This strategy has been hampered by insufficient delivery of PMO to cardiac and skeletal muscle. To overcome these limitations, we developed the FORCETM platform consisting
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The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-08 Jérémy Scutenaire, Damien Plassard, Mélody Matelot, Tommaso Villa, Julie Zumsteg, Domenico Libri, Bertrand Séraphin
N6-Methyladenosine (m6A), one of the most abundant internal modification of eukaryotic mRNAs, participates in the post-transcriptional control of gene expression through recruitment of specific m6A readers. In Saccharomyces cerevisiae, the m6A methyltransferase Ime4 is expressed only during meiosis and its deletion impairs this process. To elucidate how m6A control gene expression, we investigated
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Role for DNA double strand end-resection activity of RecBCD in control of aberrant chromosomal replication initiation in Escherichia coli Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-05 Sayantan Goswami, Jayaraman Gowrishankar
Replication of the circular bacterial chromosome is initiated from a locus oriC with the aid of an essential protein DnaA. One approach to identify factors acting to prevent aberrant oriC-independent replication initiation in Escherichia coli has been that to obtain mutants which survive loss of DnaA. Here, we show that a ΔrecD mutation, associated with attenuation of RecBCD’s DNA double strand end-resection
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SRRM2 organizes splicing condensates to regulate alternative splicing Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-05 Shaohai Xu, Soak-Kuan Lai, Donald Yuhui Sim, Warren Shou Leong Ang, Hoi Yeung Li, Xavier Roca
SRRM2 is a nuclear-speckle marker containing multiple disordered domains, whose dysfunction is associated with several human diseases. Using mainly EGFP-SRRM2 knock-in HEK293T cells, we show that SRRM2 forms biomolecular condensates satisfying most hallmarks of liquid-liquid phase separation, including spherical shape, dynamic rearrangement, coalescence and concentration dependence supported by in
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Construction of a cross-species cell landscape at single-cell level Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-05 Renying Wang, Peijing Zhang, Jingjing Wang, Lifeng Ma, Weigao E, Shengbao Suo, Mengmeng Jiang, Jiaqi Li, Haide Chen, Huiyu Sun, Lijiang Fei, Ziming Zhou, Yincong Zhou, Yao Chen, Weiqi Zhang, Xinru Wang, Yuqing Mei, Zhongyi Sun, Chengxuan Yu, Jikai Shao, Yuting Fu, Yanyu Xiao, Fang Ye, Xing Fang, Hanyu Wu, Qile Guo, Xiunan Fang, Xia Li, Xianzhi Gao, Dan Wang, Peng-Fei Xu, Rui Zeng, Gang Xu, Lijun Zhu
Individual cells are basic units of life. Despite extensive efforts to characterize the cellular heterogeneity of different organisms, cross-species comparisons of landscape dynamics have not been achieved. Here, we applied single-cell RNA sequencing (scRNA-seq) to map organism-level cell landscapes at multiple life stages for mice, zebrafish and Drosophila. By integrating the comprehensive dataset
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Transcription-coupled donor DNA expression increases homologous recombination for efficient genome editing Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-05 Kaixuan Gao, Xuedi Zhang, Zhenwu Zhang, Xiangyu Wu, Yan Guo, Pengchong Fu, Angyang Sun, Ju Peng, Jie Zheng, Pengfei Yu, Tengfei Wang, Qinying Ye, Jingwei Jiang, Haopeng Wang, Chao-Po Lin, Guanjun Gao
Genomes can be edited by homologous recombination stimulated by CRISPR/Cas9 [clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated peptide 9]-induced DNA double-strand breaks. However, this approach is inefficient for inserting or deleting long fragments in mammalian cells. Here, we describe a simple genome-editing method, termed transcription-coupled Cas9-mediated editing
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The convergent xenogeneic silencer MucR predisposes α-proteobacteria to integrate AT-rich symbiosis genes Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-04 Wen-Tao Shi, Biliang Zhang, Meng-Lin Li, Ke-Han Liu, Jian Jiao, Chang-Fu Tian
Bacterial adaptation is largely shaped by horizontal gene transfer, xenogeneic silencing mediated by lineage-specific DNA bridgers (H-NS, Lsr2, MvaT and Rok), and various anti-silencing mechanisms. No xenogeneic silencing DNA bridger is known for α-proteobacteria, from which mitochondria evolved. By investigating α-proteobacterium Sinorhizobium fredii, a facultative legume microsymbiont, here we report
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Efficient detection and assembly of non-reference DNA sequences with synthetic long reads Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-04 Dmitry Meleshko, Rui Yang, Patrick Marks, Stephen Williams, Iman Hajirasouliha
Recent pan-genome studies have revealed an abundance of DNA sequences in human genomes that are not present in the reference genome. A lion’s share of these non-reference sequences (NRSs) cannot be reliably assembled or placed on the reference genome. Improvements in long-read and synthetic long-read (aka linked-read) technologies have great potential for the characterization of NRSs. While synthetic
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FOXL2 and FOXA1 cooperatively assemble on the TP53 promoter in alternative dimer configurations Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-03 Yuri Choi, Yongyang Luo, Seunghwa Lee, Hanyong Jin, Hye-Jin Yoon, Yoonsoo Hahn, Jeehyeon Bae, Hyung Ho Lee
Although both the p53 and forkhead box (FOX) family proteins are key transcription factors associated with cancer progression, their direct relationship is unknown. Here, we found that FOX family proteins bind to the non-canonical homotypic cluster of the p53 promoter region (TP53). Analysis of crystal structures of FOX proteins (FOXL2 and FOXA1) bound to the p53 homotypic cluster indicated that they
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Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-03 Suchintak Dash, Cristina S D Palma, Ines S C Baptista, Bilena L B Almeida, Mohamed N M Bahrudeen, Vatsala Chauhan, Rahul Jagadeesan, Andre S Ribeiro
Cold shock adaptability is a key survival skill of gut bacteria of warm-blooded animals. Escherichia coli cold shock responses are controlled by a complex multi-gene, timely-ordered transcriptional program. We investigated its underlying mechanisms. Having identified short-term, cold shock repressed genes, we show that their responsiveness is unrelated to their transcription factors or global regulators
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Intratracheally administered LNA gapmer antisense oligonucleotides induce robust gene silencing in mouse lung fibroblasts Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-03 Minwook Shin, Io Long Chan, Yuming Cao, Alisha M Gruntman, Jonathan Lee, Jacquelyn Sousa, Tomás C Rodríguez, Dimas Echeverria, Gitali Devi, Alexandre J Debacker, Michael P Moazami, Pranathi Meda Krishnamurthy, Julia M Rembetsy-Brown, Karen Kelly, Onur Yukselen, Elisa Donnard, Teagan J Parsons, Anastasia Khvorova, Erik J Sontheimer, René Maehr, Manuel Garber, Jonathan K Watts
The lung is a complex organ with various cell types having distinct roles. Antisense oligonucleotides (ASOs) have been studied in the lung, but it has been challenging to determine their effectiveness in each cell type due to the lack of appropriate analytical methods. We employed three distinct approaches to study silencing efficacy within different cell types. First, we used lineage markers to identify
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ABC portal: a single-cell database and web server for blood cells Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-03 Xin Gao, Fang Hong, Zhenyu Hu, Zilong Zhang, Yang Lei, Xiaoyun Li, Tao Cheng
ABC portal (http://abc.sklehabc.com) is a database and web portal containing 198 single-cell transcriptomic datasets of development, differentiation and disorder of blood/immune cells. All the datasets were re-annotated with a manually curated and unified single-cell reference, especially for the haematopoietic stem and progenitor cells. ABC portal provides web-based interactive analysis modules, especially
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A versatile Cas12k-based genetic engineering toolkit (C12KGET) for metabolic engineering in genetic manipulation-deprived strains Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-03 Yali Cui, Huina Dong, Baisong Tong, Huiying Wang, Xipeng Chen, Guangqing Liu, Dawei Zhang
The genetic modification of microorganisms is conducive to the selection of high-yield producers of high-value-added chemicals, but a lack of genetic tools hinders the industrialization of most wild species. Therefore, it is crucial to develop host-independent gene editing tools that can be used for genetic manipulation-deprived strains. The Tn7-like transposon from Scytonema hofmanni has been shown
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Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-03 Dmitrii M Bubnov, Tigran V Yuzbashev, Andrey A Khozov, Olga E Melkina, Tatiana V Vybornaya, Guy-Bart Stan, Sergey P Sineoky
Despite advances in bacterial genome engineering, delivery of large synthetic constructs remains challenging in practice. In this study, we propose a straightforward and robust approach for the markerless integration of DNA fragments encoding whole metabolic pathways into the genome. This approach relies on the replacement of a counterselection marker with cargo DNA cassettes via λRed recombineering
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Molecular basis of anti-CRISPR operon repression by Aca10 Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-03 So Yeon Lee, Nils Birkholz, Peter C Fineran, Hyun Ho Park
CRISPR-Cas systems are bacterial defense systems for fighting against invaders such as bacteriophages and mobile genetic elements. To escape destruction by these bacterial immune systems, phages have co-evolved multiple anti-CRISPR (Acr) proteins, which inhibit CRISPR-Cas function. Many acr genes form an operon with genes encoding transcriptional regulators, called anti-CRISPR-associated (Aca) proteins
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Cluster-independent marker feature identification from single-cell omics data using SEMITONES Nucleic Acids Res. (IF 19.16) Pub Date : 2022-08-01 Anna Hendrika Cornelia Vlot, Setareh Maghsudi, Uwe Ohler
Identification of cell identity markers is an essential step in single-cell omics data analysis. Current marker identification strategies typically rely on cluster assignments of cells. However, cluster assignment, particularly for developmental data, is nontrivial, potentially arbitrary, and commonly relies on prior knowledge. In response, we present SEMITONES, a principled method for cluster-free
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Identification of a novel deFADding activity in human, yeast and bacterial 5′ to 3′ exoribonucleases Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-29 Sunny Sharma, Jun Yang, Selom K Doamekpor, Ewa Grudizen-Nogalska, Liang Tong, Megerditch Kiledjian
Identification of metabolite caps including FAD on the 5′ end of RNA has uncovered a previously unforeseen intersection between cellular metabolism and gene expression. To understand the function of FAD caps in cellular physiology, we characterised the proteins interacting with FAD caps in budding yeast. Here we demonstrate that highly conserved 5′-3′ exoribonucleases, Xrn1 and Rat1, physically interact
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The HDAC7–TET2 epigenetic axis is essential during early B lymphocyte development Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-29 Alba Azagra, Ainara Meler, Oriol de Barrios, Laureano Tomás-Daza, Olga Collazo, Beatriz Monterde, Mireia Obiols, Llorenç Rovirosa, Maria Vila-Casadesús, Mónica Cabrera-Pasadas, Mar Gusi-Vives, Thomas Graf, Ignacio Varela, José Luis Sardina, Biola M Javierre, Maribel Parra
Correct B cell identity at each stage of cellular differentiation during B lymphocyte development is critically dependent on a tightly controlled epigenomic landscape. We previously identified HDAC7 as an essential regulator of early B cell development and its absence leads to a drastic block at the pro-B to pre-B cell transition. More recently, we demonstrated that HDAC7 loss in pro-B-ALL in infants
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FACT subunit SUPT16H associates with BRD4 and contributes to silencing of interferon signaling Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-29 Dawei Zhou, Zhenyu Wu, Jun-Gyu Park, Guillaume N Fiches, Tai-Wei Li, Qin Ma, Huachao Huang, Ayan Biswas, Luis Martinez-Sobrido, Netty G Santoso, Jian Zhu
FACT (FAcilitates Chromatin Transcription) is a heterodimeric protein complex composed of SUPT16H and SSRP1, and a histone chaperone participating in chromatin remodeling during gene transcription. FACT complex is profoundly regulated, and contributes to both gene activation and suppression. Here we reported that SUPT16H, a subunit of FACT, is acetylated in both epithelial and natural killer (NK) cells
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sRNA-controlled iron sparing response in Staphylococci Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-29 Rodrigo H Coronel-Tellez, Mateusz Pospiech, Maxime Barrault, Wenfeng Liu, Valérie Bordeau, Christelle Vasnier, Brice Felden, Bruno Sargueil, Philippe Bouloc
Staphylococcus aureus, a human opportunist pathogen, adjusts its metabolism to cope with iron deprivation within the host. We investigated the potential role of small non-coding RNAs (sRNAs) in dictating this process. A single sRNA, named here IsrR, emerged from a competition assay with tagged-mutant libraries as being required during iron starvation. IsrR is iron-repressed and predicted to target
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Stochastically multimerized ParB orchestrates DNA assembly as unveiled by single-molecule analysis Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-29 Lijuan Guo, Yilin Zhao, Qian Zhang, Ying Feng, Lulu Bi, Xia Zhang, Teng Wang, Cong Liu, Hanhui Ma, Bo Sun
The tripartite ParABS system mediates chromosome segregation in a wide range of bacteria. Dimeric ParB was proposed to nucleate on parS sites and spread to neighboring DNA. However, how properly distributed ParB dimers further compact chromosomal DNA into a higher-order nucleoprotein complex for partitioning remains poorly understood. Here, using a single-molecule approach, we show that tens of Bacillus
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TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-29 Paul Stolz, Angelo Salazar Mantero, Andrey Tvardovskiy, Enes Ugur, Lucas E Wange, Christopher B Mulholland, Yuying Cheng, Michael Wierer, Wolfgang Enard, Robert Schneider, Till Bartke, Heinrich Leonhardt, Simon J Elsässer, Sebastian Bultmann
DNA methylation (5-methylcytosine (5mC)) is critical for genome stability and transcriptional regulation in mammals. The discovery that ten-eleven translocation (TET) proteins catalyze the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) revolutionized our perspective on the complexity and regulation of DNA modifications. However, to what extent
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Structural assembly of the nucleic-acid-binding Thp3–Csn12–Sem1 complex functioning in mRNA splicing Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-29 Zhiling Kuang, Jiyuan Ke, Jiong Hong, Zhongliang Zhu, Liwen Niu
PCI domain proteins play important roles in post-transcriptional gene regulation. In the TREX-2 complex, PCI domain-containing Sac3 and Thp1 proteins and accessory Sem1 protein form a ternary complex required for mRNA nuclear export. In contrast, structurally related Thp3–Csn12–Sem1 complex mediates pre-mRNA splicing. In this study, we determined the structure of yeast Thp3186–470–Csn12–Sem1 ternary
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DNA circuits compatible encoder and demultiplexer based on a single biomolecular platform with DNA strands as outputs Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-29 Tianci Xie, Yuhan Deng, Jiarui Zhang, Zhen Zhang, Zhe Hu, Tongbo Wu
A series of multiple logic circuits based on a single biomolecular platform is constructed to perform nonarithmetic and arithmetic functions, including 4-to-2 encoder, 1-to-2 demultiplexer, 1-to-4 demultiplexer, and multi-input OR gate. The encoder to a DNA circuit is the equivalent of a sensory receptor to a reflex arc. They all function to encode information from outside the pathway (DNA circuit
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Top3α is the replicative topoisomerase in mitochondrial DNA replication Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-29 Anu Hangas, Nina J Kekäläinen, Alisa Potter, Craig Michell, Kauko J Aho, Chiara Rutanen, Johannes N Spelbrink, Jaakko L Pohjoismäki, Steffi Goffart
Mitochondrial DNA has been investigated for nearly fifty years, but many aspects of the maintenance of this essential small genome remain unknown. Like any genome, mammalian mitochondrial DNA requires the function of topoisomerases to counter and regulate the topological tension arising during replication, transcription, segregation, and repair. However, the functions of the different mitochondrial
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SOX9 reprograms endothelial cells by altering the chromatin landscape Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-29 Bettina M Fuglerud, Sibyl Drissler, Jeremy Lotto, Tabea L Stephan, Avinash Thakur, Rebecca Cullum, Pamela A Hoodless
The transcription factor SOX9 is activated at the onset of endothelial-to-mesenchymal transition (EndMT) during embryonic development and in pathological conditions. Its roles in regulating these processes, however, are not clear. Using human umbilical vein endothelial cells (HUVECs) as an EndMT model, we show that SOX9 expression alone is sufficient to activate mesenchymal genes and steer endothelial
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CGG repeats trigger translational frameshifts that generate aggregation-prone chimeric proteins Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-29 Shannon E Wright, Caitlin M Rodriguez, Jeremy Monroe, Jiazheng Xing, Amy Krans, Brittany N Flores, Venkatesha Barsur, Magdalena I Ivanova, Kristin S Koutmou, Sami J Barmada, Peter K Todd
CGG repeat expansions in the FMR1 5’UTR cause the neurodegenerative disease Fragile X-associated tremor/ataxia syndrome (FXTAS). These repeats form stable RNA secondary structures that support aberrant translation in the absence of an AUG start codon (RAN translation), producing aggregate-prone peptides that accumulate within intranuclear neuronal inclusions and contribute to neurotoxicity. Here, we
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MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-29 Naoko Fujiwara, Maki Shigemoto, Mizuki Hirayama, Ken-ichi Fujita, Shigeto Seno, Hideo Matsuda, Masami Nagahama, Seiji Masuda
Recent in vitro reconstitution analyses have proven that the physical interaction between the exosome core and MTR4 helicase, which promotes the exosome activity, is maintained by either MPP6 or RRP6. However, knowledge regarding the function of MPP6 with respect to in vivo exosome activity remains scarce. Here, we demonstrate a facilitative function of MPP6 that composes a specific part of MTR4-dependent
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Precise tuning of bacterial translation initiation by non-equilibrium 5′-UTR unfolding observed in single mRNAs Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-27 Sujay Ray, Shiba S Dandpat, Surajit Chatterjee, Nils G Walter
Noncoding, structured 5′-untranslated regions (5′-UTRs) of bacterial messenger RNAs (mRNAs) can control translation efficiency by forming structures that either recruit or repel the ribosome. Here we exploit a 5′-UTR embedded preQ1-sensing, pseudoknotted translational riboswitch to probe how binding of a small ligand controls recruitment of the bacterial ribosome to the partially overlapping Shine-Dalgarno
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Uncovering translation roadblocks during the development of a synthetic tRNA Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-27 Arjun Prabhakar, Natalie Krahn, Jingji Zhang, Oscar Vargas-Rodriguez, Miri Krupkin, Ziao Fu, Francisco J Acosta-Reyes, Xueliang Ge, Junhong Choi, Ana Crnković, Måns Ehrenberg, Elisabetta Viani Puglisi, Dieter Söll, Joseph Puglisi
Ribosomes are remarkable in their malleability to accept diverse aminoacyl-tRNA substrates from both the same organism and other organisms or domains of life. This is a critical feature of the ribosome that allows the use of orthogonal translation systems for genetic code expansion. Optimization of these orthogonal translation systems generally involves focusing on the compatibility of the tRNA, aminoacyl-tRNA
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The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-26 Sophie Hertel, Richard E Spinney, Stephanie Y Xu, Thomas E Ouldridge, Richard G Morris, Lawrence K Lee
The kinetics of DNA hybridization are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridize at different rates are not well understood. Secondary structure is one predictable factor that influences hybridization rates but is not sufficient on its own to fully explain the observed sequence-dependent
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Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-26 Tanxi Bai, Jiayi Zhang, Kai Huang, Wen Wang, Bowen Chen, Yujie Li, Mengyao Zhao, Suoyu Zhang, Chenyou Zhu, Dongsheng Liu, Bryan Wei
Enzymatic ligation is a popular method in DNA nanotechnology for structural enforcement. When employed as stability switch for chosen components, ligation can be applied to induce DNA nanostructure reconfiguration. In this study, we investigate the reinforcement effect of ligation on addressable DNA nanostructures assembled entirely from short synthetic strands as the basis of structural reconfiguration
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Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-25 Gopika Gopan, Zhaleh Ghaemi, Caitlin M Davis, Martin Gruebele
The RNA recognition motif (RRM) occurs widely in RNA-binding proteins, but does not always by itself support full binding. For example, it is known that binding of SL1 RNA to the protein U1-70K in the U1 spliceosomal particle is reduced when a region flanking the RRM is truncated. How the RRM flanking regions that together with the RRM make up an ‘extended RRM’ (eRRM) contribute to complex stability
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Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Roshan Satange, Shih-Hao Kao, Ching-Ming Chien, Shan-Ho Chou, Chi-Chien Lin, Stephen Neidle, Ming-Hon Hou
The use of multiple drugs simultaneously targeting DNA is a promising strategy in cancer therapy for potentially overcoming single drug resistance. In support of this concept, we report that a combination of actinomycin D (ActD) and echinomycin (Echi), can interact in novel ways with native and mismatched DNA sequences, distinct from the structural effects produced by either drug alone. Changes in
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SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Veronique Fischer, Vincent Hisler, Elisabeth Scheer, Elisabeth Lata, Bastien Morlet, Damien Plassard, Dominique Helmlinger, Didier Devys, László Tora, Stéphane D Vincent
Coactivator complexes regulate chromatin accessibility and transcription. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved coactivator complex. The core module scaffolds the entire SAGA complex and adopts a histone octamer-like structure, which consists of six histone-fold domain (HFD)-containing proteins forming three histone-fold (HF) pairs, to which the double HFD-containing SUPT3H
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Human RNase 4 improves mRNA sequence characterization by LC–MS/MS Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Eric J Wolf, Sebastian Grünberg, Nan Dai, Tien-Hao Chen, Bijoyita Roy, Erbay Yigit, Ivan R Corrêa
With the rapid growth of synthetic messenger RNA (mRNA)-based therapeutics and vaccines, the development of analytical tools for characterization of long, complex RNAs has become essential. Tandem liquid chromatography–mass spectrometry (LC–MS/MS) permits direct assessment of the mRNA primary sequence and modifications thereof without conversion to cDNA or amplification. It relies upon digestion of
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CMDB: the comprehensive population genome variation database of China Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Zhichao Li, Xiaosen Jiang, Mingyan Fang, Yong Bai, Siyang Liu, Shujia Huang, Xin Jin
A high-quality genome variation database derived from a large-scale population is one of the most important infrastructures for genomics, clinical and translational medicine research. Here, we developed the Chinese Millionome Database (CMDB), a database that contains 9.04 million single nucleotide variants (SNV) with allele frequency information derived from low-coverage (0.06×–0.1×) whole-genome sequencing
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Decoding YAP dependent transcription in the liver Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Francesca Biagioni, Ottavio Croci, Silvia Sberna, Elisa Donato, Arianna Sabò, Andrea Bisso, Laura Curti, Arianna Chiesa, Stefano Campaner
The transcriptional coactivator YAP is emerging as a master regulator of cell growth. In the liver, YAP activity is linked to hepatomegaly, regeneration, dedifferentiation, and aggressive tumor growth. Here we present genomic studies to address how YAP may elicit such profound biological changes in murine models. YAP bound the genome in a TEAD-dependent manner, either at loci constitutively occupied
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Structural basis of AlpA-dependent transcription antitermination Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Aijia Wen, Minxing Zhao, Sha Jin, Yuan-Qiang Lu, Yu Feng
AlpA positively regulates a programmed cell death pathway linked to the virulence of Pseudomonas aeruginosa by recognizing an AlpA binding element within the promoter, then binding RNA polymerase directly and allowing it to bypass an intrinsic terminator positioned downstream. Here, we report the single-particle cryo-electron microscopy structures of both an AlpA-loading complex and an AlpA-loaded
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Structural basis of Streptomyces transcription activation by zinc uptake regulator Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Xu Yang, Yiqun Wang, Guiyang Liu, Zixin Deng, Shuangjun Lin, Jianting Zheng
Streptomyces coelicolor (Sc) is a model organism of actinobacteria to study morphological differentiation and production of bioactive metabolites. Sc zinc uptake regulator (Zur) affects both processes by controlling zinc homeostasis. It activates transcription by binding to palindromic Zur-box sequences upstream of −35 elements. Here we deciphered the molecular mechanism by which ScZur interacts with
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Efficient quantitative monitoring of translational initiation by RelE cleavage Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Caroline M Focht, Scott A Strobel
The sequences of the 5′ untranslated regions (5′-UTRs) of mRNA alter gene expression across domains of life. Transcriptional modulators can be easily assayed through transcription termination, but translational regulators often require indirect, laborious methods. We have leveraged RelE’s ribosome-dependent endonuclease activity to develop a quantitative assay to monitor translation initiation of cis-regulatory
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Staphylococcal self-loading helicases couple the staircase mechanism with inter domain high flexibility Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Cuncun Qiao, Gianluca Debiasi-Anders, Ignacio Mir-Sanchis
Replication is a crucial cellular process. Replicative helicases unwind DNA providing the template strand to the polymerase and promoting replication fork progression. Helicases are multi-domain proteins which use an ATPase domain to couple ATP hydrolysis with translocation, however the role that the other domains might have during translocation remains elusive. Here, we studied the unexplored self-loading
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R-loop-induced irreparable DNA damage evades checkpoint detection in the C. elegans germline Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Tara Hicks, Emily Koury, Caleb McCabe, Cameron Williams, Caroline Crahan, Sarit Smolikove
Accumulation of DNA–RNA hybrids in the form of R-loops can result in replication–transcription conflict that leads to the formation of DNA double strand breaks (DSBs). Using null mutants for the two Caenorhabditis elegans genes encoding for RNaseH1 and RNaseH2, we identify novel effects of R-loop accumulation in the germline. R-loop accumulation leads, as expected, to replication stress, followed by
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Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Christine A Roden, Yifan Dai, Catherine A Giannetti, Ian Seim, Myungwoon Lee, Rachel Sealfon, Grace A McLaughlin, Mark A Boerneke, Christiane Iserman, Samuel A Wey, Joanne L Ekena, Olga G Troyanskaya, Kevin M Weeks, Lingchong You, Ashutosh Chilkoti, Amy S Gladfelter
Nucleocapsid protein (N-protein) is required for multiple steps in betacoronaviruses replication. SARS-CoV-2-N-protein condenses with specific viral RNAs at particular temperatures making it a powerful model for deciphering RNA sequence specificity in condensates. We identify two separate and distinct double-stranded, RNA motifs (dsRNA stickers) that promote N-protein condensation. These dsRNA stickers
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Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1 Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Mathieu Lussier-Price, Haytham M Wahba, Xavier H Mascle, Laurent Cappadocia, Veronique Bourdeau, Christina Gagnon, Sebastian Igelmann, Kazuyasu Sakaguchi, Gerardo Ferbeyre, James G Omichinski
SUMO proteins are important regulators of many key cellular functions in part through their ability to form interactions with other proteins containing SUMO interacting motifs (SIMs). One characteristic feature of all SUMO proteins is the presence of a highly divergent intrinsically disordered region at their N-terminus. In this study, we examine the role of this N-terminal region of SUMO proteins
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The L1-ORF1p coiled coil enables formation of a tightly compacted nucleic acid-bound complex that is associated with retrotransposition Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Ben A Cashen, M Nabuan Naufer, Michael Morse, Charles E Jones, Mark C Williams, Anthony V Furano
Long interspersed nuclear element 1 (L1) parasitized most vertebrates and constitutes ∼20% of the human genome. It encodes ORF1p and ORF2p which form an L1-ribonucleoprotein (RNP) with their encoding transcript that is copied into genomic DNA (retrotransposition). ORF1p binds single-stranded nucleic acid (ssNA) and exhibits NA chaperone activity. All vertebrate ORF1ps contain a coiled coil (CC) domain
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HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Sebastian Gregoricchio, Lélia Polit, Michela Esposito, Jérémy Berthelet, Laure Delestré, Emilie Evanno, M’Boyba Diop, Isabelle Gallais, Hanna Aleth, Mathilde Poplineau, Wilbert Zwart, Frank Rosenbauer, Fernando Rodrigues-Lima, Estelle Duprez, Valentina Boeva, Christel Guillouf
Although originally described as transcriptional activator, SPI1/PU.1, a major player in haematopoiesis whose alterations are associated with haematological malignancies, has the ability to repress transcription. Here, we investigated the mechanisms underlying gene repression in the erythroid lineage, in which SPI1 exerts an oncogenic function by blocking differentiation. We show that SPI1 represses
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mRNA- and factor-driven dynamic variability controls eIF4F-cap recognition for translation initiation Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Burak Çetin, Seán E O’Leary
mRNA 5′ cap recognition by eIF4F is a key element of eukaryotic translational control. Kinetic differences in eIF4F–mRNA interactions have long been proposed to mediate translation-efficiency differences between mRNAs, and recent transcriptome-wide studies have revealed significant heterogeneity in eIF4F engagement with differentially-translated mRNAs. However, detailed kinetic information exists only
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Cooperative engagement and subsequent selective displacement of SR proteins define the pre-mRNA 3D structural scaffold for early spliceosome assembly Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-24 Kaushik Saha, Gourisankar Ghosh
We recently reported that serine–arginine-rich (SR) protein-mediated pre-mRNA structural remodeling generates a pre-mRNA 3D structural scaffold that is stably recognized by the early spliceosomal components. However, the intermediate steps between the free pre-mRNA and the assembled early spliceosome are not yet characterized. By probing the early spliceosomal complexes in vitro and RNA-protein interactions
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Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer–promoter interactions Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-18 Kaiyuan Wang, Mario Escobar, Jing Li, Barun Mahata, Jacob Goell, Spencer Shah, Madeleine Cluck, Isaac B Hilton
Nuclease-inactivated CRISPR/Cas-based (dCas-based) systems have emerged as powerful technologies to synthetically reshape the human epigenome and gene expression. Despite the increasing adoption of these platforms, their relative potencies and mechanistic differences are incompletely characterized, particularly at human enhancer–promoter pairs. Here, we systematically compared the most widely adopted
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Cap-independent translation and a precisely located RNA sequence enable SARS-CoV-2 to control host translation and escape anti-viral response Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-18 Boris Slobodin, Urmila Sehrawat, Anastasia Lev, Daniel Hayat, Binyamin Zuckerman, Davide Fraticelli, Ariel Ogran, Amir Ben-Shmuel, Elad Bar-David, Haim Levy, Igor Ulitsky, Rivka Dikstein
Translation of SARS-CoV-2-encoded mRNAs by the host ribosomes is essential for its propagation. Following infection, the early expressed viral protein NSP1 binds the ribosome, represses translation, and induces mRNA degradation, while the host elicits an anti-viral response. The mechanisms enabling viral mRNAs to escape this multifaceted repression remain obscure. Here we show that expression of NSP1
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Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-18 Jinfeng Chen, Jingfei Cheng, Xiufei Chen, Masato Inoue, Yibin Liu, Chun-Xiao Song
Long-read sequencing provides valuable information on difficult-to-map genomic regions, which can complement short-read sequencing to improve genome assembly, yet limited methods are available to accurately detect DNA methylation over long distances at a whole-genome scale. By combining our recently developed TET-assisted pyridine borane sequencing (TAPS) method, which enables direct detection of 5-methylcytosine
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Exploration of DNA processing features unravels novel properties of ICE conjugation in Gram-positive bacteria Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-18 Haifa Laroussi, Yanis Aoudache, Emilie Robert, Virginie Libante, Louise Thiriet, Dominique Mias-Lucquin, Badreddine Douzi, Yvonne Roussel, Isaure Chauvot de Beauchêne, Nicolas Soler, Nathalie Leblond-Bourget
Integrative and conjugative elements (ICEs) are important drivers of horizontal gene transfer in prokaryotes. They are responsible for antimicrobial resistance spread, a major current health concern. ICEs are initially processed by relaxases that recognize the binding site of oriT sequence and nick at a conserved nic site. The ICESt3/Tn916/ICEBs1 superfamily, which is widespread among Firmicutes, encodes
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Role of EXO1 nuclease activity in genome maintenance, the immune response and tumor suppression in Exo1D173A mice Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-18 Shanzhi Wang, Kyeryoung Lee, Stephen Gray, Yongwei Zhang, Catherine Tang, Rikke B Morrish, Elena Tosti, Johanna van Oers, Mohammad Ruhul Amin, Paula E Cohen, Thomas MacCarthy, Sergio Roa, Matthew D Scharff, Winfried Edelmann, Richard Chahwan
DNA damage response pathways rely extensively on nuclease activity to process DNA intermediates. Exonuclease 1 (EXO1) is a pleiotropic evolutionary conserved DNA exonuclease involved in various DNA repair pathways, replication, antibody diversification, and meiosis. But, whether EXO1 facilitates these DNA metabolic processes through its enzymatic or scaffolding functions remains unclear. Here, we dissect
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LncRNA CTBP1-DT-encoded microprotein DDUP sustains DNA damage response signalling to trigger dual DNA repair mechanisms Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-18 Ruyuan Yu, Yameng Hu, Shuxia Zhang, Xincheng Li, Miaoling Tang, Meisongzhu Yang, Xingui Wu, Ziwen Li, Xinyi Liao, Yingru Xu, Man Li, Suwen Chen, Wanying Qian, Li-Yun Gong, Libing Song, Jun Li
Sustaining DNA damage response (DDR) signalling via retention of DDR factors at damaged sites is important for transmitting damage-sensing and repair signals. Herein, we found that DNA damage provoked the association of ribosomes with IRES region in lncRNA CTBP1-DT, which overcame the negative effect of upstream open reading frames (uORFs), and elicited the novel microprotein DNA damage-upregulated
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Elucidation of structure–function relationships in Methanocaldococcus jannaschii RNase P, a multi-subunit catalytic ribonucleoprotein Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-18 Hong-Duc Phan, Andrew S Norris, Chen Du, Kye Stachowski, Bela H Khairunisa, Vaishnavi Sidharthan, Biswarup Mukhopadhyay, Mark P Foster, Vicki H Wysocki, Venkat Gopalan
RNase P is a ribonucleoprotein (RNP) that catalyzes removal of the 5′ leader from precursor tRNAs in all domains of life. A recent cryo-EM study of Methanocaldococcus jannaschii (Mja) RNase P produced a model at 4.6-Å resolution in a dimeric configuration, with each holoenzyme monomer containing one RNase P RNA (RPR) and one copy each of five RNase P proteins (RPPs; POP5, RPP30, RPP21, RPP29, L7Ae)
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Melanoma RBPome identification reveals PDIA6 as an unconventional RNA-binding protein involved in metastasis Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-18 Neus Mestre-Farràs, Santiago Guerrero, Nadine Bley, Ezequiel Rivero, Olga Coll, Eva Borràs, Eduard Sabidó, Alberto Indacochea, Carlos Casillas-Serra, Aino I Järvelin, Baldomero Oliva, Alfredo Castello, Stefan Hüttelmaier, Fátima Gebauer
RNA-binding proteins (RBPs) have been relatively overlooked in cancer research despite their contribution to virtually every cancer hallmark. Here, we use RNA interactome capture (RIC) to characterize the melanoma RBPome and uncover novel RBPs involved in melanoma progression. Comparison of RIC profiles of a non-tumoral versus a metastatic cell line revealed prevalent changes in RNA-binding capacities
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Insights into innate immune activation via PS-ASO–protein–TLR9 interactions Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-18 Adam J Pollak, Luyi Zhao, Timothy A Vickers, Ian J Huggins, Xue-Hai Liang, Stanley T Crooke
Non-CpG PS-ASOs can activate the innate immune system, leading to undesired outcomes. This response can vary—in part—as a function of 2′modifications and sequence. Here we investigated the molecular steps involved in the varied effects of PS-ASOs on the innate immune system. We found that pro-inflammatory PS-ASOs require TLR9 signaling based on the experimental systems used. However, the innate immunity
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Notch-dependent and -independent functions of transcription factor RBPJ Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-18 Tobias Friedrich, Francesca Ferrante, Léo Pioger, Andrea Nist, Thorsten Stiewe, Jean-Christophe Andrau, Marek Bartkuhn, Benedetto Daniele Giaimo, Tilman Borggrefe
Signal transduction pathways often involve transcription factors that promote activation of defined target gene sets. The transcription factor RBPJ is the central player in Notch signaling and either forms an activator complex with the Notch intracellular domain (NICD) or a repressor complex with corepressors like KYOT2/FHL1. The balance between these two antagonizing RBPJ-complexes depends on the
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Editor's Note to 'Transcription activation by targeted recruitment of the RNA polymerase II CTD phosphatase FCP1'. Nucleic Acids Res. (IF 19.16) Pub Date : 2022-07-15