Works matching IS 03051048 AND DT 2021 AND VI 49 AND IP 1

Results: 50

Strand antagonism in RNAi: an explanation of differences in potency between intracellularly expressed siRNA and shRNA.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 600, doi. 10.1093/nar/gkaa1217

By:

Jin, Xin;
Sun, Tingting;
Zhao, Chuanke;
Zheng, Yongxiang;
Zhang, Yufan;
Cai, Weijing;
He, Qiuchen;
Taira, Kaz;
Zhang, Lihe;
Zhou, Demin

Publication type:

Article

Chromatin remodeler Ino80C acts independently of H2A.Z to evict promoter nucleosomes and stimulate transcription of highly expressed genes in yeast.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 599, doi. 10.1093/nar/gkaa1212

By:

Qiu, Hongfang;
Biernat, Emily;
Govind, Chhabi K;
Rawal, Yashpal;
Chereji, Răzvan V;
Clark, David J;
Hinnebusch, Alan G

Publication type:

Article

Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 596, doi. 10.1093/nar/gkaa1211

By:

Wu, Jian;
Zhou, Cuiji;
Li, James;
Li, Chun;
Tao, Xiaorong;
Leontis, Neocles B;
Zirbel, Craig L;
Bisaro, David M;
Ding, Biao

Publication type:

Article

Multiple competing RNA structures dynamically control alternative splicing in the human ATE1 gene.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 479, doi. 10.1093/nar/gkaa1208

By:

Kalinina, Marina;
Skvortsov, Dmitry;
Kalmykova, Svetlana;
Ivanov, Timofei;
Dontsova, Olga;
Pervouchine, Dmitri D

Publication type:

Article

G-quadruplex–R-loop interactions and the mechanism of anticancer G-quadruplex binders.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 595, doi. 10.1093/nar/gkaa1206

By:

Miglietta, Giulia;
Russo, Marco;
Capranico, Giovanni

Publication type:

Article

DNA damage alters nuclear mechanics through chromatin reorganization.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 340, doi. 10.1093/nar/gkaa1202

By:

dos Santos, Ália;
Cook, Alexander W;
Gough, Rosemarie E;
Schilling, Martin;
Olszok, Nora A;
Brown, Ian;
Wang, Lin;
Aaron, Jesse;
Martin-Fernandez, Marisa L;
Rehfeldt, Florian;
Toseland, Christopher P

Publication type:

Article

APOBEC1 cytosine deaminase activity on single-stranded DNA is suppressed by replication protein A.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 322, doi. 10.1093/nar/gkaa1201

By:

Wong, Lai;
Vizeacoumar, Frederick S;
Vizeacoumar, Franco J;
Chelico, Linda

Publication type:

Article

A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 206, doi. 10.1093/nar/gkaa1200

By:

Rodríguez-Galán, Olga;
García-Gómez, Juan J;
Rosado, Iván V;
Wei, Wu;
Méndez-Godoy, Alfonso;
Pillet, Benjamin;
Alekseenko, Alisa;
Steinmetz, Lars M;
Pelechano, Vicent;
Kressler, Dieter;
de la Cruz, Jesús

Publication type:

Article

Structural basis for inhibition of the type I-F CRISPR–Cas surveillance complex by AcrIF4, AcrIF7 and AcrIF14.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 584, doi. 10.1093/nar/gkaa1199

By:

Gabel, Clinton;
Li, Zhuang;
Zhang, Heng;
Chang, Leifu

Publication type:

Article

Structural basis for guide RNA trimming by RNase D ribonuclease in Trypanosoma brucei.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 568, doi. 10.1093/nar/gkaa1197

By:

Gao, Yanqing;
Liu, Hehua;
Zhang, Chong;
Su, Shichen;
Chen, Yiqing;
Chen, Xi;
Li, Yangyang;
Shao, Zhiwei;
Zhang, Yixi;
Shao, Qiyuan;
Li, Jixi;
Huang, Zhen;
Ma, Jinbiao;
Gan, Jianhua

Publication type:

Article

Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 547, doi. 10.1093/nar/gkaa1195

By:

Jha, Vikash;
Roy, Bappaditya;
Jahagirdar, Dushyant;
McNutt, Zakkary A;
Shatoff, Elan A;
Boleratz, Bethany L;
Watkins, Dean E;
Bundschuh, Ralf;
Basu, Kaustuv;
Ortega, Joaquin;
Fredrick, Kurt

Publication type:

Article

The versatile interactome of chloroplast ribosomes revealed by affinity purification mass spectrometry.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 400, doi. 10.1093/nar/gkaa1192

By:

Westrich, Lisa Désirée;
Gotsmann, Vincent Leon;
Herkt, Claudia;
Ries, Fabian;
Kazek, Tanja;
Trösch, Raphael;
Armbruster, Laura;
Mühlenbeck, Jens Stephan;
Ramundo, Silvia;
Nickelsen, Jörg;
Finkemeier, Iris;
Wirtz, Markus;
Storchová, Zuzana;
Räschle, Markus;
Willmund, Felix

Publication type:

Article

Histone methyltransferase ATX1 dynamically regulates fiber secondary cell wall biosynthesis in Arabidopsis inflorescence stem.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 190, doi. 10.1093/nar/gkaa1191

By:

Wang, Xianqiang;
Wang, Denghui;
Xu, Wenjian;
Kong, Lingfei;
Ye, Xiao;
Zhuang, Qianye;
Fan, Di;
Luo, Keming

Publication type:

Article

Systematic evaluation of the effects of genetic variants on PIWI-interacting RNA expression across 33 cancer types.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 90, doi. 10.1093/nar/gkaa1190

By:

Xin, Junyi;
Du, Mulong;
Jiang, Xia;
Wu, Yanling;
Ben, Shuai;
Zheng, Rui;
Chu, Haiyan;
Li, Shuwei;
Zhang, Zhengdong;
Wang, Meilin

Publication type:

Article

The mTOR regulated RNA-binding protein LARP1 requires PABPC1 for guided mRNA interaction.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 458, doi. 10.1093/nar/gkaa1189

By:

Smith, Ewan M;
Benbahouche, Nour El Houda;
Morris, Katherine;
Wilczynska, Ania;
Gillen, Sarah;
Schmidt, Tobias;
Meijer, Hedda A;
Jukes-Jones, Rebekah;
Cain, Kelvin;
Jones, Carolyn;
Stoneley, Mark;
Waldron, Joseph A;
Bell, Cameron;
Fonseca, Bruno D;
Blagden, Sarah;
Willis, Anne E;
Bushell, Martin

Publication type:

Article

An atypical BRCT–BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIα within a flexible DNA repair complex.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 306, doi. 10.1093/nar/gkaa1188

By:

Hammel, Michal;
Rashid, Ishtiaque;
Sverzhinsky, Aleksandr;
Pourfarjam, Yasin;
Tsai, Miaw-Sheue;
Ellenberger, Tom;
Pascal, John M;
Kim, In-Kwon;
Tainer, John A;
Tomkinson, Alan E

Publication type:

Article

Ribosome association primes the stringent factor Rel for tRNA-dependent locking in the A-site and activation of (p)ppGpp synthesis.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 444, doi. 10.1093/nar/gkaa1187

By:

Takada, Hiraku;
Roghanian, Mohammad;
Caballero-Montes, Julien;
Van Nerom, Katleen;
Jimmy, Steffi;
Kudrin, Pavel;
Trebini, Fabio;
Murayama, Rikinori;
Akanuma, Genki;
Garcia-Pino, Abel;
Hauryliuk, Vasili

Publication type:

Article

Single-molecule visualization of human RECQ5 interactions with single-stranded DNA recombination intermediates.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 285, doi. 10.1093/nar/gkaa1184

By:

Xue, Chaoyou;
Molnarova, Lucia;
Steinfeld, Justin B;
Zhao, Weixing;
Ma, Chujian;
Spirek, Mario;
Kaniecki, Kyle;
Kwon, Youngho;
Beláň, Ondrej;
Krejci, Katerina;
Boulton, Simon J;
Sung, Patrick;
Greene, Eric C;
Krejci, Lumir

Publication type:

Article

Basic mechanisms and kinetics of pause-interspersed transcript elongation.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 15, doi. 10.1093/nar/gkaa1182

By:

Qian, Jin;
Dunlap, David;
Finzi, Laura

Publication type:

Article

Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogen Agrobacterium fabrum.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 529, doi. 10.1093/nar/gkaa1181

By:

Vigouroux, Armelle;
Meyer, Thibault;
Naretto, Anaïs;
Legrand, Pierre;
Aumont-Nicaise, Magali;
Di Cicco, Aurélie;
Renoud, Sébastien;
Doré, Jeanne;
Lévy, Daniel;
Vial, Ludovic;
Lavire, Céline;
Moréra, Solange

Publication type:

Article

Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 383, doi. 10.1093/nar/gkaa1180

By:

Rubio, Angela;
Ghosh, Sanjay;
Mülleder, Michael;
Ralser, Markus;
Mata, Juan

Publication type:

Article

Pseudouridine-mediated translation control of mRNA by methionine aminoacyl tRNA synthetase.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 432, doi. 10.1093/nar/gkaa1178

By:

Levi, Ofri;
Arava, Yoav S

Publication type:

Article

Water spines and networks in G-quadruplex structures.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 519, doi. 10.1093/nar/gkaa1177

By:

Li, Kevin;
Yatsunyk, Liliya;
Neidle, Stephen

Publication type:

Article

Identification of lysine isobutyrylation as a new histone modification mark.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 177, doi. 10.1093/nar/gkaa1176

By:

Zhu, Zhesi;
Han, Zhen;
Halabelian, Levon;
Yang, Xiangkun;
Ding, Jun;
Zhang, Nawei;
Ngo, Liza;
Song, Jiabao;
Zeng, Hong;
He, Maomao;
Zhao, Yingming;
Arrowsmith, Cheryl H;
Luo, Minkui;
Bartlett, Michael G;
Zheng, Y George

Publication type:

Article

A skipping rope translocation mechanism in a widespread family of DNA repair helicases.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 504, doi. 10.1093/nar/gkaa1174

By:

Roske, Johann J;
Liu, Sunbin;
Loll, Bernhard;
Neu, Ursula;
Wahl, Markus C

Publication type:

Article

G-Quadruplex loops regulate PARP-1 enzymatic activation.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 416, doi. 10.1093/nar/gkaa1172

By:

Edwards, Andrea D;
Marecki, John C;
Byrd, Alicia K;
Gao, Jun;
Raney, Kevin D

Publication type:

Article

Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 158, doi. 10.1093/nar/gkaa1169

By:

Broche, Julian;
Kungulovski, Goran;
Bashtrykov, Pavel;
Rathert, Philipp;
Jeltsch, Albert

Publication type:

Article

Flanking sequence preference modulates de novo DNA methylation in the mouse genome.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 145, doi. 10.1093/nar/gkaa1168

By:

Mallona, Izaskun;
Ilie, Ioana Mariuca;
Karemaker, Ino Dominiek;
Butz, Stefan;
Manzo, Massimiliano;
Caflisch, Amedeo;
Baubec, Tuncay

Publication type:

Article

Reconstitution of mammalian mitochondrial translation system capable of correct initiation and long polypeptide synthesis from leaderless mRNA.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 371, doi. 10.1093/nar/gkaa1165

By:

Lee, Muhoon;
Matsunaga, Noriko;
Akabane, Shiori;
Yasuda, Ippei;
Ueda, Takuya;
Takeuchi-Tomita, Nono

Publication type:

Article

The nature of the modification at position 37 of tRNA<sup>Phe</sup> correlates with acquired taxol resistance.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 38, doi. 10.1093/nar/gkaa1164

By:

Pan, Yu;
Yan, Tong-Meng;
Wang, Jing-Rong;
Jiang, Zhi-Hong

Publication type:

Article

TonEBP recognizes R-loops and initiates m6A RNA methylation for R-loop resolution.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 269, doi. 10.1093/nar/gkaa1162

By:

Kang, Hyun Je;
Cheon, Na Young;
Park, Hyun;
Jeong, Gyu Won;
Ye, Byeong Jin;
Yoo, Eun Jin;
Lee, Jun Ho;
Hur, Jin-Hoe;
Lee, Eun-A;
Kim, Hongtae;
Lee, Kyoo-young;
Choi, Soo Youn;
Lee-Kwon, Whaseon;
Myung, Kyungjae;
Lee, Ja Yil;
Kwon, Hyug Moo

Publication type:

Article

Validation of human microRNA target pathways enables evaluation of target prediction tools.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 127, doi. 10.1093/nar/gkaa1161

By:

Kern, Fabian;
Krammes, Lena;
Danz, Karin;
Diener, Caroline;
Kehl, Tim;
Küchler, Oliver;
Fehlmann, Tobias;
Kahraman, Mustafa;
Rheinheimer, Stefanie;
Aparicio-Puerta, Ernesto;
Wagner, Sylvia;
Ludwig, Nicole;
Backes, Christina;
Lenhof, Hans-Peter;
von Briesen, Hagen;
Hart, Martin;
Keller, Andreas;
Meese, Eckart

Publication type:

Article

The proto-Nucleic Acid Builder: a software tool for constructing nucleic acid analogs.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 79, doi. 10.1093/nar/gkaa1159

By:

Alenaizan, Asem;
Barnett, Joshua L;
Hud, Nicholas V;
Sherrill, C David;
Petrov, Anton S

Publication type:

Article

Deploying MMEJ using MENdel in precision gene editing applications for gene therapy and functional genomics.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 67, doi. 10.1093/nar/gkaa1156

By:

Martínez-Gálvez, Gabriel;
Joshi, Parnal;
Friedberg, Iddo;
Manduca, Armando;
Ekker, Stephen C

Publication type:

Article

Histones participate in base excision repair of 8-oxodGuo by transiently cross-linking with active repair intermediates in nucleosome core particles.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 257, doi. 10.1093/nar/gkaa1153

By:

Ren, Mengtian;
Shang, Mengdi;
Wang, Huawei;
Xi, Zhen;
Zhou, Chuanzheng

Publication type:

Article

Structural basis for the substrate specificity and catalytic features of pseudouridine kinase from Arabidopsis thaliana.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 491, doi. 10.1093/nar/gkaa1144

By:

Kim, Sang-Hoon;
Witte, Claus-Peter;
Rhee, Sangkee

Publication type:

Article

Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 53, doi. 10.1093/nar/gkaa1137

By:

Pei, Guangsheng;
Hu, Ruifeng;
Dai, Yulin;
Manuel, Astrid Marilyn;
Zhao, Zhongming;
Jia, Peilin

Publication type:

Article

The fragility of a structurally diverse duplication block triggers recurrent genomic amplification.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 244, doi. 10.1093/nar/gkaa1136

By:

Suzuki, Ryusuke;
Murata, Michael M;
Manguso, Nicholas;
Watanabe, Takaaki;
Mouakkad-Montoya, Lila;
Igari, Fumie;
Rahman, Md Maminur;
Qu, Ying;
Cui, Xiaojiang;
Giuliano, Armando E;
Takeda, Shunichi;
Tanaka, Hisashi

Publication type:

Article

Human GTPBP5 is involved in the late stage of mitoribosome large subunit assembly.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 354, doi. 10.1093/nar/gkaa1131

By:

Cipullo, Miriam;
Pearce, Sarah F;
Lopez Sanchez, Isabel G;
Gopalakrishna, Shreekara;
Krüger, Annika;
Schober, Florian;
Busch, Jakob D;
Li, Xinping;
Wredenberg, Anna;
Atanassov, Ilian;
Rorbach, Joanna

Publication type:

Article

Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 114, doi. 10.1093/nar/gkaa1130

By:

Ren, Xiangle;
Zhou, Yang;
Xue, Zhaoyu;
Hao, Ning;
Li, Yuanyuan;
Guo, Xiaohuan;
Wang, Daliang;
Shi, Xiaobing;
Li, Haitao

Publication type:

Article

The transcriptional repressors VAL1 and VAL2 recruit PRC2 for genome-wide Polycomb silencing in Arabidopsis.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 98, doi. 10.1093/nar/gkaa1129

By:

Yuan, Liangbing;
Song, Xin;
Zhang, Lu;
Yu, Yaoguang;
Liang, Zhenwei;
Lei, Yawen;
Ruan, Jiuxiao;
Tan, Bin;
Liu, Jun;
Li, Chenlong

Publication type:

Article

Heritable pattern of oxidized DNA base repair coincides with pre-targeting of repair complexes to open chromatin.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 221, doi. 10.1093/nar/gkaa1120

By:

Bacolla, Albino;
Sengupta, Shiladitya;
Ye, Zu;
Yang, Chunying;
Mitra, Joy;
De-Paula, Ruth B;
Hegde, Muralidhar L;
Ahmed, Zamal;
Mort, Matthew;
Cooper, David N;
Mitra, Sankar;
Tainer, John A

Publication type:

Article

MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 25, doi. 10.1093/nar/gkaa1117

By:

Wang, Yuluan;
Soneson, Charlotte;
Malinowska, Anna L;
Laski, Artur;
Ghosh, Souvik;
Kanitz, Alexander;
Gebert, Luca F R;
Robinson, Mark D;
Hall, Jonathan

Publication type:

Article

High-resolution visualization and quantification of nucleic acid–based therapeutics in cells and tissues using Nanoscale secondary ion mass spectrometry (NanoSIMS).

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. 1, doi. 10.1093/nar/gkaa1112

By:

He, Cuiwen;
Migawa, Michael T;
Chen, Kai;
Weston, Thomas A;
Tanowitz, Michael;
Song, Wenxin;
Guagliardo, Paul;
Iyer, K Swaminathan;
Bennett, C Frank;
Fong, Loren G;
Seth, Punit P;
Young, Stephen G;
Jiang, Haibo

Publication type:

Article

A simplified strategy for titrating gene expression reveals new relationships between genotype, environment, and bacterial growth.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. e6, doi. 10.1093/nar/gkaa1073

By:

Mathis, Andrew D;
Otto, Ryan M;
Reynolds, Kimberly A

Publication type:

Article

Optimized design of antisense oligomers for targeted rRNA depletion.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. e5, doi. 10.1093/nar/gkaa1072

By:

Phelps, Wesley A;
Carlson, Anne E;
Lee, Miler T

Publication type:

Article

Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. e4, doi. 10.1093/nar/gkaa1052

By:

Georgakopoulos-Soares, Ilias;
Mouratidis, Ioannis;
Parada, Guillermo E;
Matharu, Navneet;
Hemberg, Martin;
Ahituv, Nadav

Publication type:

Article

A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. e3, doi. 10.1093/nar/gkaa1041

By:

Shin, Junha;
Marx, Harald;
Richards, Alicia;
Vaneechoutte, Dries;
Jayaraman, Dhileepkumar;
Maeda, Junko;
Chakraborty, Sanhita;
Sussman, Michael;
Vandepoele, Klaas;
Ané, Jean-Michel;
Coon, Joshua;
Roy, Sushmita

Publication type:

Article

e-MutPath: computational modeling reveals the functional landscape of genetic mutations rewiring interactome networks.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. e2, doi. 10.1093/nar/gkaa1015

By:

Li, Yongsheng;
Burgman, Brandon;
Khatri, Ishaani S;
Pentaparthi, Sairahul R;
Su, Zhe;
McGrail, Daniel J;
Li, Yang;
Wu, Erxi;
Eckhardt, S Gail;
Sahni, Nidhi;
Yi, S Stephen

Publication type:

Article

TENET: gene network reconstruction using transfer entropy reveals key regulatory factors from single cell transcriptomic data.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 1, p. e1, doi. 10.1093/nar/gkaa1014

By:

Kim, Junil;
T. Jakobsen, Simon;
Natarajan, Kedar N;
Won, Kyoung-Jae

Publication type:

Article