Subject: Nucleic Acids Research Table of Contents for 24 June 2024 Oxford Academic
 
 
 
Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Celebrating 50 years of NAR
 

Nucleic Acids Research is celebrating its 50th anniversary this year. We owe our success to the incredible work of the three founding editors, Richard T. Walker and A. Stanley Jones at the University of Birmingham in the UK, and Dieter Söll at Yale University in the USA. Their vision and dedication have been carried forward by the editors who followed them, as well as our authors and reviewers. Today, NAR remains one of the leading journals in the biological sciences. 

Celebrate our 50th anniversary with us
 
 
 
 
Nucleic Acids Research  
Volume 52 Issue 11
 
24 June 2024
 
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Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
A programmable dual-targeting siRNA scaffold supports potent two-gene modulation in the central nervous system border= 
 
Jillian Belgrad, Qi Tang, Sam Hildebrand, Ashley Summers, Ellen Sapp ...
 
 
 
Computational Biology
 
 
 
 
SCTC: inference of developmental potential from single-cell transcriptional complexity border= 
 
Hai Lin, Huan Hu, Zhen Feng, Fei Xu, Jie Lyu ...
 
 
 
asteRIa enables robust interaction modeling between chromatin modifications and epigenetic readers border= 
 
Mara Stadler, Saulius Lukauskas, Till Bartke, Christian L Müller
 
 
 
Species-specific design of artificial promoters by transfer-learning based generative deep-learning model border= 
 
Yan Xia, Xiaowen Du, Bin Liu, Shuyuan Guo, Yi-Xin Huo
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
H3.1/3.2 regulate the initial progression of the gene expression program border= 
 
Satoshi Funaya, Yusuke Takahashi, Masataka G Suzuki, Yutaka Suzuki, Fugaku Aoki
 
 
 
 
HELLS regulates transcription in T-cell lymphomas by reducing unscheduled R-loops and by facilitating RNAPII progression border= 
 
Annalisa Tameni, Selene Mallia, Veronica Manicardi, Benedetta Donati, Federica Torricelli ...
 
 
 
The long non-coding RNA Meg3 mediates imprinted gene expression during stem cell differentiation border= 
 
Sabina Farhadova, Amani Ghousein, François Charon, Caroline Surcis, Melisa Gomez-Velazques ...
 
 
 
KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons border= 
 
Matanel Yheskel, Hayden A M Hatch, Erika Pedrosa, Bethany K Terry, Aubrey A Siebels ...
 
 
 
Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes border= 
 
Wael R Abdel-Fattah, Mattias Carlsson, Guo-Zhen Hu, Ajeet Singh, Alexander Vergara ...
 
 
 
Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome border= 
 
Ilya A Pletenev, Maria Bazarevich, Diana R Zagirova, Anna D Kononkova, Alexander V Cherkasov ...
 
 
 
 
Interaction between a J-domain co-chaperone and a specific Argonaute protein contributes to microRNA function in animals border= 
 
Pierre-Marc Frédérick, Guillaume Jannot, Isabelle Banville, Martin J Simard
 
 
 
Proximal telomeric decompaction due to telomere shortening drives FOXC1-dependent myocardial senescence border= 
 
Bin Li, Weiyao Xiong, Wu Zuo, Yuanyuan Shi, Teng Wang ...
 
 
 
Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing border= 
 
Basile Leduque, Alejandro Edera, Clémentine Vitte, Leandro Quadrana
 
 
 
Senescence of human pancreatic beta cells enhances functional maturation through chromatin reorganization and promotes interferon responsiveness border= 
 
Milan Patra, Agnes Klochendler, Reba Condiotti, Binyamin Kaffe, Sharona Elgavish ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
Cdc13 exhibits dynamic DNA strand exchange in the presence of telomeric DNA border= 
 
David G Nickens, Zhitong Feng, Jiangchuan Shen, Spencer J Gray, Robert H Simmons, III ...
 
 
 
Interplay of the Tfb1 pleckstrin homology domain with Rad2 and Rad4 in transcription coupled and global genomic nucleotide excision repair border= 
 
Wenzhi Gong, Hannah Holmberg, Cheng Lu, Michelle Huang, Shisheng Li
 
 
 
Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB border= 
 
Kelly A Manthei, Lia M Munson, Jayakrishnan Nandakumar, Lyle A Simmons
 
 
 
DNA-PK participates in pre-rRNA biogenesis independent of DNA double-strand break repair border= 
 
Peng Li, Xiaochen Gai, Qilin Li, Qianqian Yang, Xiaochun Yu
 
 
 
EXO1 and DNA2-mediated ssDNA gap expansion is essential for ATR activation and to maintain viability in BRCA1-deficient cells border= 
 
Néstor García-Rodríguez, Iria Domínguez-García, María del Carmen Domínguez-Pérez, Pablo Huertas
 
 
 
Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements border= 
 
Phuong Pham, Elizabeth A Wood, Emma L Dunbar, Michael M Cox, Myron F Goodman
 
 
 
Stress-induced nucleoid remodeling in Deinococcus radiodurans is associated with major changes in Heat Unstable (HU) protein dynamics border= 
 
Pierre Vauclare, Jip Wulffelé, Françoise Lacroix, Pascale Servant, Fabrice Confalonieri ...
 
 
 
The TIMELESS and PARP1 interaction suppresses replication-associated DNA gap accumulation border= 
 
Joanne Saldanha, Julie Rageul, Jinal A Patel, Amy L Phi, Natalie Lo ...
 
 
 
Molecular Biology
 
 
 
 
Despite the odds: formation of the SARS-CoV-2 methylation complex border= 
 
Alex Matsuda, Jacek Plewka, MichaÅ‚ Rawski, André Mourão, Weronika Zajko ...
 
 
 
AcrIIA28 is a metalloprotein that specifically inhibits targeted-DNA loading to SpyCas9 by binding to the REC3 domain border= 
 
Gi Eob Kim, Hyun Ho Park
 
 
 
Orphan nuclear receptors-induced ALT-associated PML bodies are targets for ALT inhibition border= 
 
Venus Marie Gaela, Hsuan-Yu Hsia, Nithila A Joseph, Wan-Yi Tzeng, Pin-Chao Ting ...
 
 
 
Single-molecule imaging reveals a direct role of CTCF's zinc fingers in SA interaction and cluster-dependent RNA recruitment border= 
 
Jonas Huber, Nicoleta-Loredana Tanasie, Sarah Zernia, Johannes Stigler
 
 
 
Kinetics of programmed and spontaneous ribosome sliding along the mRNA border=  
 
Tamara Senyushkina, Ekaterina Samatova, Maria Klimova, Marina V Rodnina
 
 
 
rAAV capsid mutants eliminate leaky expression from DNA donor template for homologous recombination border= 
 
Chen Ling, Chenghui Yu, Cong Wang, Ming Yang, Hengbin Yang ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Visualization of oxidized guanine nucleotides accumulation in living cells with split MutT border= 
 
Yoshihiro Fujikawa, Hidehiko Kawai, Tetsuya Suzuki, Hiroyuki Kamiya
 
 
 
Two residues in the DNA binding site of Pif1 helicase are essential for nuclear functions but dispensable for mitochondrial respiratory growth border= 
 
Jun Gao, David R Proffitt, John C Marecki, Reine U Protacio, Wayne P Wahls ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
MIWI N-terminal arginines orchestrate generation of functional pachytene piRNAs and spermiogenesis border= 
 
Nicholas Vrettos, Jan Oppelt, Ansgar Zoch, Paraskevi Sgourdou, Haruka Yoshida ...
 
 
 
Distinct and overlapping RNA determinants for binding and target-primed reverse transcription by Bombyx mori R2 retrotransposon protein border= 
 
Anthony Rodríguez-Vargas, Kathleen Collins
 
 
 
Fine-tuning the tRNA anticodon arm for multiple/consecutive incorporations of beta -amino acids and analogs border= 
 
Takayuki Katoh, Hiroaki Suga
 
 
 
The RNA secondary structure of androgen receptor-FL and V7 transcripts reveals novel regulatory regions border= 
 
Warren B Rouse, Van S Tompkins, Collin A O'Leary, Walter N Moss
 
 
 
Ribosomal RNA modification enzymes stimulate large ribosome subunit assembly in E. coli border= 
 
Rya Ero, Margus Leppik, Kaspar Reier, Aivar Liiv, Jaanus Remme
 
 
 
Mitolnc controls cardiac BCAA metabolism and heart hypertrophy by allosteric activation of BCKDH border= 
 
Maria Weiss, Sara Hettrich, Theresa Hofmann, Salma Hachim, Stefan Günther ...
 
 
 
Assembly of SARS-CoV-2 nucleocapsid protein with nucleic acid 
 
Huaying Zhao, Abdullah M Syed, Mir M Khalid, Ai Nguyen, Alison Ciling ...
 
 
 
The clade-specific target recognition mechanisms of plant RISCs border=  
 
Hiro-oki Iwakawa
 
 
 
RNase E searches for cleavage sites in RNA by linear diffusion: direct evidence from single-molecule FRET border= 
 
Tithi Banerjee, Eli Rothenberg, Joel G Belasco
 
 
 
Structural Biology
 
 
 
 
Structure of an internal loop motif with three consecutive U¢U mismatches from stem'loop 1 in the 3²-UTR of the SARS-CoV-2 genomic RNA border= 
 
Jennifer Vögele, Elke Duchardt-Ferner, Jasleen Kaur Bains, Bozana Knezic, Anna Wacker ...
 
 
 
Antisense RNA C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms a triplex-like structure and binds small synthetic ligand border= 
 
Leszek BÅ‚aszczyk, Marcin Ryczek, Bimolendu Das, Martyna Mateja-Pluta, Magdalena Bejger ...
 
 
 
Structural basis for double-stranded RNA recognition by SID1 border=  
 
Runhao Wang, Ye Cong, Dandan Qian, Chuangye Yan, Deshun Gong
 
 
 
Corrections
 
 
 
 
Correction to ˜RNase E searches for cleavage sites in RNA by linear diffusion: direct evidence from single-molecule FRET' border= 
 
 
 
 
Correction to ˜Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery' border= 
 
 
 
 
Correction to ˜The Uba4 domain interplay is mediated via a thioester that is critical for tRNA thiolation through Urm1 thiocarboxylation' border=  
 
 
 
 
Correction to ˜Senescence of human pancreatic beta cells enhances functional maturation through chromatin reorganization and promotes interferon responsiveness' border= 
 
 
 
 
Methods
 
 
 
 
Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA border= 
 
Jordan C Cheng, Neeti Swarup, Marco Morselli, Wei-Lun Huang, Mohammad Aziz ...
 
 
 
SpatialSPM: statistical parametric mapping for the comparison of gene expression pattern images in multiple spatial transcriptomic datasets border= 
 
Jungyoon Ohn, Mi-Kyoung Seo, Jeongbin Park, Daeseung Lee, Hongyoon Choi
 
 
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