Volume 49, Issue 16
20 September 2021
Cover image
Cover image
Cover: Abnormal expansion of G4C2 hexanucleotide repeats, often associated with the formation of secondary structures such as hairpins and quadruplexes within the intron of C9orf71, causes neurodegenerative diseases: Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD). The image above shows crystal structures of G4C2 repeat-related DNA (blue) and RNA/DNA hybrid (red-blue) duplex motifs as novel targets for drug development against ALS/FTD.
For more information see the article by Jhan C.R. et al., pages 9526–9538, in this issue.
For more information see the article by Jhan C.R. et al., pages 9526–9538, in this issue.
ISSN 0305-1048
EISSN 1362-4962
Issue navigation
Volume 49, Issue 16, 20 September 2021
NAR Breakthrough Article
RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9007–9025, https://doi.org/10.1093/nar/gkab367
Chemical Biology and Nucleic Acid Chemistry
Towards next generation antisense oligonucleotides: mesylphosphoramidate modification improves therapeutic index and duration of effect of gapmer antisense oligonucleotides
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9026–9041, https://doi.org/10.1093/nar/gkab718
Expanding the chemical functionality of DNA nanomaterials generated by rolling circle amplification
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9042–9052, https://doi.org/10.1093/nar/gkab720
Computational Biology
A simple model explains the cell cycle-dependent assembly of centromeric nucleosomes in holocentric species
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9053–9065, https://doi.org/10.1093/nar/gkab648
The lane-switch mechanism for nucleosome repositioning by DNA translocase
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9066–9076, https://doi.org/10.1093/nar/gkab664
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9077–9096, https://doi.org/10.1093/nar/gkab688
Data Resources and Analyses
Autosomal sex-associated co-methylated regions predict biological sex from DNA methylation
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9097–9116, https://doi.org/10.1093/nar/gkab682
Computational resources to define alleles and altered regulatory motifs at genomically edited candidate response elements
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9117–9131, https://doi.org/10.1093/nar/gkab700
Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9132–9153, https://doi.org/10.1093/nar/gkab710
Gene Regulation, Chromatin and Epigenetics
RbAp46/48LIN-53 and HAT-1 are required for initial CENP-AHCP-3 deposition and de novo holocentromere formation on artificial chromosomes in Caenorhabditis elegans embryos
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9154–9173, https://doi.org/10.1093/nar/gkab217
Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9174–9193, https://doi.org/10.1093/nar/gkab690
Antisense ribosomal siRNAs inhibit RNA polymerase I-directed transcription in C. elegans
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9194–9210, https://doi.org/10.1093/nar/gkab662
Expression of the ISPpu9 transposase of Pseudomonas putida KT2440 is regulated by two small RNAs and the secondary structure of the mRNA 5′-untranslated region
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9211–9228, https://doi.org/10.1093/nar/gkab672
A phage-encoded nucleoid associated protein compacts both host and phage DNA and derepresses H-NS silencing
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9229–9245, https://doi.org/10.1093/nar/gkab678
Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9246–9263, https://doi.org/10.1093/nar/gkab679
A cascade of transcriptional repression determines sexual commitment and development in Plasmodium falciparum
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9264–9279, https://doi.org/10.1093/nar/gkab683
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9280–9293, https://doi.org/10.1093/nar/gkab691
Genome Integrity, Repair and Replication
A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9294–9309, https://doi.org/10.1093/nar/gkab692
Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9310–9326, https://doi.org/10.1093/nar/gkab693
Handcuffing intrinsically disordered regions in Mlh1–Pms1 disrupts mismatch repair
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9327–9341, https://doi.org/10.1093/nar/gkab694
De-dimerization of PTB is catalyzed by PDI and is involved in the regulation of p53 translation
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9342–9352, https://doi.org/10.1093/nar/gkab708
ESA1 regulates meiotic chromosome axis and crossover frequency via acetylating histone H4
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9353–9373, https://doi.org/10.1093/nar/gkab722
Molecular Biology
Photo-activatable Ub-PCNA probes reveal new structural features of the Saccharomyces cerevisiae Polη/PCNA complex
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9374–9388, https://doi.org/10.1093/nar/gkab646
Cooperative DNA binding mediated by KicGAS/ORF52 oligomerization allows inhibition of DNA-induced phase separation and activation of cGAS
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9389–9403, https://doi.org/10.1093/nar/gkab689
Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9404–9423, https://doi.org/10.1093/nar/gkab729
RNA and RNA-protein complexes
SDE2 is an essential gene required for ribosome biogenesis and the regulation of alternative splicing
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9424–9443, https://doi.org/10.1093/nar/gkab647
Protein cofactors and substrate influence Mg2+-dependent structural changes in the catalytic RNA of archaeal RNase P
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9444–9458, https://doi.org/10.1093/nar/gkab655
Genetic depletion of the RNA helicase DDX3 leads to impaired elongation of translating ribosomes triggering co-translational quality control of newly synthesized polypeptides
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9459–9478, https://doi.org/10.1093/nar/gkab667
Cyclic mismatch binding ligands interact with disease-associated CGG trinucleotide repeats in RNA and suppress their translation
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9479–9495, https://doi.org/10.1093/nar/gkab669
Arabidopsis retains vertebrate-type telomerase accessory proteins via a plant-specific assembly
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9496–9507, https://doi.org/10.1093/nar/gkab699
The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR–Cas immune systems
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9508–9525, https://doi.org/10.1093/nar/gkab704
Structural Biology
Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9526–9538, https://doi.org/10.1093/nar/gkab227
Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9539–9547, https://doi.org/10.1093/nar/gkab665
The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9548–9559, https://doi.org/10.1093/nar/gkab681
Ribosome-binding and anti-microbial studies of the mycinamicins, 16-membered macrolide antibiotics from Micromonospora griseorubida
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9560–9573, https://doi.org/10.1093/nar/gkab684
Context-sensitivity of isosteric substitutions of non-Watson–Crick basepairs in recurrent RNA 3D motifs
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9574–9593, https://doi.org/10.1093/nar/gkab703
Synthetic Biology and Bioengineering
Development of a base editor for protein evolution via in situ mutation in vivo
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Pages 9594–9605, https://doi.org/10.1093/nar/gkab673
Corrigendum
Correction to ‘Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA’
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Page 9606, https://doi.org/10.1093/nar/gkab742
Methods Online
Cell type hierarchy reconstruction via reconciliation of multi-resolution cluster tree
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Page e91, https://doi.org/10.1093/nar/gkab481
Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Page e92, https://doi.org/10.1093/nar/gkab485
Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Page e93, https://doi.org/10.1093/nar/gkab516
A transferrable and integrative type I-F Cascade for heterologous genome editing and transcription modulation
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Page e94, https://doi.org/10.1093/nar/gkab521
Harnessing self-labeling enzymes for selective and concurrent A-to-I and C-to-U RNA base editing
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Page e95, https://doi.org/10.1093/nar/gkab541
CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations
Nucleic Acids Research, Volume 49, Issue 16, 20 September 2021, Page e96, https://doi.org/10.1093/nar/gkab543
