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New issue alert
New Impact Factor Announced
We are delighted to reveal that the latest Impact Factor for Nucleic Acids Research has risen to 16.971. To celebrate this new Impact Factor, we have curated a collection of highly cited articles from recent years.
Nucleic Acids Research  
Volume 49 Issue 22
16 December 2021
NAR Breakthrough Article
Mapping yeast mitotic 5² resection at base resolution reveals the sequence and positional dependence of nucleases in vivo border= 
Dominic Bazzano; Stephanie Lomonaco; Thomas E Wilson
Chemical Biology and Nucleic Acid Chemistry
Constrained peptides mimic a viral suppressor of RNA silencing border= 
Arne Kuepper; Niall M McLoughlin; Saskia Neubacher; Alejandro Yeste-Vázquez ; Estel Collado Camps ...
Regulation of PDGFR-beta gene expression by targeting the G-vacancy bearing G-quadruplex in promoter border= 
Juan-nan Chen; Yi-de He; Hui-ting Liang ; Ting-ting Cai; Qi Chen ...
BrdU immuno-tagged G-quadruplex ligands: a new ligand-guided immunofluorescence approach for tracking G-quadruplexes in cells border= 
Thibaut Masson; Corinne Landras Guetta; Eugénie Laigre ; Anne Cucchiarini; Patricia Duchambon ...
Computational Biology
CoCoNet'boosting RNA contact prediction by convolutional neural networks border= 
Mehari B Zerihun; Fabrizio Pucci; Alexander Schug
Decoding the effects of synonymous variants border= 
Zishuo Zeng; Ariel A Aptekmann; Yana Bromberg
DNA methylation variation along the cancer epigenome and the identification of novel epigenetic driver events border= 
Richard Heery; Martin H Schaefer
Gene Regulation, Chromatin and Epigenetics
Inhibitor of growth protein 3 epigenetically silences endogenous retroviral elements and prevents innate immune activation border= 
Yanhua Song; Gaopeng Hou; Jonathan Diep ; Yaw Shin Ooi; Natalia S Akopyants ...
A set of accessible enhancers enables the initial response of breast cancer cells to physiological progestin concentrations border= 
Roser Zaurin; Roberto Ferrari; Ana Silvina Nacht ; Jose Carbonell; Francois Le Dily ...
An archaeal histone-like protein regulates gene expression in response to salt stress border= 
Saaz Sakrikar; Amy K Schmid
Complexities in the role of acetylation dynamics in modifying inducible gene activation parameters border= 
Samantha Carrera; Amanda O'Donnell; Yaoyong Li ; Karol Nowicki-Osuch; Shen-Hsi Yang ...
Single-molecule mitochondrial DNA sequencing shows no evidence of CpG methylation in human cells and tissues border= 
Iacopo Bicci; Claudia Calabrese; Zoe J Golder ; Aurora Gomez-Duran; Patrick F Chinnery
Genome Integrity, Repair and Replication
Elongating RNA polymerase II and RNA:DNA hybrids hinder fork progression and gene expression at sites of head-on replication-transcription collisions border= 
Luca Zardoni; Eleonora Nardini; Alessandra Brambati ; Chiara Lucca; Ramveer Choudhary ...
VID22 counteracts G-quadruplex-induced genome instability border= 
Elena Galati; Maria C Bosio; Daniele Novarina; Matteo Chiara ; Giulia M Bernini ...
Division of labor between SOS and PafBC in mycobacterial DNA repair and mutagenesis border= 
Oyindamola O Adefisayo; Pierre Dupuy; Astha Nautiyal ; James M Bean; Michael S Glickman
Negative feedback for DARS2'Fis complex by ATP'DnaA supports the cell cycle-coordinated regulation for chromosome replication border= 
Kenya Miyoshi; Yuka Tatsumoto; Shogo Ozaki ; Tsutomu Katayama
Cockayne syndrome group B protein regulates fork restart, fork progression and MRE11-dependent fork degradation in BRCA1/2-deficient cells border= 
Nicole L Batenburg; Sofiane Y Mersaoui; John R Walker ; Yan Coulombe; Ian Hammond-Martel ...
Loss of MED12 activates the TGFbeta pathway to promote chemoresistance and replication fork stability in BRCA-deficient cells border= 
Lindsey M Jackson; Ashna Dhoonmoon; Anastasia Hale ; Kady A Dennis; Emily M Schleicher ...
Molecular Biology
Cytosine base modifications regulate DNA duplex stability and metabolism border= 
Cathia Rausch; Peng Zhang; Corella S Casas-Delucchi; Julia L Daiß ; Christoph Engel ...
MLL1 is regulated by KSHV LANA and is important for virus latency border= 
Min Tan; Shijun Li; Franceline Juillard; Rute Chitas ; Tânia F Custódio ...
Controlled RISC loading efficiency of miR168 defined by miRNA duplex structure adjusts ARGONAUTE1 homeostasis border= 
Ágnes Dalmadi; Fabio Miloro; Jeannette Bálint ; Éva Várallyay; Zoltán Havelda
A distinct complex of PRP19-related and trypanosomatid-specific proteins is required for pre-mRNA splicing in trypanosomes border= 
Ankita Srivastava; Daniela L Ambrósio; Monika Tasak ; Ujwala Gosavi; Arthur Günzl
Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning border= 
Patrick J Carmody; Matthew H Zimmer; Charles P Kuntz ; Haley R Harrington; Kate E Duckworth ...
Functional role and ribosomal position of the unique N-terminal region of DHX29, a factor required for initiation on structured mammalian mRNAs border= 
Trevor R Sweeney; Vidya Dhote; Ewelina Guca ; Christopher U T Hellen; Yaser Hashem ...
Perinuclear positioning of endosomes can affect PS-ASO activities border= 
Xue-hai Liang; Joshua G Nichols; Dario Tejera; Stanley T Crooke
Dynamic queuosine changes in tRNA couple nutrient levels to codon choice in Trypanosoma brucei border= 
Sameer Dixit; Alan C Kessler; Jeremy Henderson ; Xiaobei Pan; Ruoxia Zhao ...
Nucleic Acid Enzymes
TIN2 is an architectural protein that facilitates TRF2-mediated trans- and cis-interactions on telomeric DNA border= 
Parminder Kaur; Ryan Barnes; Hai Pan ; Ariana C Detwiler; Ming Liu ...
The SARS-CoV-2 RNA polymerase is a viral RNA capping enzyme border= 
Alexander P Walker; Haitian Fan; Jeremy R Keown; Michael L Knight ; Jonathan M Grimes ...
Zippered G-quadruplex/hemin DNAzyme: exceptional catalyst for universal bioanalytical applications border= 
Jia Li; Haiping Wu; Yurong Yan ; Taixian Yuan; Yue Shu ...
RNA and RNA-protein complexes
Position 34 of tRNA is a discriminative element for m5C38 modification by human DNMT2 border= 
Zhi-Xuan Huang; Jing Li; Qing-Ping Xiong ; Hao Li; En-Duo Wang ...
Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length border= 
Jonathan Bohlen; Mykola Roiuk; Aurelio A Teleman
Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition border= 
Ute A Hoffmann; Florian Heyl; Said N Rogh ; Thomas Wallner; Rolf Backofen ...
Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs border= 
Mahmoud-Reza Rafiee; Julian A Zagalak; Sviatoslav Sidorov ; Sebastian Steinhauser; Karen Davey ...
FARS2 deficiency in Drosophila reveals the developmental delay and seizure manifested by aberrant mitochondrial tRNA metabolism border= 
Wenlu Fan; Xiaoye Jin; Man Xu ; Yongmei Xi; Weiguo Lu ...
Specificity and sensitivity of an RNA targeting type III CRISPR complex coupled with a NucC endonuclease effector border= 
Sabine Grüschow; Catherine S Adamson; Malcolm F White
Structural Biology
Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination border= 
Jingfei Xu; Lingyun Zhao; Sijia Peng ; Huiying Chu; Rui Liang ...
Chromosome segregation in Archaea: SegA' and SegB'DNA complex structures provide insights into segrosome assembly border= 
Cheng-Yi Yen; Min-Guan Lin; Bo-Wei Chen ; Irene W Ng; Nicholas Read ...
Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis border= 
Brittany L Carroll; Karl E Zahn; John P Hanley ; Susan S Wallace; Julie A Dragon ...
Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands 
Monalisa Swain; Abeer A Ageeli; Wojciech K Kasprzak; Mi Li ; Jennifer T Miller ...
Structure of CRL2Lrr1, the E3 ubiquitin ligase that promotes DNA replication termination in vertebrates border= 
Haixia Zhou ; Manal S Zaher; Johannes C Walter; Alan Brown
Methods Online
MLG: multilayer graph clustering for multi-condition scRNA-seq data border= 
Shan Lu; Daniel J Conn; Shuyang Chen; Kirby D Johnson ; Emery H Bresnick ...
Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment border= 
Kaihao Tang; Weiquan Wang; Yamin Sun ; Yiqing Zhou; Pengxia Wang ...
BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models border= 
Hong-Liang Li; Yi-He Pang; Bin Liu
MetaPlatanus: a metagenome assembler that combines long-range sequence links and species-specific features border= 
Rei Kajitani; Hideki Noguchi; Yasuhiro Gotoh ; Yoshitoshi Ogura; Dai Yoshimura ...
A simple and rapid method for enzymatic synthesis of CRISPR-Cas9 sgRNA libraries border= 
Joshua D Yates; Robert C Russell; Nathaniel J Barton ; H Joseph Yost; Jonathon T Hill
RNA-based cooperative protein labeling that permits direct monitoring of the intracellular concentration change of an endogenous protein border= 
Kathleen Beverly Alog Pe; Kenji Yatsuzuka; Hayase Hakariya ; Tomoki Kida; Yousuke Katsuda ...
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