Volume 50, Issue 14
12 August 2022
Cover image
Cover image
Cover: The proper partitioning of genetic material during cell division is essential to the maintenance of cellular and organismal fitness. In this issue, Hedouin et al. identify the transcriptional landscape around centromeres and discover a roadblock mediated by the Cbf1 centromere protein. The cover illustration is an abstract depiction of chromosomes attached to the mitotic spindle and is inspired by images taken by Julie Canman. Cover artwork by Michelle Peterson.
For more information see article by Hedouin, S. et al., pages 7801–7815 in this issue.
For more information see article by Hedouin, S. et al., pages 7801–7815 in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 50, Issue 14, 12 August 2022
NAR Breakthrough Article
A transcriptional roadblock protects yeast centromeres
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 7801–7815, https://doi.org/10.1093/nar/gkac117
Chemical Biology and Nucleic Acid Chemistry
Retracted: G-quadruplex structural transition driven by a platinum compound
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 7816–7828, https://doi.org/10.1093/nar/gkac572
The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 7829–7841, https://doi.org/10.1093/nar/gkac590
Gene Regulation, Chromatin and Epigenetics
Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer–promoter interactions
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 7842–7855, https://doi.org/10.1093/nar/gkac582
PHF20 is crucial for epigenetic control of starvation-induced autophagy through enhancer activation
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 7856–7872, https://doi.org/10.1093/nar/gkac584
DBC1 is a key positive regulator of enhancer epigenomic writers KMT2D and p300
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 7873–7888, https://doi.org/10.1093/nar/gkac585
Induction of senescence upon loss of the Ash2l core subunit of H3K4 methyltransferase complexes
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 7889–7905, https://doi.org/10.1093/nar/gkac591
NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 7906–7924, https://doi.org/10.1093/nar/gkac600
Notch-dependent and -independent functions of transcription factor RBPJ
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 7925–7937, https://doi.org/10.1093/nar/gkac601
HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 7938–7958, https://doi.org/10.1093/nar/gkac613
Decoding YAP dependent transcription in the liver
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 7959–7971, https://doi.org/10.1093/nar/gkac624
SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 7972–7990, https://doi.org/10.1093/nar/gkac637
Genome Integrity, Repair and Replication
In vitro reconstitution reveals a key role of human mitochondrial EXOG in RNA primer processing
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 7991–8007, https://doi.org/10.1093/nar/gkac581
Strand annealing and motor driven activities of SMARCAL1 and ZRANB3 are stimulated by RAD51 and the paralog complex
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8008–8022, https://doi.org/10.1093/nar/gkac583
Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ϵ variants at low dNTP levels
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8023–8040, https://doi.org/10.1093/nar/gkac602
R-loop-induced irreparable DNA damage evades checkpoint detection in the C. elegans germline
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8041–8059, https://doi.org/10.1093/nar/gkac621
Molecular Biology
LncRNA CTBP1-DT-encoded microprotein DDUP sustains DNA damage response signalling to trigger dual DNA repair mechanisms
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8060–8079, https://doi.org/10.1093/nar/gkac611
Cap-independent translation and a precisely located RNA sequence enable SARS-CoV-2 to control host translation and escape anti-viral response
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8080–8092, https://doi.org/10.1093/nar/gkac615
Role of EXO1 nuclease activity in genome maintenance, the immune response and tumor suppression in Exo1D173A mice
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8093–8106, https://doi.org/10.1093/nar/gkac616
Insights into innate immune activation via PS-ASO–protein–TLR9 interactions
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8107–8126, https://doi.org/10.1093/nar/gkac618
Nucleic Acid Enzymes
Exploration of DNA processing features unravels novel properties of ICE conjugation in Gram-positive bacteria
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8127–8142, https://doi.org/10.1093/nar/gkac607
RNA and RNA-protein complexes
Small molecule-based detection of non-canonical RNA G-quadruplex structures that modulate protein translation
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8143–8153, https://doi.org/10.1093/nar/gkac580
Elucidation of structure–function relationships in Methanocaldococcus jannaschii RNase P, a multi-subunit catalytic ribonucleoprotein
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8154–8167, https://doi.org/10.1093/nar/gkac595
Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8168–8192, https://doi.org/10.1093/nar/gkac596
Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8193–8206, https://doi.org/10.1093/nar/gkac599
Melanoma RBPome identification reveals PDIA6 as an unconventional RNA-binding protein involved in metastasis
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8207–8225, https://doi.org/10.1093/nar/gkac605
The silencing of ets-4 mRNA relies on the functional cooperation between REGE-1/Regnase-1 and RLE-1/Roquin-1
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8226–8239, https://doi.org/10.1093/nar/gkac609
mRNA- and factor-driven dynamic variability controls eIF4F-cap recognition for translation initiation
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8240–8261, https://doi.org/10.1093/nar/gkac631
Cooperative engagement and subsequent selective displacement of SR proteins define the pre-mRNA 3D structural scaffold for early spliceosome assembly
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8262–8278, https://doi.org/10.1093/nar/gkac636
Structural Biology
Structure of the human RAD17–RFC clamp loader and 9–1–1 checkpoint clamp bound to a dsDNA–ssDNA junction
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8279–8289, https://doi.org/10.1093/nar/gkac588
Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8290–8301, https://doi.org/10.1093/nar/gkac589
Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8302–8320, https://doi.org/10.1093/nar/gkac597
Structural basis of AlpA-dependent transcription antitermination
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8321–8330, https://doi.org/10.1093/nar/gkac608
Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8331–8348, https://doi.org/10.1093/nar/gkac620
Staphylococcal self-loading helicases couple the staircase mechanism with inter domain high flexibility
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8349–8362, https://doi.org/10.1093/nar/gkac625
Structural basis of Streptomyces transcription activation by zinc uptake regulator
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8363–8376, https://doi.org/10.1093/nar/gkac627
Synthetic Biology and Bioengineering
Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8377–8391, https://doi.org/10.1093/nar/gkac578
Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Pages 8392–8398, https://doi.org/10.1093/nar/gkac606
Editor's Note
Editor's Note to ‘Transcription activation by targeted recruitment of the RNA polymerase II CTD phosphatase FCP1’
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Page 8399, https://doi.org/10.1093/nar/gkac622
Editor's Note to ‘Identification of peptide inhibitors of pre-mRNA splicing derived from the essential interaction domains of CDC5L and PLRG1’
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Page 8400, https://doi.org/10.1093/nar/gkac623
Methods Online
Oligo targeting for profiling drug resistance mutations in the parasitic trypanosomatids
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Page e79, https://doi.org/10.1093/nar/gkac319
Cell type identification in spatial transcriptomics data can be improved by leveraging cell-type-informative paired tissue images using a Bayesian probabilistic model
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Page e80, https://doi.org/10.1093/nar/gkac320
Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Page e81, https://doi.org/10.1093/nar/gkac326
Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Page e82, https://doi.org/10.1093/nar/gkac333
vRhyme enables binning of viral genomes from metagenomes
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Page e83, https://doi.org/10.1093/nar/gkac341
Inert Pepper aptamer-mediated endogenous mRNA recognition and imaging in living cells
Nucleic Acids Research, Volume 50, Issue 14, 12 August 2022, Page e84, https://doi.org/10.1093/nar/gkac368
