Volume 51, Issue 21
27 November 2023
Cover image
Cover image
Cover: Mitochondrial DNA and RNA both condense into distinct foci inside mitochondria and these foci numbers vary from cell to cell. In this cover image, mitochondrial DNA foci are visible from anti-dsDNA antibody-staining (magenta) inside mitochondria (green) of a 3t3 mouse cell, with Hoechst staining highlighting the nucleus (blue). mtFociCounter software allows to quantify mitochondrial foci content in single cells from superresolution images (i.e. SIM2) like this one, or confocal microscopy.
For more information see article by Rey, T. et al., pages e107 in this issue.
For more information see article by Rey, T. et al., pages e107 in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 51, Issue 21, 27 November 2023
Chemical Biology and Nucleic Acid Chemistry
‘SAXS-osmometer’ method provides measurement of DNA pressure in viral capsids and delivers an empirical equation of state
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11415–11427, https://doi.org/10.1093/nar/gkad852
Superanionic DNA: enzymatic synthesis of hypermodified DNA bearing four different anionic substituents at all four nucleobases
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11428–11438, https://doi.org/10.1093/nar/gkad893
Selective targeting of parallel G-quadruplex structure using L-RNA aptamer
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11439–11452, https://doi.org/10.1093/nar/gkad900
Computational Biology
The landscape of human SVA retrotransposons
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11453–11465, https://doi.org/10.1093/nar/gkad821
RNA sequestration driven by amyloid formation: the alpha synuclein case
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11466–11478, https://doi.org/10.1093/nar/gkad857
Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11479–11503, https://doi.org/10.1093/nar/gkad879
Data Resources and Analyses
StORF-Reporter: finding genes between genes
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11504–11517, https://doi.org/10.1093/nar/gkad814
Gene Regulation, Chromatin and Epigenetics
Different elongation factors distinctly modulate RNA polymerase II transcription in Arabidopsis
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11518–11533, https://doi.org/10.1093/nar/gkad825
Low RNA stability signifies strong expression regulatability of tumor suppressors
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11534–11548, https://doi.org/10.1093/nar/gkad838
The N-terminus of Spt16 anchors FACT to MCM2–7 for parental histone recycling
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11549–11567, https://doi.org/10.1093/nar/gkad846
Sea-ATI unravels novel vocabularies of plant active cistrome
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11568–11583, https://doi.org/10.1093/nar/gkad853
Hypoxia-induced transcriptional stress is mediated by ROS-induced R-loops
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11584–11599, https://doi.org/10.1093/nar/gkad858
High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11600–11612, https://doi.org/10.1093/nar/gkad872
DNA elements tether canonical Polycomb Repressive Complex 1 to human genes
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11613–11633, https://doi.org/10.1093/nar/gkad889
BRD9-mediated control of the TGF-β/Activin/Nodal pathway regulates self-renewal and differentiation of human embryonic stem cells and progression of cancer cells
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11634–11651, https://doi.org/10.1093/nar/gkad907
LSM14B is essential for oocyte meiotic maturation by regulating maternal mRNA storage and clearance
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11652–11667, https://doi.org/10.1093/nar/gkad919
Genome Integrity, Repair and Replication
ADAR1 links R-loop homeostasis to ATR activation in replication stress response
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11668–11687, https://doi.org/10.1093/nar/gkad839
Rad53 regulates the lifetime of Rdh54 at homologous recombination intermediates
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11688–11705, https://doi.org/10.1093/nar/gkad848
The SAP domain of Ku facilitates its efficient loading onto DNA ends
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11706–11716, https://doi.org/10.1093/nar/gkad850
RAD51 paralogs synergize with RAD51 to protect reversed forks from cellular nucleases
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11717–11731, https://doi.org/10.1093/nar/gkad856
Structural and functional basis of inositol hexaphosphate stimulation of NHEJ through stabilization of Ku-XLF interaction
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11732–11747, https://doi.org/10.1093/nar/gkad863
GSE1 links the HDAC1/CoREST co-repressor complex to DNA damage
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11748–11769, https://doi.org/10.1093/nar/gkad911
Genomics
A high-resolution haplotype-resolved Reference panel constructed from the China Kadoorie Biobank Study
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11770–11782, https://doi.org/10.1093/nar/gkad779
Molecular Biology
An archaeal virus-encoded anti-CRISPR protein inhibits type III-B immunity by inhibiting Cas RNP complex turnover
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11783–11796, https://doi.org/10.1093/nar/gkad804
BOLA3 and NFU1 link mitoribosome iron–sulfur cluster assembly to multiple mitochondrial dysfunctions syndrome
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11797–11812, https://doi.org/10.1093/nar/gkad842
Two mitochondrial HMG-box proteins, Cim1 and Abf2, antagonistically regulate mtDNA copy number in Saccharomyces cerevisiae
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11813–11835, https://doi.org/10.1093/nar/gkad849
Comparison of cell response to chromatin and DNA damage
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11836–11855, https://doi.org/10.1093/nar/gkad865
Dynamic ParB–DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11856–11875, https://doi.org/10.1093/nar/gkad868
RNA and RNA-protein complexes
Dynamics of ribosome composition and ribosomal protein phosphorylation in immune signaling in Arabidopsis thaliana
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11876–11892, https://doi.org/10.1093/nar/gkad827
A conserved isoleucine in the binding pocket of RIG-I controls immune tolerance to mitochondrial RNA
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11893–11910, https://doi.org/10.1093/nar/gkad835
Long non-coding RNA generated from CDKN1A gene by alternative polyadenylation regulates p21 expression during DNA damage response
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11911–11926, https://doi.org/10.1093/nar/gkad899
Structural Biology
Molecular insight into the specific enzymatic properties of TREX1 revealing the diverse functions in processing RNA and DNA/RNA hybrids
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11927–11940, https://doi.org/10.1093/nar/gkad910
Structural and functional investigation of GajB protein in Gabija anti-phage defense
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11941–11951, https://doi.org/10.1093/nar/gkad951
Synthetic Biology and Bioengineering
Design of a sorbitol-activated nitrogen metabolism-dependent regulatory system for redirection of carbon metabolism flow in Bacillus licheniformis
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11952–11966, https://doi.org/10.1093/nar/gkad859
Design and deep learning of synthetic B-cell-specific promoters
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Pages 11967–11979, https://doi.org/10.1093/nar/gkad930
Correction
Correction to ‘Four additional natural 7-deazaguanine derivatives in phages and how to make them’
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Page 11980, https://doi.org/10.1093/nar/gkad983
Methods
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Page e106, https://doi.org/10.1093/nar/gkad843
mtFociCounter for automated single-cell mitochondrial nucleoid quantification and reproducible foci analysis
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Page e107, https://doi.org/10.1093/nar/gkad864
Shortcut barcoding and early pooling for scalable multiplex single-cell reduced-representation CpG methylation sequencing at single nucleotide resolution
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Page e108, https://doi.org/10.1093/nar/gkad892
Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Page e109, https://doi.org/10.1093/nar/gkad909
A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder
Nucleic Acids Research, Volume 51, Issue 21, 27 November 2023, Page e110, https://doi.org/10.1093/nar/gkad929
