Works in Nucleic Acids Research, 2024, Vol 52, Issue 5

Results: 49

Correction to 'HDGFRP3 interaction with 53BP1 promotes DNA double-strand break repair'.

Published in:: 2024
Publication type:: Correction Notice

When Paul Berg meets Donald Crothers: an achiral connection through protein biosynthesis.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2130, doi. 10.1093/nar/gkae117

By:

Kumar, Pradeep;
Sankaranarayanan, Rajan

Publication type:

Article

The SMC5/6 complex: folding chromosomes back into shape when genomes take a break.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2112, doi. 10.1093/nar/gkae103

By:

Roy, Shamayita;
Adhikary, Hemanta;
D'Amours, Damien

Publication type:

Article

G-quadruplex-mediated genomic instability drives SNVs in cancer.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2198, doi. 10.1093/nar/gkae098

By:

Richl, Tilmann;
Kuper, Jochen;
Kisker, Caroline

Publication type:

Article

Prediction of DNA i-motifs via machine learning.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2188, doi. 10.1093/nar/gkae092

By:

Yang, Bibo;
Guneri, Dilek;
Yu, Haopeng;
Wright, Elisé P;
Chen, Wenqian;
Waller, Zoë A E;
Ding, Yiliang

Publication type:

Article

Transient states during the annealing of mismatched and bulged oligonucleotides.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2174, doi. 10.1093/nar/gkae091

By:

Todisco, Marco;
Ding, Dian;
Szostak, Jack W

Publication type:

Article

Molecular and thermodynamic determinants of self-assembly and hetero-oligomerization in the enterobacterial thermo-osmo-regulatory protein H-NS.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2157, doi. 10.1093/nar/gkae090

By:

Lukose, Bincy;
Maruno, Takahiro;
Faidh, Mohammed A;
Uchiyama, Susumu;
Naganathan, Athi N

Publication type:

Article

RNAvigate: efficient exploration of RNA chemical probing datasets.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2231, doi. 10.1093/nar/gkae089

By:

Irving, Patrick S;
Weeks, Kevin M

Publication type:

Article

Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2212, doi. 10.1093/nar/gkae086

By:

Wu, Zhikun;
Li, Tong;
Jiang, Zehang;
Zheng, Jingjing;
Gu, Yizhou;
Liu, Yizhi;
Liu, Yun;
Xie, Zhi

Publication type:

Article

Correction to 'PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs'.

Published in:: 2024
Publication type:: Correction Notice

G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2142, doi. 10.1093/nar/gkae073

By:

Liang, Hui-ting;
Yan, Jiang-yu;
Yao, Hao-jun;
Zhang, Xue-nan;
Xing, Zhi-ming;
Liu, Lin;
Chen, Yao-qing;
Li, Guo-rui;
Huang, Jing;
He, Yi-de;
Zheng, Ke-wei

Publication type:

Article

The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2519, doi. 10.1093/nar/gkae063

By:

Dong, Hai-Long;
Zhang, Chen;
Dai, Liang;
Zhang, Yan;
Zhang, Xing-Hua;
Tan, Zhi-Jie

Publication type:

Article

Selection-free precise gene repair using high-capacity adenovector delivery of advanced prime editing systems rescues dystrophin synthesis in DMD muscle cells.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2740, doi. 10.1093/nar/gkae057

By:

Wang, Qian;
Capelletti, Sabrina;
Liu, Jin;
Janssen, Josephine M;
Gonçalves, Manuel A F V

Publication type:

Article

Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. e28, doi. 10.1093/nar/gkae056

By:

Nanni, Adalena;
Titus-McQuillan, James;
Bankole, Kinfeosioluwa S;
Pardo-Palacios, Francisco;
Signor, Sarah;
Vlaho, Srna;
Moskalenko, Oleksandr;
Morse, Alison M;
Rogers, Rebekah L;
Conesa, Ana;
McIntyre, Lauren M

Publication type:

Article

Xrp1 governs the stress response program to spliceosome dysfunction.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2093, doi. 10.1093/nar/gkae055

By:

Stanković, Dimitrije;
Tain, Luke S;
Uhlirova, Mirka

Publication type:

Article

Two birds with one stone: SGI1 can stabilize itself and expel the IncC helper by hijacking the plasmid parABS system.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2498, doi. 10.1093/nar/gkae050

By:

Murányi, Gábor;
Szabó, Mónika;
Acsai, Károly;
Kiss, János

Publication type:

Article

Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in Pseudomonas fluorescens SBW25.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2446, doi. 10.1093/nar/gkae049

By:

Khomarbaghi, Zahra;
Ngan, Wing Y;
Ayan, Gökçe B;
Lim, Sungbin;
Dechow-Seligmann, Gunda;
Nandy, Pabitra;
Gallie, Jenna

Publication type:

Article

Mage transposon: a novel gene delivery system for mammalian cells.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2724, doi. 10.1093/nar/gkae048

By:

Tian, Jinghan;
Tong, Doudou;
Li, Zhendong;
Wang, Erqiang;
Yu, Yifei;
Lv, Hangya;
Hu, Zhendan;
Sun, Fang;
Wang, Guoping;
He, Min;
Xia, Tian

Publication type:

Article

The unique dual targeting of AGO1 by two types of PRMT enzymes promotes phasiRNA loading in Arabidopsis thaliana.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2480, doi. 10.1093/nar/gkae045

By:

Barre-Villeneuve, Clément;
Laudié, Michèle;
Carpentier, Marie-Christine;
Kuhn, Lauriane;
Lagrange, Thierry;
Azevedo-Favory, Jacinthe

Publication type:

Article

EquiPNAS: improved protein–nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. e27, doi. 10.1093/nar/gkae039

By:

Roche, Rahmatullah;
Moussad, Bernard;
Shuvo, Md Hossain;
Tarafder, Sumit;
Bhattacharya, Debswapna

Publication type:

Article

SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. e26, doi. 10.1093/nar/gkae038

By:

Aydin, Jens;
Gabel, Alexander;
Zielinski, Sebastian;
Ganskih, Sabina;
Schmidt, Nora;
Hartigan, Christina R;
Schenone, Monica;
Carr, Steven A;
Munschauer, Mathias

Publication type:

Article

Structural insights into the HDAC4–MEF2A–DNA complex and its implication in long-range transcriptional regulation.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2711, doi. 10.1093/nar/gkae036

By:

Dai, Shuyan;
Guo, Liang;
Dey, Raja;
Guo, Ming;
Zhang, Xiangqian;
Bates, Darren;
Cayford, Justin;
Jiang, Longying;
Wei, Hudie;
Chen, Zhuchu;
Zhang, Ye;
Chen, Lin;
Chen, Yongheng

Publication type:

Article

Ribosomal frameshifting at normal codon repeats recodes functional chimeric proteins in human.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2463, doi. 10.1093/nar/gkae035

By:

Ren, Guiping;
Gu, Xiaoqian;
Zhang, Lu;
Gong, Shimin;
Song, Shuang;
Chen, Shunkai;
Chen, Zhenjing;
Wang, Xiaoyan;
Li, Zhanbiao;
Zhou, Yingshui;
Li, Longxi;
Yang, Jiao;
Lai, Fan;
Dang, Yunkun

Publication type:

Article

Structural investigation of pathogenic RFC1 AAGGG pentanucleotide repeats reveals a role of G-quadruplex in dysregulated gene expression in CANVAS.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2698, doi. 10.1093/nar/gkae032

By:

Wang, Yang;
Wang, Junyan;
Yan, Zhenzhen;
Hou, Jianing;
Wan, Liqi;
Yang, Yingquan;
Liu, Yu;
Yi, Jie;
Guo, Pei;
Han, Da

Publication type:

Article

Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2434, doi. 10.1093/nar/gkae030

By:

Teyssonniere, Elie M;
Shichino, Yuichi;
Mito, Mari;
Friedrich, Anne;
Iwasaki, Shintaro;
Schacherer, Joseph

Publication type:

Article

MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. e25, doi. 10.1093/nar/gkae029

By:

Tang, Li;
Liao, Jiaqi;
Hill, Matthew C;
Hu, Jiaxin;
Zhao, Yichao;
Ellinor, Patrick T;
Li, Min

Publication type:

Article

Understanding intercalative modulation of G-rich sequence folding: solution structure of a TINA-conjugated antiparallel DNA triplex.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2686, doi. 10.1093/nar/gkae028

By:

Garavís, Miguel;
Edwards, Patrick J B;
Serrano-Chacón, Israel;
Doluca, Osman;
Filichev, Vyacheslav V;
González, Carlos

Publication type:

Article

NMR measurements of transient low-populated tautomeric and anionic Watson–Crick-like G·T/U in RNA:DNA hybrids: implications for the fidelity of transcription and CRISPR/Cas9 gene editing.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2672, doi. 10.1093/nar/gkae027

By:

Szekely, Or;
Rangadurai, Atul Kaushik;
Gu, Stephanie;
Manghrani, Akanksha;
Guseva, Serafima;
Al-Hashimi, Hashim M

Publication type:

Article

Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. e24, doi. 10.1093/nar/gkae023

By:

Xiong, Xiong;
Chen, Hengye;
Zhang, Qifan;
Liu, Yangying;
Xu, Chenhuan

Publication type:

Article

Smoother: on-the-fly processing of interactome data using prefix sums.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. e23, doi. 10.1093/nar/gkae008

By:

Schmidt, Markus R;
Barcons-Simon, Anna;
Rabuffo, Claudia;
Siegel, T Nicolai

Publication type:

Article

Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2578, doi. 10.1093/nar/gkae007

By:

Pavankumar, Theetha L;
Wong, C Jason;
Wong, Yun Ka;
Spies, Maria;
Kowalczykowski, Stephen C

Publication type:

Article

Site-specific acetylation of polynucleotide kinase 3′-phosphatase regulates its distinct role in DNA repair pathways.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2416, doi. 10.1093/nar/gkae002

By:

Islam, Azharul;
Chakraborty, Anirban;
Sarker, Altaf H;
Aryal, Uma K;
Pan, Lang;
Sharma, Gulshan;
Boldogh, Istvan;
Hazra, Tapas

Publication type:

Article

STIM1 translocation to the nucleus protects cells from DNA damage.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2389, doi. 10.1093/nar/gkae001

By:

Sanchez-Lopez, Irene;
Orantos-Aguilera, Yolanda;
Pozo-Guisado, Eulalia;
Alvarez-Barrientos, Alberto;
Lilla, Sergio;
Zanivan, Sara;
Lachaud, Christophe;
Martin-Romero, Francisco Javier

Publication type:

Article

Homology recognition without double-stranded DNA-strand separation in D-loop formation by RecA.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2565, doi. 10.1093/nar/gkad1260

By:

Shibata, Takehiko;
Ikawa, Shukuko;
Iwasaki, Wakana;
Sasanuma, Hiroyuki;
Masai, Hisao;
Hirota, Kouji

Publication type:

Article

Thiolutin has complex effects in vivo but is a direct inhibitor of RNA polymerase II in vitro.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2546, doi. 10.1093/nar/gkad1258

By:

Qiu, Chenxi;
Arora, Payal;
Malik, Indranil;
Laperuta, Amber J;
Pavlovic, Emily M;
Ugochukwu, Scott;
Naik, Mandar;
Kaplan, Craig D

Publication type:

Article

Aberrant DNA repair reveals a vulnerability in histone H3.3-mutant brain tumors.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2372, doi. 10.1093/nar/gkad1257

By:

Giacomini, Giulia;
Piquet, Sandra;
Chevallier, Odile;
Dabin, Juliette;
Bai, Siau-Kun;
Kim, Byungjin;
Siddaway, Robert;
Raught, Brian;
Coyaud, Etienne;
Shan, Chun-Min;
Reid, Robert J D;
Toda, Takenori;
Rothstein, Rodney;
Barra, Viviana;
Wilhelm, Therese;
Hamadat, Sabah;
Bertin, Chloé;
Crane, Alexander;
Dubois, Frank;
Forne, Ignasi

Publication type:

Article

Rif2 interaction with Rad50 counteracts Tel1 functions in checkpoint signalling and DNA tethering by releasing Tel1 from MRX binding.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2355, doi. 10.1093/nar/gkad1246

By:

Pizzul, Paolo;
Casari, Erika;
Rinaldi, Carlo;
Gnugnoli, Marco;
Mangiagalli, Marco;
Tisi, Renata;
Longhese, Maria Pia

Publication type:

Article

piRNA generation is associated with the pioneer round of translation in stem cells.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2590, doi. 10.1093/nar/gkad1212

By:

Allikka Parambil, Sudheesh;
Li, Danyan;
Zelko, Michael;
Poulet, Axel;
van Wolfswinkel, Josien C

Publication type:

Article

The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2530, doi. 10.1093/nar/gkad1241

By:

Manakova, Elena;
Golovinas, Edvardas;
Pocevičiūtė, Reda;
Sasnauskas, Giedrius;
Silanskas, Arunas;
Rutkauskas, Danielis;
Jankunec, Marija;
Zagorskaitė, Evelina;
Jurgelaitis, Edvinas;
Grybauskas, Algirdas;
Venclovas, Česlovas;
Zaremba, Mindaugas

Publication type:

Article

USP1-dependent nucleolytic expansion of PRIMPOL-generated nascent DNA strand discontinuities during replication stress.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2340, doi. 10.1093/nar/gkad1237

By:

Nusawardhana, Alexandra;
Pale, Lindsey M;
Nicolae, Claudia M;
Moldovan, George-Lucian

Publication type:

Article

Heterogeneous nuclear ribonucleoprotein K promotes cap-independent translation initiation of retroviral mRNAs.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2625, doi. 10.1093/nar/gkad1221

By:

Fuentes, Yazmín;
Olguín, Valeria;
López-Ulloa, Brenda;
Mendonça, Dafne;
Ramos, Hade;
Abdalla, Ana Luiza;
Guajardo-Contreras, Gabriel;
Niu, Meijuan;
Rojas-Araya, Barbara;
Mouland, Andrew J;
López-Lastra, Marcelo

Publication type:

Article

The disordered N-terminal tail of SARS-CoV-2 Nucleocapsid protein forms a dynamic complex with RNA.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2609, doi. 10.1093/nar/gkad1215

By:

Cubuk, Jasmine;
Alston, Jhullian J;
Incicco, J Jeremías;
Holehouse, Alex S;
Hall, Kathleen B;
Stuchell-Brereton, Melissa D;
Soranno, Andrea

Publication type:

Article

METTL3 drives telomere targeting of TERRA lncRNA through m<sup>6</sup>A-dependent R-loop formation: a therapeutic target for ALT-positive neuroblastoma.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2648, doi. 10.1093/nar/gkad1242

By:

Vaid, Roshan;
Thombare, Ketan;
Mendez, Akram;
Burgos-Panadero, Rebeca;
Djos, Anna;
Jachimowicz, Daniel;
Lundberg, Kristina Ihrmark;
Bartenhagen, Christoph;
Kumar, Navinder;
Tümmler, Conny;
Sihlbom, Carina;
Fransson, Susanne;
Johnsen, John Inge;
Kogner, Per;
Martinsson, Tommy;
Fischer, Matthias;
Mondal, Tanmoy

Publication type:

Article

Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2323, doi. 10.1093/nar/gkad1211

By:

McQuail, Josh;
Matera, Gianluca;
Gräfenhan, Tom;
Bischler, Thorsten;
Haberkant, Per;
Stein, Frank;
Vogel, Jörg;
Wigneshweraraj, Sivaramesh

Publication type:

Article

PRC1 directs PRC2-H3K27me3 deposition to shield adult spermatogonial stem cells from differentiation.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2306, doi. 10.1093/nar/gkad1203

By:

Hu, Mengwen;
Yeh, Yu-Han;
Maezawa, So;
Nakagawa, Toshinori;
Yoshida, Shosei;
Namekawa, Satoshi H

Publication type:

Article

G-quadruplexes control hepatitis B virus replication by promoting cccDNA transcription and phase separation in hepatocytes.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2290, doi. 10.1093/nar/gkad1200

By:

Giraud, Guillaume;
Rodà, Mélanie;
Huchon, Pélagie;
Michelet, Maud;
Maadadi, Sarah;
Jutzi, Daniel;
Montserret, Roland;
Ruepp, Marc-David;
Parent, Romain;
Combet, Christophe;
Zoulim, Fabien;
Testoni, Barbara

Publication type:

Article

Histone lactylation-boosted ALKBH3 potentiates tumor progression and diminished promyelocytic leukemia protein nuclear condensates by m<sup>1</sup>A demethylation of SP100A.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2273, doi. 10.1093/nar/gkad1193

By:

Gu, Xiang;
Zhuang, Ai;
Yu, Jie;
Yang, Ludi;
Ge, Shengfang;
Ruan, Jing;
Jia, Renbing;
Fan, Xianqun;
Chai, Peiwei

Publication type:

Article

Intrinsically disordered regions of the Msn2 transcription factor encode multiple functions using interwoven sequence grammars.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2260, doi. 10.1093/nar/gkad1191

By:

Mindel, Vladimir;
Brodsky, Sagie;
Cohen, Aileen;
Manadre, Wajd;
Jonas, Felix;
Carmi, Miri;
Barkai, Naama

Publication type:

Article

Yeast zinc cluster transcription factors involved in the switch from fermentation to respiration show interdependency for DNA binding revealing a novel type of DNA recognition.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 5, p. 2242, doi. 10.1093/nar/gkad1185

By:

Martinez, Karla Páez;
Gasmi, Najla;
Jeronimo, Célia;
Klimova, Natalia;
Robert, François;
Turcotte, Bernard

Publication type:

Article