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Nucleic Acids Research  
Volume 50 Issue 13
 
22 July 2022
 
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Editorial
 
 
 
Editorial: Critical reviews and perspectives in Nucleic Acids Research border= 
 
David R Corey; Helle D Ulrich
 
 
 
NAR Breakthrough Article
 
 
 
Membrane-dependent relief of translation elongation arrest on pseudouridine- and N1-methyl-pseudouridine-modified mRNAs border= 
 
Yuri V Svitkin; Anne-Claude Gingras; Nahum Sonenberg
 
 
 
Critical Reviews and Perspectives
 
 
 
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey border= 
 
Stanley T Crooke
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Identification of nucleobase chemical modifications that reduce the hepatotoxicity of gapmer antisense oligonucleotides border= 
 
Tokuyuki Yoshida; Kunihiko Morihiro; Yuki Naito ; Atsushi Mikami; Yuuya Kasahara ...
 
 
Conjugation of chemical handles and functional moieties to DNA during solid phase synthesis with sulfonyl azides border= 
 
Angel Santorelli; Kurt V Gothelf
 
 
 
Short LNA-modified oligonucleotide probes as efficient disruptors of DNA G-quadruplexes border= 
 
Souroprobho Chowdhury; Jiayi Wang; Sabrina Pia Nuccio ; Hanbin Mao; Marco Di Antonio
 
 
 
Computational Biology
 
 
 
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions border= 
 
Henry E Miller; Daniel Montemayor; Jebriel Abdul ; Anna Vines; Simon A Levy ...
 
 
Quantitative contribution of the spacer length in the supercoiling-sensitivity of bacterial promoters border= 
 
Raphaël Forquet; William Nasser; Sylvie Reverchon ; Sam Meyer
 
 
Systemic approaches using single cell transcriptome reveal that C/EBPgamma regulates autophagy under amino acid starved condition border= 
 
Dongha Kim; Junil Kim; Young Suk Yu ; Yong Ryoul Kim; Sung Hee Baek ...
 
 
 
Data Resources and Analyses
 
 
 
Regulation of both transcription and RNA turnover contribute to germline specification border= 
 
Kun Tan; Miles F Wilkinson
 
 
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates border= 
 
Tushar Warrier; Chadi El Farran; Yingying Zeng ; Benedict Shao Quan Ho; Qiuye Bao ...
 
 
Dual role of histone variant H3.3B in spermatogenesis: positive regulation of piRNA transcription and implication in X-chromosome inactivation border= 
 
Emeline Fontaine; Christophe Papin; Guillaume Martinez ; Stéphanie Le Gras; Roland Abi Nahed ...
 
 
OCT4 activates a Suv39h1-repressive antisense lncRNA to couple histone H3 Lysine 9 methylation to pluripotency border= 
 
Laure D Bernard; Agnès Dubois; Victor Heurtier ; Véronique Fischer; Inma Gonzalez ...
 
 
Characterization of an autonomous pathway complex that promotes flowering in Arabidopsis border= 
 
Pei-Lin Qi; Hao-Ran Zhou; Qiang-Qiang Zhao ; Chao Feng; Yong-Qiang Ning ...
 
 
On the stability of stalled RNA polymerase and its removal by RapA border= 
 
James R Portman; M Zuhaib Qayyum; Katsuhiko S Murakami; Terence R Strick
 
 
 
Genome Integrity, Repair and Replication
 
 
 
A combinatorial system to examine the enzymatic repair of multiply damaged DNA substrates border= 
 
Chia Wei Hsu; James W Conrad; Mark L Sowers ; Tuvshintugs Baljinnyam; Jason L Herring ...
 
 
Division of labor within the DNA damage tolerance system reveals non-epistatic and clinically actionable targets for precision cancer medicine border= 
 
Aldo Spanjaard; Ronak Shah; Daniël de Groot ; Olimpia Alessandra Buoninfante; Ben Morris ...
 
 
Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation border= 
 
Guillaume Guilbaud; Pierre Murat; Helen S Wilkes ; Leticia Koch Lerner; Julian E Sale ...
 
 
Acetaldehyde makes a distinct mutation signature in single-stranded DNA border= 
 
Sriram Vijayraghavan; Latarsha Porcher; Piotr A Mieczkowski; Natalie Saini
 
 
Characterization of sequence contexts that favor alternative end joining at Cas9-induced double-strand breaks border= 
 
Terrence Hanscom; Nicholas Woodward; Rebecca Batorsky ; Alexander J Brown; Steven A Roberts ...
 
 
 
Genomics
 
 
 
De novo assembly of human genome at single-cell levels border= 
 
Haoling Xie; Wen Li; Yuqiong Hu; Cheng Yang ; Jiansen Lu ...
 
 
 
Molecular Biology
 
 
 
Selective pericentromeric heterochromatin dismantling caused by TP53 activation during senescence border= 
 
Aaron Mendez-Bermudez; Liudmyla Lototska; Melanie Pousse ; Florent Tessier; Oliver Croce ...
 
 
 
Nucleic Acid Enzymes
 
 
 
Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter border= 
 
Subhas C Bera; Pim P B America; Santeri Maatsola ; Mona Seifert; Eugeniu Ostrofet ...
 
 
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity border= 
 
Lirong Zheng; Hui Lu; Bing Zan ; Song Li; Hao Liu ...
 
 
Phosphorylation of SAMHD1 Thr592 increases C-terminal domain dynamics, tetramer dissociation and ssDNA binding kinetics border= 
 
Benjamin Orris; Kevin W Huynh; Mark Ammirati ; Seungil Han; Ben Bolaños ...
 
 
Direct adenylation from 5²-OH-terminated oligonucleotides by a fusion enzyme containing Pfu RNA ligase and T4 polynucleotide kinase border= 
 
Zhengquan Yang; Chengliang Zhang; Guojun Lian ; Shijie Dong; Menghui Song ...
 
 
 
RNA and RNA-protein complexes
 
 
 
A tRNA modifying enzyme as a tunable regulatory nexus for bacterial stress responses and virulence border= 
 
Brittany A Fleming; Matthew G Blango; Alexis A Rousek ; William M Kincannon; Alexander Tran ...
 
 
A novel, essential trans-splicing protein connects the nematode SL1 snRNP to the CBC-ARS2 complex border= 
 
Rotimi Yemi Fasimoye; Rosie Elizabeth Barker Spencer; Eva Soto-Martin ; Peter Eijlers; Haitem Elmassoudi ...
 
 
LncRNA EPR-induced METTL7A1 modulates target gene translation border= 
 
Paola Briata; Luca Caputo; Ettore Zapparoli; Elisa Marcaccini ; Mario Passalacqua ...
 
 
P-bodies directly regulate MARF1-mediated mRNA decay in human cells border= 
 
William R Brothers; Hana Fakim; Sam Kajjo; Marc R Fabian
 
 
Regulated dicing of pre-mir-144 via reshaping of its terminal loop border= 
 
Renfu Shang; Dmitry A Kretov; Scott I Adamson; Thomas Treiber ; Nora Treiber ...
 
 
 
Structural Biology
 
 
 
Molecular insights into the interaction of CAG trinucleotide RNA repeats with nucleolin and its implication in polyglutamine diseases border= 
 
Ying An; Zhefan S Chen; Ho Yin Edwin Chan ; Jacky Chi Ki Ngo
 
 
Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine border= 
 
Egor A Syroegin; Elena V Aleksandrova; Yury S Polikanov
 
 
Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction border= 
 
Anne-Sophie Banneville; Claire Bouthier de la Tour; Salvatore De Bonis ; Cécilia Hognon; Jacques-Philippe Colletier ...
 
 
Structural analysis of the basal state of the Artemis:DNA-PKcs complex border= 
 
Go Watanabe; Michael R Lieber; Dewight R Williams
 
 
Cryo neutron crystallography demonstrates influence of RNA 2²-OH orientation on conformation, sugar pucker and water structure border= 
 
Joel M Harp; Terry P Lybrand; Pradeep S Pallan ; Leighton Coates; Brendan Sullivan ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
Repurposing CRISPR RNA-guided integrases system for one-step, efficient genomic integration of ultra-long DNA sequences border= 
 
Zhou-Hua Cheng; Jie Wu; Jia-Qi Liu ; Di Min; Dong-Feng Liu ...
 
 
Activating natural product synthesis using CRISPR interference and activation systems in Streptomyces border= 
 
Andrea Ameruoso; Maria Claudia Villegas Kcam; Katherine Piper Cohen ; James Chappell
 
 
Large-scale genome editing based on high-capacity adenovectors and CRISPR-Cas9 nucleases rescues full-length dystrophin synthesis in DMD muscle cells border= 
 
Francesca Tasca; Marcella Brescia; Qian Wang ; Jin Liu; Josephine M Janssen ...
 
 
Highly efficient CRISPR-mediated large DNA docking and multiplexed prime editing using a single baculovirus border= 
 
Francesco Aulicino; Martin Pelosse; Christine Toelzer ; Julien Capin; Erwin Ilegems ...
 
 
 
Retraction
 
 
 
Retraction of ˜Protein kinase CK2 phosphorylation regulates the interaction of Kaposi's sarcoma-associated herpesvirus regulatory protein ORF57 with its multifunctional partner hnRNP K' border= 
 
 
 
 
Methods Online
 
 
 
QRNAstruct: a method for extracting secondary structural features of RNA via regression with biological activity border= 
 
Goro Terai; Kiyoshi Asai
 
 
A molecular beacon assay for monitoring RNA splicing border= 
 
Qusay Q Omran; Olga Fedorova; Tianshuo Liu; Anna M Pyle
 
 
DEPhT: a novel approach for efficient prophage discovery and precise extraction border= 
 
Christian H Gauthier; Lawrence Abad; Ananya K Venbakkam; Julia Malnak ; Daniel A Russell ...
 
 
How clear is our current view on microbial dark matter? (Re-)assessing public MAG & SAG datasets with MDMcleaner border= 
 
John Vollmers; Sandra Wiegand; Florian Lenk ; Anne-Kristin Kaster
 
 
Efficient golden gate assembly of DNA constructs for single molecule force spectroscopy and imaging border= 
 
Nicholas A W Bell; Justin E Molloy
 
 
Characterizing locus specific chromatin structure and dynamics with correlative conventional and super-resolution imaging in living cells border= 
 
Dushyant Mehra; Santosh Adhikari; Chiranjib Banerjee ; Elias M Puchner
 
 
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