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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 18
11 October 2021
NAR Breakthrough Article
The Fkh1 Forkhead associated domain promotes ORC binding to a subset of DNA replication origins in budding yeast border= 
Timothy Hoggard; Allison J Hollatz; Rachel E Cherney ; Melissa R Seman; Catherine A Fox
Critical Reviews and Perspectives
beta -CASP proteins removing RNA polymerase from DNA: when a torpedo is needed to shoot a sitting duck border= 
Jana Wiedermannová; Libor Krásný
Toward a mechanistic understanding of DNA binding by forkhead transcription factors and its perturbation by pathogenic mutations border= 
Shuyan Dai; Linzhi Qu; Jun Li ; Yongheng Chen
Chemical Biology and Nucleic Acid Chemistry
Small circular interfering RNAs (sciRNAs) as a potent therapeutic platform for gene-silencing border= 
Hartmut Jahns; Rohan Degaonkar; Peter Podbevsek ; Swati Gupta; Anna Bisbe ...
Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami border= 
Hyungmin Jun; Xiao Wang; Molly F Parsons; William P Bricker ; Torsten John ...
Dual targeting of higher-order DNA structures by azacryptands induces DNA junction-mediated DNA damage in cancer cells border= 
Joanna Zell; Katerina Duskova; Leïla Chouh ; Madeleine Bossaert; Nicolas Chéron ...
Click and Cut: a click chemistry approach to developing oxidative DNA damaging agents border= 
Natasha McStay; Creina Slator; Vandana Singh ; Alex Gibney; Fredrik Westerlund ...
Computational Biology
Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks border= 
Payam Dibaeinia; Saurabh Sinha
A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants 
Igor Fesenko; Svetlana A Shabalina; Anna Mamaeva; Andrey Knyazev ; Anna Glushkevich ...
Predict long-range enhancer regulation based on protein'protein interactions between transcription factors border= 
Hao Wang; Binbin Huang; Jianrong Wang
Data Resources and Analyses
Comprehensive characterization of somatic variants associated with intronic polyadenylation in human cancers border= 
Zhaozhao Zhao; Qiushi Xu; Ran Wei ; Leihuan Huang; Weixu Wang ...
Gene Regulation, Chromatin and Epigenetics
Designed architectural proteins that tune DNA looping in bacteria border= 
David H Tse; Nicole A Becker; Robert T Young; Wilma K Olson ; Justin P Peters ...
Integrative analysis of epigenetics data identifies gene-specific regulatory elements border= 
Florian Schmidt; Alexander Marx; Nina Baumgarten ; Marie Hebel; Martin Wegner ...
The fate of notch-1 transcript is linked to cell cycle dynamics by activity of a natural antisense transcript border= 
Filip Vujovic; Saba Rezaei-Lotfi; Neil Hunter ; Ramin M Farahani
Genomic impact of stress-induced transposable element mobility in Arabidopsis border= 
David Roquis; Marta Robertson; Liang Yu; Michael Thieme ; Magdalena Julkowska ...
Fusarium BP1 is a reader of H3K27 methylation border= 
Guangfei Tang; Jianlong Yuan; Jing Wang; Yi-Zhe Zhang ; Si-Si Xie ...
Genome Integrity, Repair and Replication
Fission yeast Stn1 maintains stability of repetitive DNA at subtelomere and ribosomal DNA regions border= 
Io Yamamoto; Hidenori Nakaoka; Masahiro Takikawa ; Sanki Tashiro; Junko Kanoh ...
TARG1 protects against toxic DNA ADP-ribosylation border= 
Callum Tromans-Coia; Andrea Sanchi; Giuliana K Moeller; Gyula Timinszky ; Massimo Lopes ...
Replication-dependent cytotoxicity and Spartan-mediated repair of trapped PARP1'DNA complexes 
Liton Kumar Saha; Yasuhisa Murai; Sourav Saha; Ukhyun Jo ; Masataka Tsuda ...
The CRL4DTL E3 ligase induces degradation of the DNA replication initiation factor TICRR/TRESLIN specifically during S phase border= 
Kimberlie A Wittig; Courtney G Sansam; Tyler D Noble ; Duane Goins; Christopher L Sansam
Suppression of liquid'liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells border= 
Sergey V Ulianov; Artem K Velichko; Mikhail D Magnitov ; Artem V Luzhin; Arkadiy K Golov ...
Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases border= 
Penghao Xu; Francesca Storici
Molecular Biology
Functional correction of CFTR mutations in human airway epithelial cells using adenine base editors border= 
Sateesh Krishnamurthy; Soumba Traore; Ashley L Cooney ; Christian M Brommel; Katarina Kulhankova ...
Nucleic Acid Enzymes
The function of twister ribozyme variants in non-LTR retrotransposition in Schistosoma mansoni border= 
Getong Liu; Hengyi Jiang; Wenxia Sun ; Jun Zhang; Dongrong Chen ...
RNA and RNA-protein complexes
A new role for SR1 from Bacillus subtilis: regulation of sporulation by inhibition of kinA translation border= 
Inam Ul Haq; Sabine Brantl; Peter Müller
Theoretical basis for stabilizing messenger RNA through secondary structure design border= 
Hannah K Wayment-Steele; Do Soon Kim; Christian A Choe ; John J Nicol; Roger Wellington-Oguri ...
Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip border= 
Marta Cela; Anne Théobald-Dietrich; Joëlle Rudinger-Thirion ; Philippe Wolff; Renaud Geslain ...
ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation border= 
Yimin Wang; Jing Fan; Jianshu Wang; Yi Zhu ; Lin Xu ...
A small regulatory RNA alters Staphylococcus aureus virulence by titrating RNAIII activity border= 
Kim Boi Le Huyen; Cintia Daniela Gonzalez; Gaëtan Pascreau ; Valérie Bordeau; Vincent Cattoir ...
Modulation of alternative splicing during early infection of human primary B lymphocytes with Epstein-Barr virus (EBV): a novel function for the viral EBNA-LP protein border= 
Evelyne Manet; Hélène Polvèche; Fabrice Mure ; Paulina Mrozek-Gorska; Florian Roisné-Hamelin ...
Divergent degeneration of creA antitoxin genes from minimal CRISPRs and the convergent strategy of tRNA-sequestering CreT toxins border= 
Feiyue Cheng; Rui Wang; Haiying Yu ; Chao Liu; Jun Yang ...
Structural Biology
The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex border= 
Subramaniyam Ravichandran; Maria Razzaq; Nazia Parveen ; Ambarnil Ghosh; Kyeong Kyu Kim
Structural basis for activation of Swi2/Snf2 ATPase RapA by RNA polymerase border= 
Wei Shi; Wei Zhou; Ming Chen; Yang Yang ; Yangbo Hu ...
Two coexisting pseudo-mirror heteromolecular telomeric G-quadruplexes in opposite loop progressions differentially recognized by a low equivalent of Thioflavin T border= 
Wenqiang Fu; Haitao Jing; Xiaojuan Xu ; Suping Xu; Tao Wang ...
Multiple hPOT1'TPP1 cooperatively unfold contiguous telomeric G-quadruplexes proceeding from 3² toward 5², a feature due to a 3²-end binding preference and to structuring of telomeric DNA border= 
Jean Chatain; Georges Hatem; Emmanuelle Delagoutte ; Jean-François Riou; Patrizia Alberti ...
Structure of an inactive RNA polymerase II dimer border= 
Shintaro Aibara; Christian Dienemann; Patrick Cramer
Structural basis of transcription activation by the global regulator Spx border= 
Jing Shi; Fangfang Li; Aijia Wen; Libing Yu ; Lu Wang ...
Novel anti-repression mechanism of H-NS proteins by a phage protein border= 
Fredj Ben Bdira; Amanda M Erkelens; Liang Qin; Alexander N Volkov ; Andrew M Lippa ...
Synthetic Biology and Bioengineering
Optimized nickase- and nuclease-based prime editing in human and mouse cells border= 
Fatwa Adikusuma; Caleb Lushington; Jayshen Arudkumar; Gelshan I Godahewa ; Yu C J Chey ...
Correction to ˜Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition' border= 
Dipanwita Banerjee; Hisae Tateishi-Karimata; Tatsuya Ohyama ; Saptarshi Ghosh; Tamaki Endoh ...
Correction to ˜The STRING database in 2021: customizable protein'protein networks, and functional characterization of user-uploaded gene/measurement sets' border= 
Damian Szklarczyk; Annika L Gable; Katerina C Nastou ; David Lyon; Rebecca Kirsch ...
Correction to ˜DrugCombDB: a comprehensive database of drug combinations toward the discovery of combinatorial therapy' border= 
Hui Liu; Wenhao Zhang; Bo Zou ; Jinxian Wang; Yuanyuan Deng ...
Correction to ˜DNA polymerase gamma mutations that impair holoenzyme stability cause catalytic subunit depletion' border= 
Pedro Silva-Pinheiro; Carlos Pardo-Hernández; Aurelio Reyes ; Lisa Tilokani; Anup Mishra ...
Correction to ˜Cis regulation within a cluster of viral microRNAs' border= 
Monika Vilimova; Maud Contrant; Ramy Randrianjafy; Philippe Dumas ; Endrit Elbasani ...
Correction to ˜Structure of the bacteriophage PhiKZ non-virion RNA polymerase' border= 
Natàlia de Martín Garrido; Mariia Orekhova; Yuen Ting Emilie Lai Wan Loong; Anna Litvinova ; Kailash Ramlaul ...
Methods Online
Single-cell nucleic acid profiling in droplets (SNAPD) enables high-throughput analysis of heterogeneous cell populations border= 
Leland B Hyman; Clare R Christopher; Philip A Romero
Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data border= 
Natsu Nakajima; Tomoatsu Hayashi; Katsunori Fujiki ; Katsuhiko Shirahige; Tetsu Akiyama ...
capCLIP: a new tool to probe translational control in human cells through capture and identification of the eIF4E'mRNA interactome border= 
Kirk B Jensen; B Kate Dredge; John Toubia ; Xin Jin; Valentina Iadevaia ...
Aberration-corrected ultrafine analysis of miRNA reads at single-base resolution: a k-mer lattice approach border= 
Xuan Zhang; Pengyao Ping; Gyorgy Hutvagner ; Michael Blumenstein; Jinyan Li
Visualization and characterization of RNA'protein interactions in living cells border= 
Ningjun Duan; Maria Arroyo; Wen Deng; M Cristina Cardoso ; Heinrich Leonhardt
TSMiner: a novel framework for generating time-specific gene regulatory networks from time-series expression profiles border= 
Mingfei Han; Xian Liu; Wen Zhang ; Mengnan Wang; Wenjing Bu ...
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