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Nucleic Acids Research  
Volume 50 Issue 12
8 July 2022
NAR Breakthrough Article
Deficiency of ribosomal proteins reshapes the transcriptional and translational landscape in human cells border= 
Yizhao Luan; Nan Tang; Jiaqi Yang ; Shuting Liu; Chichi Cheng ...
Critical Reviews and Perspectives
Anatomy of four human Argonaute proteins border= 
Kotaro Nakanishi
Chemical Biology and Nucleic Acid Chemistry
The cotranscriptional folding landscape for two cyclic di-nucleotide-sensing riboswitches with highly homologous aptamer domains acting either as ON- or OFF-switches border= 
Tom Landgraf; Albrecht Eduard Völklein; Boris Fürtig ; Harald Schwalbe
From bench to bedside: Improving the clinical safety of GalNAc'siRNA conjugates using seed-pairing destabilization border= 
Mark K Schlegel; Maja M Janas; Yongfeng Jiang ; Joseph D Barry; Wendell Davis ...
Computational Biology
Torsional behaviour of supercoiled DNA regulates recognition of architectural protein Fis on minicircle DNA border= 
Anupam Mondal; Sangeeta; Arnab Bhattacherjee
Gene Regulation, Chromatin and Epigenetics
Genome-wide CRISPR/Cas9 transcriptional activation screen identifies a histone acetyltransferase inhibitor complex as a regulator of HIV-1 integration border= 
Qiong Zhang; Shaobo Wang; Wanyu Li ; Edwin Yau; Hui Hui ...
Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression border= 
Avital Sarusi Portuguez; Ivana Grbesa; Moran Tal ; Rachel Deitch; Dana Raz ...
AtNusG, a chloroplast nucleoid protein of bacterial origin linking chloroplast transcriptional and translational machineries, is required for proper chloroplast gene expression in Arabidopsis thaliana border= 
Hai-Bo Xiong; Hui-Min Pan; Qiao-Ying Long ; Zi-Yuan Wang; Wan-Tong Qu ...
Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo border= 
Maria Derakhshan; Noah J Kessler; Miho Ishida ; Charalambos Demetriou; Nicolas Brucato ...
Synthesis of the NarP response regulator of nitrate respiration in Escherichia coli is regulated at multiple levels by Hfq and small RNAs border= 
Anaïs Brosse; Pierre Boudry; Anne Walburger ; Axel Magalon; Maude Guillier
Body temperature variation controls pre-mRNA processing and transcription of antiviral genes and SARS-CoV-2 replication border= 
Bruna Los; Marco Preußner; Kathrin Eschke ; Ricardo Martin Vidal; Azza Abdelgawad ...
H3K36me2 methyltransferase NSD2 orchestrates epigenetic reprogramming during spermatogenesis border= 
Zhiming Li; Xinzong Zhang; Shiming Xie ; Xingping Liu; Caifeng Fei ...
The transcription factor network of E. coli steers global responses to shifts in RNAP concentration border= 
Bilena L.B. Almeida; Mohamed N M. Bahrudeen; Vatsala Chauhan ; Suchintak Dash; Vinodh Kandavalli ...
Genome Integrity, Repair and Replication
TEB/POLQ plays dual roles in protecting Arabidopsis from NO-induced DNA damage border= 
Qiang Lv; Shuang Han; Lei Wang ; Jinchan Xia; Peng Li ...
Mechanism of lesion verification by the human XPD helicase in nucleotide excision repair border= 
Iwen Fu; Hong Mu; Nicholas E Geacintov ; Suse Broyde
Host cell RecA activates a mobile element-encoded mutagenic DNA polymerase border= 
Debika Ojha; Malgorzata M Jaszczur; Adhirath Sikand; John P McDonald ; Andrew Robinson ...
Migrating bubble synthesis promotes mutagenesis through lesions in its template border= 
Beth Osia; Jerzy Twarowski; Tyler Jackson; Kirill Lobachev ; Liping Liu ...
Ribodysgenesis: sudden genome instability in the yeast Saccharomyces cerevisiae arising from RNase H2 cleavage at genomic-embedded ribonucleotides border= 
Yang Sui; Anastasiya Epstein; Margaret Dominska ; Dao-Qiong Zheng; Thomas D Petes ...
Molecular Biology
TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in glioma border= 
Lee Admoni-Elisha; Tzofit Elbaz; Anand Chopra ; Guy Shapira; Mark T Bedford ...
Experimental paradigms revisited: oxidative stress-induced tRNA fragmentation does not correlate with stress granule formation but is associated with delayed cell death border= 
Nasim Sanadgol; Lisa König; Aleksej Drino ; Michaela Jovic; Matthias R Schaefer
Decoding phage resistance by mpr and its role in survivability of Mycobacterium smegmatis border= 
Surya Pratap Seniya; Vikas Jain
DNA G-quadruplex structure participates in regulation of lipid metabolism through acyl-CoA binding protein border= 
Lijun Xiang; Kangkang Niu; Yuling Peng ; Xiaojuan Zhang; Xiaoyu Li ...
Nucleic Acid Enzymes
Insights into the product release mechanism of dengue virus NS3 helicase border= 
Natalia S Adler; Leila A Cababie; Carolina Sarto; Claudio N Cavasotto ; Leopoldo G Gebhard ...
Direct tracking of reverse-transcriptase speed and template sensitivity: implications for sequencing and analysis of long RNA molecules border= 
Li-Tao Guo; Sara Olson; Shivali Patel ; Brenton R Graveley; Anna Marie Pyle
HSP90 and Aha1 modulate microRNA maturation through promoting the folding of Dicer1 border= 
Xiaochuan Liu; Yen-Yu Yang; Yinsheng Wang
Identification of flexible Pif1'DNA interactions and their impacts on enzymatic activities border= 
Jinghua Li; Jianbing Ma; Vikash Kumar ; Hang Fu; Chunhua Xu ...
A dual-activity topoisomerase complex regulates mRNA translation and turnover 
Shuaikun Su; Yutong Xue; Alexei Sharov; Yongqing Zhang ; Seung Kyu Lee ...
RNA and RNA-protein complexes
The dsRBP Staufen2 governs RNP assembly of neuronal Argonaute proteins border= 
Janina Ehses; Melina Schlegel; Luise Schröger; Rico Schieweck ; Sophia Derdak ...
PUMILIO competes with AUF1 to control DICER1 RNA levels and miRNA processing border= 
Swetha Rajasekaran; Eshan Khan; Samuel R Ching; Misbah Khan ; Jalal K Siddiqui ...
The Drosophila hnRNP F/H homolog Glorund recruits dFMRP to inhibit nanos translation elongation border= 
Yingshi Peng; Elizabeth R Gavis
A new bacterial tRNA enhances antibiotic production in Streptomyces by circumventing inefficient wobble base-pairing border= 
Ximing Chen; Shuyan Li; Binglin Zhang ; Haili Sun; Jinxiu Wang ...
TRIM25 inhibits influenza A virus infection, destabilizes viral mRNA, but is redundant for activating the RIG-I pathway border= 
Nila Roy Choudhury; Ivan Trus; Gregory Heikel ; Magdalena Wolczyk; Jacek Szymanski ...
LncRNA OIP5-AS1-directed miR-7 degradation promotes MYMX production during human myogenesis 
Jen-Hao Yang; Ming-Wen Chang; Dimitrios Tsitsipatis; Xiaoling Yang ; Jennifer L Martindale ...
Structural Biology
G-quadruplex structure of the C. elegans telomeric repeat: a two tetrads basket type conformation stabilized by a non-canonical C'T base-pair border= 
Julien Marquevielle; Aurore De Rache; Brune Vialet ; Estelle Morvan; Jean-Louis Mergny ...
Structural and dynamic studies of DNA recognition by NF-kappa B p50 RHR homodimer using methyl NMR spectroscopy border= 
Amrinder Singh; Maria A Martinez-Yamout; Peter E Wright ; H Jane Dyson
Guiding the folding of G-quadruplexes through loop residue interactions border= 
Jagannath Jana; Yoanes Maria Vianney; Nina Schröder; Klaus Weisz
Synthetic Biology and Bioengineering
Utilizing RNA origami scaffolds in Saccharomyces cerevisiae for dCas9-mediated transcriptional control border= 
Georgios Pothoulakis; Michael T A Nguyen; Ebbe S Andersen
Controllable assembly of synthetic constructs with programmable ternary DNA interaction border= 
Huangchen Cui; Tianqing Zhang; Yuhan Kong ; Hang Xing; Bryan Wei
Correction to ˜Effects of chain length and geometry on the activation of DNA damage bypass by polyubiquitylated PCNA' and ˜Structural basis of ubiquitin recognition by the winged-helix domain of Cockayne syndrome group B protein' border= 
Correction to ˜SynergyFinder 2.0: visual analytics of multi-drug combination synergies' border= 
Correction to ˜Deep sequencing of non-enzymatic RNA primer extension' border= 
Expression of Concern
Expression of Concern on ˜DICER-dependent biogenesis of let-7 miRNAs affects human cell response to DNA damage via targeting p21/p27' border= 
Methods Online
Expanding the DNA-encoded library toolbox: identifying small molecules targeting RNA border= 
Qiuxia Chen; You Li; Chunrong Lin ; Liu Chen; Hao Luo ...
Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3 information border= 
James M Heather; Matthew J Spindler; Marta Herrero Alonso; Yifang Ivana Shui ; David G Millar ...
Optical control of protein delivery and partitioning in the nucleolus border= 
Peng Tan; Tingting Hong; Xiaoli Cai; Wenbo Li ; Yun Huang ...
EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants border= 
Saeid Parvandeh; Lawrence A Donehower; Katsonis Panagiotis ; Teng-Kuei Hsu; Jennifer K Asmussen ...
MarcoPolo: a method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering border= 
Chanwoo Kim; Hanbin Lee; Juhee Jeong ; Keehoon Jung; Buhm Han
Joint dimension reduction and clustering analysis of single-cell RNA-seq and spatial transcriptomics data border= 
Wei Liu; Xu Liao; Yi Yang; Huazhen Lin; Joe Yeong ...
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