Volume 49, Issue 9
21 May 2021
Cover image
Cover image
Cover: Visualization of model-generated gene regulatory network for the malaria parasite Plasmodium falciparum genome. Ring segments represent chromosomes. Orange and blue lines inside segments indicate genomic locations of ApiAP2 and non-ApiAP2 transcriptional regulators, respectively. Edges indicate regulator-target interactions positioned according to the location of their genes.
For more information see article by Neal, M.L. et al., pages 4891–4906 in this issue.
For more information see article by Neal, M.L. et al., pages 4891–4906 in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 49, Issue 9, 21 May 2021
NAR Breakthrough Article
microRNA-mediated translation repression through GYF-1 and IFE-4 in C. elegans development
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4803–4815, https://doi.org/10.1093/nar/gkab162
Survey and Summary
G-Quadruplexes as pathogenic drivers in neurodegenerative disorders
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4816–4830, https://doi.org/10.1093/nar/gkab164
Repriming DNA synthesis: an intrinsic restart pathway that maintains efficient genome replication
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4831–4847, https://doi.org/10.1093/nar/gkab176
Untangling the crosstalk between BRCA1 and R-loops during DNA repair
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4848–4863, https://doi.org/10.1093/nar/gkab178
Chemical Biology and Nucleic Acid Chemistry
Short DNA/RNA heteroduplex oligonucleotide interacting proteins are key regulators of target gene silencing
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4864–4876, https://doi.org/10.1093/nar/gkab258
The human tRNA-guanine transglycosylase displays promiscuous nucleobase preference but strict tRNA specificity
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4877–4890, https://doi.org/10.1093/nar/gkab289
Computational Biology
A systems-level gene regulatory network model for Plasmodium falciparum
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4891–4906, https://doi.org/10.1093/nar/gkaa1245
Asymmetry in histone rotation in forced unwrapping and force quench rewrapping in a nucleosome
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4907–4918, https://doi.org/10.1093/nar/gkab263
A unified computational view of DNA duplex, triplex, quadruplex and their donor–acceptor interactions
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4919–4933, https://doi.org/10.1093/nar/gkab285
MoiRNAiFold: a novel tool for complex in silico RNA design
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4934–4943, https://doi.org/10.1093/nar/gkab331
Gene Regulation, Chromatin and Epigenetics
Opposite roles of transcription elongation factors Spt4/5 and Elf1 in RNA polymerase II transcription through B-form versus non-B DNA structures
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4944–4953, https://doi.org/10.1093/nar/gkab240
Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4954–4970, https://doi.org/10.1093/nar/gkab245
Cistrome analysis of YY1 uncovers a regulatory axis of YY1:BRD2/4-PFKP during tumorigenesis of advanced prostate cancer
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4971–4988, https://doi.org/10.1093/nar/gkab252
Structural variation affecting DNA backbone interactions underlies adaptation of B3 DNA binding domains to constraints imposed by protein architecture
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 4989–5002, https://doi.org/10.1093/nar/gkab257
HPF1-dependent PARP activation promotes LIG3-XRCC1-mediated backup pathway of Okazaki fragment ligation
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5003–5016, https://doi.org/10.1093/nar/gkab269
Slow chromatin dynamics enhances promoter accessibility to transcriptional condensates
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5017–5027, https://doi.org/10.1093/nar/gkab275
Solution structure(s) of trinucleosomes from contrast variation SAXS
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5028–5037, https://doi.org/10.1093/nar/gkab290
ERG transcription factors have a splicing regulatory function involving RBFOX2 that is altered in the EWS-FLI1 oncogenic fusion
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5038–5056, https://doi.org/10.1093/nar/gkab305
Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5057–5073, https://doi.org/10.1093/nar/gkab322
Genome Integrity, Repair and Replication
Inhibition of DNA replication initiation by silver nanoclusters
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5074–5083, https://doi.org/10.1093/nar/gkab271
Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5084–5094, https://doi.org/10.1093/nar/gkab276
Marker-free quantification of repair pathway utilization at Cas9-induced double-strand breaks
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5095–5105, https://doi.org/10.1093/nar/gkab299
HDAC3 controls male fertility through enzyme-independent transcriptional regulation at the meiotic exit of spermatogenesis
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5106–5123, https://doi.org/10.1093/nar/gkab313
Molecular Biology
Estimation of peptide elongation times from ribosome profiling spectra
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5124–5142, https://doi.org/10.1093/nar/gkab260
Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5143–5158, https://doi.org/10.1093/nar/gkab265
eIF4E3 forms an active eIF4F complex during stresses (eIF4FS) targeting mTOR and re-programs the translatome
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5159–5176, https://doi.org/10.1093/nar/gkab267
Evolving origin-of-transfer sequences on staphylococcal conjugative and mobilizable plasmids—who’s mimicking whom?
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5177–5188, https://doi.org/10.1093/nar/gkab303
Folding and persistence times of intramolecular G-quadruplexes transiently embedded in a DNA duplex
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5189–5201, https://doi.org/10.1093/nar/gkab306
Increased expression of tryptophan and tyrosine tRNAs elevates stop codon readthrough of reporter systems in human cell lines
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5202–5215, https://doi.org/10.1093/nar/gkab315
Nucleic Acid Enzymes
A nucleotide-sensing endonuclease from the Gabija bacterial defense system
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5216–5229, https://doi.org/10.1093/nar/gkab277
DNA polymerase gamma mutations that impair holoenzyme stability cause catalytic subunit depletion
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5230–5248, https://doi.org/10.1093/nar/gkab282
RNase R is associated in a functional complex with the RhpA DEAD-box RNA helicase in Helicobacter pylori
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5249–5264, https://doi.org/10.1093/nar/gkab283
E. coli RNase I exhibits a strong Ca2+-dependent inherent double-stranded RNase activity
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5265–5277, https://doi.org/10.1093/nar/gkab284
Decoupling the bridge helix of Cas12a results in a reduced trimming activity, increased mismatch sensitivity and impaired conformational transitions
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5278–5293, https://doi.org/10.1093/nar/gkab286
RNA and RNA-protein complexes
A ribonuclease III involved in virulence of Mucorales fungi has evolved to cut exclusively single-stranded RNA
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5294–5307, https://doi.org/10.1093/nar/gkab238
Translational accuracy of a tethered ribosome
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5308–5318, https://doi.org/10.1093/nar/gkab259
In vivo targets of Salmonella FinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5319–5335, https://doi.org/10.1093/nar/gkab281
DDX3 depletion represses translation of mRNAs with complex 5′ UTRs
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5336–5350, https://doi.org/10.1093/nar/gkab287
Structural Biology
Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5351–5368, https://doi.org/10.1093/nar/gkab272
PIN and CCCH Zn-finger domains coordinate RNA targeting in ZC3H12 family endoribonucleases
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5369–5381, https://doi.org/10.1093/nar/gkab316
Crystal structure of SARS-CoV-2 nsp10 bound to nsp14-ExoN domain reveals an exoribonuclease with both structural and functional integrity
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5382–5392, https://doi.org/10.1093/nar/gkab320
Synthetic Biology and Bioengineering
Topologies of synthetic gene circuit for optimal fold change activation
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Pages 5393–5406, https://doi.org/10.1093/nar/gkab253
Methods Online
Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Page e49, https://doi.org/10.1093/nar/gkab038
SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Page e50, https://doi.org/10.1093/nar/gkab043
GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Page e51, https://doi.org/10.1093/nar/gkab044
Engineering nucleosomes for generating diverse chromatin assemblies
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Page e52, https://doi.org/10.1093/nar/gkab070
KERA: analysis tool for multi-process, multi-state single-molecule data
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Page e53, https://doi.org/10.1093/nar/gkab087
Independent component analysis based gene co-expression network inference (ICAnet) to decipher functional modules for better single-cell clustering and batch integration
Nucleic Acids Research, Volume 49, Issue 9, 21 May 2021, Page e54, https://doi.org/10.1093/nar/gkab089
