Volume 52, Issue 21
27 November 2024
Cover image
Cover image
Cover: STK19 (green) is a missing piece of the transcription-coupled repair (TCR) puzzle. In the original model, TCR is initiated by lesion-stalled RNA polymerase II (red) associating with ELOF1 (purple), then classical TCR factors CSB (orange), CSA (dark blue) and UVSSA (light blue) are sequentially recruited, followed by the loading of TFIIH (yellow) as a scaffold. Our findings demonstrate STK19 is a fundamental TCR factor interacting with PolII, CSA and TFIIH. STK19 is recruited in parallel with UVSSA in a CSA-dependent way, and plays an indispensable role in the proper loading of TFIIH together with UVSSA. The identification and further investigation of STK19 promise to complete the longstanding puzzle of TCR mechanisms.
For more information see article by Tan, Y. et al., pages 12767–12783 in this issue.
For more information see article by Tan, Y. et al., pages 12767–12783 in this issue.
ISSN 0305-1048
EISSN 1362-4962
Issue navigation
Volume 52, Issue 21, 27 November 2024
NAR Breakthrough Article
STK19 is a transcription-coupled repair factor that participates in UVSSA ubiquitination and TFIIH loading
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12767–12783, https://doi.org/10.1093/nar/gkae787
Chemical Biology and Nucleic Acid Chemistry
Differential redox sensitivity of tRNA dihydrouridylation
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12784–12797, https://doi.org/10.1093/nar/gkae964
Computational Biology
Towards the genomic sequence code of DNA fragility for machine learning
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12798–12816, https://doi.org/10.1093/nar/gkae914
Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12817–12830, https://doi.org/10.1093/nar/gkae966
Gene Regulation, Chromatin and Epigenetics
ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12831–12849, https://doi.org/10.1093/nar/gkae926
The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12850–12877, https://doi.org/10.1093/nar/gkae941
YY1 is a transcriptional activator of the mouse LINE-1 Tf subfamily
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12878–12894, https://doi.org/10.1093/nar/gkae949
Recruitment of homodimeric proneural factors by conserved CAT–CAT E-boxes drives major epigenetic reconfiguration in cortical neurogenesis
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12895–12917, https://doi.org/10.1093/nar/gkae950
PWOs repress gene transcription by regulating chromatin structures in Arabidopsis
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12918–12929, https://doi.org/10.1093/nar/gkae958
A bacterial transcription activator dedicated to the expression of the enzyme catalyzing the first committed step in fatty acid biosynthesis
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12930–12944, https://doi.org/10.1093/nar/gkae960
NusG-dependent RNA polymerase pausing is a common feature of riboswitch regulatory mechanisms
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12945–12960, https://doi.org/10.1093/nar/gkae981
Genome Integrity, Repair and Replication
RAD52-mediated repair of DNA double-stranded breaks at inactive centromeres leads to subsequent apoptotic cell death
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12961–12975, https://doi.org/10.1093/nar/gkae852
Various plasmid strategies limit the effect of bacterial restriction–modification systems against conjugation
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12976–12986, https://doi.org/10.1093/nar/gkae896
Pathogen-encoded Rum DNA polymerase drives rapid bacterial drug resistance
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 12987–13002, https://doi.org/10.1093/nar/gkae899
SNF2L suppresses nascent DNA gap formation to promote DNA synthesis
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13003–13018, https://doi.org/10.1093/nar/gkae903
PCNA-binding activity separates RNF168 functions in DNA replication and DNA double-stranded break signaling
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13019–13035, https://doi.org/10.1093/nar/gkae918
Tetrameric INTS6-SOSS1 complex facilitates DNA:RNA hybrid autoregulation at double-strand breaks
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13036–13056, https://doi.org/10.1093/nar/gkae937
EGFR-mediated HSP70 phosphorylation facilitates PCNA association with chromatin and DNA replication
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13057–13072, https://doi.org/10.1093/nar/gkae938
Genomics
Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13073–13093, https://doi.org/10.1093/nar/gkae871
Unveiling host–parasite relationships through conserved MITEs in prokaryote and viral genomes
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13094–13109, https://doi.org/10.1093/nar/gkae906
Global coupling of R-loop dynamics with RNA polymerase II modulates gene expression and early development of Drosophila
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13110–13127, https://doi.org/10.1093/nar/gkae933
Insertion sequence elements and unique symmetrical genomic regions mediate chromosomal inversions in Streptococcus pyogenes
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13128–13137, https://doi.org/10.1093/nar/gkae948
Molecular and Structural Biology
A compact stem-loop DNA aptamer _targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13138–13151, https://doi.org/10.1093/nar/gkae874
Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13152–13173, https://doi.org/10.1093/nar/gkae886
Coronavirus S protein alters dsRNA accumulation and stress granule formation through regulation of ADAR1-p150 expression
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13174–13191, https://doi.org/10.1093/nar/gkae921
Structural basis of transcriptional regulation by UrtR in response to uric acid
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13192–13205, https://doi.org/10.1093/nar/gkae922
GTSF1 is required for transposon silencing in the unicellular eukaryote Paramecium tetraurelia
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13206–13223, https://doi.org/10.1093/nar/gkae925
RNA G-quadruplex formation in biologically important transcribed regions: can two-tetrad intramolecular RNA quadruplexes be formed?
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13224–13242, https://doi.org/10.1093/nar/gkae927
Stacking correlation length in single-stranded DNA
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13243–13254, https://doi.org/10.1093/nar/gkae934
DNA supercoiling enhances DNA condensation by ParB proteins
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13255–13268, https://doi.org/10.1093/nar/gkae936
ALS-associated FUS mutation reshapes the RNA and protein composition of stress granules
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13269–13289, https://doi.org/10.1093/nar/gkae942
Uncoupling FRUITFULL’s functions through modification of a protein motif identified by co-ortholog analysis
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13290–13304, https://doi.org/10.1093/nar/gkae963
Nucleic Acid Enzymes
A genomic database furnishes minimal functional glycyl-tRNA synthetases homologous to other, designed class II urzymes
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13305–13324, https://doi.org/10.1093/nar/gkae992
RNA and RNA-protein complexes
Modulation of UPF1 catalytic activity upon interaction of SARS-CoV-2 Nucleocapsid protein with factors involved in nonsense mediated-mRNA decay
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13325–13339, https://doi.org/10.1093/nar/gkae829
Optimized periphery-core interface increases fitness of the Bacillus subtilis glmS ribozyme
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13340–13350, https://doi.org/10.1093/nar/gkae830
Taurine hypomodification underlies mitochondrial tRNATrp-related genetic diseases
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13351–13367, https://doi.org/10.1093/nar/gkae854
Human selenocysteine synthase, SEPSECS, has evolved to optimize binding of a tRNA-based substrate
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13368–13385, https://doi.org/10.1093/nar/gkae875
RNase W, a conserved ribonuclease family with a novel active site
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13386–13401, https://doi.org/10.1093/nar/gkae907
Systematic analysis of the _target recognition and repression by the Pumilio proteins
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13402–13418, https://doi.org/10.1093/nar/gkae929
Alternative substrate kinetics of SARS-CoV-2 Nsp15 endonuclease reveals a specificity landscape dominated by RNA structure
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13419–13433, https://doi.org/10.1093/nar/gkae939
Structural Biology
Structural insights into human ELAC2 as a tRNA 3′ processing enzyme
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13434–13446, https://doi.org/10.1093/nar/gkae1014
Synthetic Biology and Bioengineering
A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13447–13468, https://doi.org/10.1093/nar/gkae912
Synthetic translational coupling element for multiplexed signal processing and cellular control
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13469–13483, https://doi.org/10.1093/nar/gkae980
Correction
Correction to ‘Solution structures and effects of a platinum compound successively bound MYC G-quadruplex’
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Page 13484, https://doi.org/10.1093/nar/gkae1012
Methods
MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylated regions from whole-genome datasets
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Page e98, https://doi.org/10.1093/nar/gkae880
OmicsFootPrint: a framework to integrate and interpret multi-omics data using circular images and deep neural networks
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Page e99, https://doi.org/10.1093/nar/gkae915
Aptamer-based assay for high-throughput substrate profiling of RNA decapping enzymes
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Page e100, https://doi.org/10.1093/nar/gkae919
Spatial pattern and differential expression analysis with spatial transcriptomic data
Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Page e101, https://doi.org/10.1093/nar/gkae962
