Works in Nucleic Acids Research, 2019, Vol 47, Issue 1

Results: 43

A tightly regulated and adjustable CRISPR-dCas9 based AND gate in yeast.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 509, doi. 10.1093/nar/gky1191

By:

Hofmann, Anja;
Falk, Johannes;
Prangemeier, Tim;
Happel, Dominic;
Köber, Adrian;
Christmann, Andreas;
Koeppl, Heinz;
Kolmar, Harald

Publication type:

Article

TOE1 acts as a 3′ exonuclease for telomerase RNA and regulates telomere maintenance.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 391, doi. 10.1093/nar/gky1019

By:

Deng, Tingting;
Huang, Yan;
Weng, Kai;
Lin, Song;
Li, Yujing;
Shi, Guang;
Chen, Yali;
Huang, Junjiu;
Liu, Dan;
Ma, Wenbin;
Songyang, Zhou

Publication type:

Article

Trypanosomes can initiate nuclear export co-transcriptionally.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 266, doi. 10.1093/nar/gky1136

By:

Goos, Carina;
Dejung, Mario;
Wehman, Ann M;
M-Natus, Elisabeth;
Schmidt, Johannes;
Sunter, Jack;
Engstler, Markus;
Butter, Falk;
Kramer, Susanne

Publication type:

Article

Telomere shortening by transgenerational transmission of TNF-α-induced TERRA via ATF7.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 283, doi. 10.1093/nar/gky1149

By:

Liu, Binbin;
Maekawa, Toshio;
Yoshida, Keisuke;
Ly, Nhung Hong;
Inoue, Kimiko;
Hasegawa, Ayumi;
Chatton, Bruno;
Ogura, Atsuo;
Ishii, Shunsuke

Publication type:

Article

TDP-43 enhances translation of specific mRNAs linked to neurodegenerative disease.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 341, doi. 10.1093/nar/gky972

By:

Neelagandan, Nagammal;
Gonnella, Giorgio;
Dang, Stefan;
Janiesch, Philipp C;
Miller, Katharine K;
Küchler, Katrin;
Marques, Rita F;
Indenbirken, Daniela;
Alawi, Malik;
Grundhoff, Adam;
Kurtz, Stefan;
Duncan, Kent E

Publication type:

Article

Targeting individual cells by barcode in pooled sequence libraries.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. e4, doi. 10.1093/nar/gky856

By:

Ranu, Navpreet;
Villani, Alexandra-Chloé;
Hacohen, Nir;
Blainey, Paul C

Publication type:

Article

Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 450, doi. 10.1093/nar/gky1059

By:

Shen, Betty W;
Doyle, Lindsey;
Bradley, Phil;
Heiter, Daniel F;
Lunnen, Keith D;
Wilson, Geoffrey G;
Stoddard, Barry L

Publication type:

Article

Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 15, doi. 10.1093/nar/gky1110

By:

Gustmann, Henrik;
Segler, Anna-Lena J;
Gophane, Dnyaneshwar B;
Reuss, Andreas J;
Grünewald, Christian;
Braun, Markus;
Weigand, Julia E;
Sigurdsson, Snorri Th;
Wachtveitl, Josef

Publication type:

Article

Structural insights into a unique preference for 3′ terminal guanine of mirtron in Drosophila TUTase tailor.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 495, doi. 10.1093/nar/gky1116

By:

Cheng, Lin;
Li, Fudong;
Jiang, Yiyang;
Yu, Hailong;
Xie, Changlin;
Shi, Yunyu;
Gong, Qingguo

Publication type:

Article

Structural analysis of fungal CENP-H/I/K homologs reveals a conserved assembly mechanism underlying proper chromosome alignment.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 468, doi. 10.1093/nar/gky1108

By:

Hu, Liqiao;
Huang, Hao;
Hei, Mohan;
Yang, Yang;
Li, Sheng;
Liu, Yunshan;
Dou, Zhen;
Wu, Mengying;
Li, Jie;
Wang, Guang-zhong;
Yao, Xuebiao;
Liu, Hong;
He, Xiaojing;
Tian, Wei

Publication type:

Article

Single-molecule imaging of DNA gyrase activity in living Escherichia coli.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 210, doi. 10.1093/nar/gky1143

By:

Stracy, Mathew;
Wollman, Adam J M;
Kaja, Elzbieta;
Gapinski, Jacek;
Lee, Ji-Eun;
Leek, Victoria A;
McKie, Shannon J;
Mitchenall, Lesley A;
Maxwell, Anthony;
Sherratt, David J;
Leake, Mark C;
Zawadzki, Pawel

Publication type:

Article

RNA polymerase III subunits C37/53 modulate rU:dA hybrid 3′ end dynamics during transcription termination.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 310, doi. 10.1093/nar/gky1109

By:

Mishra, Saurabh;
Maraia, Richard J

Publication type:

Article

Ribosomal protein eL24, involved in two intersubunit bridges, stimulates translation initiation and elongation.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 406, doi. 10.1093/nar/gky1083

By:

Kisly, Ivan;
Remme, Jaanus;
Tamm, Tiina

Publication type:

Article

Ribose-Map: a bioinformatics toolkit to map ribonucleotides embedded in genomic DNA.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. e5, doi. 10.1093/nar/gky874

By:

Gombolay, Alli L;
Vannberg, Fredrik O;
Storici, Francesca

Publication type:

Article

Resting cells rely on the DNA helicase component MCM2 to build cilia.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 134, doi. 10.1093/nar/gky945

By:

Casar Tena, Teresa;
Maerz, Lars D;
Szafranski, Karol;
Groth, Marco;
Blätte, Tamara J;
Donow, Cornelia;
Matysik, Sabrina;
Walther, Paul;
Jeggo, Penelope A;
Burkhalter, Martin D;
Philipp, Melanie

Publication type:

Article

The RecB helicase-nuclease tether mediates Chi hotspot control of RecBCD enzyme.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 197, doi. 10.1093/nar/gky1132

By:

Amundsen, Susan K;
Smith, Gerald R

Publication type:

Article

ProGeM: a framework for the prioritization of candidate causal genes at molecular quantitative trait loci.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. e3, doi. 10.1093/nar/gky837

By:

Stacey, David;
Fauman, Eric B;
Ziemek, Daniel;
Sun, Benjamin B;
Harshfield, Eric L;
Wood, Angela M;
Butterworth, Adam S;
Suhre, Karsten;
Paul, Dirk S

Publication type:

Article

N6-methyladenosine modification and METTL3 modulate enterovirus 71 replication.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 362, doi. 10.1093/nar/gky1007

By:

Hao, Haojie;
Hao, Sujuan;
Chen, Honghe;
Chen, Zhen;
Zhang, Yanfang;
Wang, Jun;
Wang, Hanzhong;
Zhang, Bo;
Qiu, Jianming;
Deng, Fei;
Guan, Wuxiang

Publication type:

Article

Methylation of UHRF1 by SET7 is essential for DNA double-strand break repair.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 184, doi. 10.1093/nar/gky975

By:

Hahm, Ja Young;
Kim, Ji-Young;
Park, Jin Woo;
Kang, Joo-Young;
Kim, Kee-Beom;
Kim, Se-Ryeon;
Cho, Hana;
Seo, Sang-Beom

Publication type:

Article

Kinetic pathways of topology simplification by Type-II topoisomerases in knotted supercoiled DNA.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 69, doi. 10.1093/nar/gky1174

By:

Ziraldo, Riccardo;
Hanke, Andreas;
Levene, Stephen D

Publication type:

Article

Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 93, doi. 10.1093/nar/gky1189

By:

Lee, Jae Young;
Kim, Young-Joo;
Lee, Chanseok;
Lee, Jae Gyung;
Yagyu, Hiromasa;
Tabata, Osamu;
Kim, Do-Nyun

Publication type:

Article

Inosine induces context-dependent recoding and translational stalling.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 3, doi. 10.1093/nar/gky1163

By:

Licht, Konstantin;
Hartl, Markus;
Amman, Fabian;
Anrather, Dorothea;
Janisiw, Michael P;
Jantsch, Michael F

Publication type:

Article

IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 375, doi. 10.1093/nar/gky1012

By:

Müller, Simon;
Glaß, Markus;
Singh, Anurag K;
Haase, Jacob;
Bley, Nadine;
Fuchs, Tommy;
Lederer, Marcell;
Dahl, Andreas;
Huang, Huilin;
Chen, Jianjun;
Posern, Guido;
Hüttelmaier, Stefan

Publication type:

Article

Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 122, doi. 10.1093/nar/gky937

By:

Tellier, Michael;
Chalmers, Ronald

Publication type:

Article

Genome-wide mapping of 8-oxo-7,8-dihydro-2′-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 221, doi. 10.1093/nar/gky1152

By:

Amente, Stefano;
Di Palo, Giacomo;
Scala, Giovanni;
Castrignanò, Tiziana;
Gorini, Francesca;
Cocozza, Sergio;
Moresano, Angela;
Pucci, Piero;
Ma, Bin;
Stepanov, Irina;
Lania, Luigi;
Pelicci, Pier Giuseppe;
Dellino, Gaetano Ivan;
Majello, Barbara

Publication type:

Article

A genetic screen pinpoints ribonucleotide reductase residues that sustain dNTP homeostasis and specifies a highly mutagenic type of dNTP imbalance.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 237, doi. 10.1093/nar/gky1154

By:

Schmidt, Tobias T;
Sharma, Sushma;
Reyes, Gloria X;
Gries, Kerstin;
Gross, Maike;
Zhao, Boyu;
Yuan, Jui-Hung;
Wade, Rebecca;
Chabes, Andrei;
Hombauer, Hans

Publication type:

Article

Editorial: Preprints, citations and Nucleic Acids Research.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 1, doi. 10.1093/nar/gky1229

By:

Stoddard, Barry L;
Fox, Keith R

Publication type:

Article

E. coli gene regulatory networks are inconsistent with gene expression data.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 85, doi. 10.1093/nar/gky1176

By:

Larsen, Simon J;
Röttger, Richard;
Schmidt, Harald H H W;
Baumbach, Jan

Publication type:

Article

A dual-functional priming-capping loop of rhabdoviral RNA polymerases directs terminal de novo initiation and capping intermediate formation.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 299, doi. 10.1093/nar/gky1058

By:

Ogino, Minako;
Gupta, Nirmala;
Green, Todd J;
Ogino, Tomoaki

Publication type:

Article

DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 168, doi. 10.1093/nar/gky953

By:

Franz, Henriette;
Villarreal, Alejandro;
Heidrich, Stefanie;
Videm, Pavankumar;
Kilpert, Fabian;
Mestres, Ivan;
Calegari, Federico;
Backofen, Rolf;
Manke, Thomas;
Vogel, Tanja

Publication type:

Article

Dom34 mediates targeting of exogenous RNA in the antiviral OAS/RNase L pathway.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 432, doi. 10.1093/nar/gky1087

By:

Nogimori, Takuto;
Nishiura, Kyutatsu;
Kawashima, Sho;
Nagai, Takahiro;
Oishi, Yuka;
Hosoda, Nao;
Imataka, Hiroaki;
Kitamura, Yoshiaki;
Kitade, Yukio;
Hoshino, Shin-ichi

Publication type:

Article

DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 152, doi. 10.1093/nar/gky947

By:

Veland, Nicolas;
Lu, Yue;
Hardikar, Swanand;
Gaddis, Sally;
Zeng, Yang;
Liu, Bigang;
Estecio, Marcos R;
Takata, Yoko;
Lin, Kevin;
Tomida, Mary W;
Shen, Jianjun;
Saha, Debapriya;
Gowher, Humaira;
Zhao, Hongbo;
Chen, Taiping

Publication type:

Article

A combinatorial code for mRNA 3′-UTR-mediated translational control in the mouse oocyte.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 328, doi. 10.1093/nar/gky971

By:

Dai, Xing-Xing;
Jiang, Jun-Chao;
Sha, Qian-Qian;
Jiang, Yu;
Ou, Xiang-Hong;
Fan, Heng-Yu

Publication type:

Article

Detection of epigenetic field defects using a weighted epigenetic distance-based method.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. e6, doi. 10.1093/nar/gky882

By:

Wang, Ya;
Qian, Min;
Ruan, Peifeng;
Teschendorff, Andrew E;
Wang, Shuang

Publication type:

Article

Deducing putative ancestral forms of GNRA/receptor interactions from the ribosome.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 480, doi. 10.1093/nar/gky1111

By:

Calkins, Erin R;
Zakrevsky, Paul;
Keleshian, Vasken L;
Aguilar, Eduardo G;
Geary, Cody;
Jaeger, Luc

Publication type:

Article

De novo clustering of long reads by gene from transcriptomics data.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. e2, doi. 10.1093/nar/gky834

By:

Marchet, Camille;
Lecompte, Lolita;
Silva, Corinne Da;
Cruaud, Corinne;
Aury, Jean-Marc;
Nicolas, Jacques;
Peterlongo, Pierre

Publication type:

Article

CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. e1, doi. 10.1093/nar/gky820

By:

Lee, Jeewon;
Lim, Hyeonseob;
Jang, Hoon;
Hwang, Byungjin;
Lee, Joon Ho;
Cho, Junhyuk;
Lee, Ji Hyun;
Bang, Duhee

Publication type:

Article

BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 253, doi. 10.1093/nar/gky1125

By:

Gordeeva, Julia;
Morozova, Natalya;
Sierro, Nicolas;
Isaev, Artem;
Sinkunas, Tomas;
Tsvetkova, Ksenia;
Matlashov, Mikhail;
Truncaitė, Lidija;
Morgan, Richard D;
Ivanov, Nikolai V;
Siksnys, Virgis;
Zeng, Lanying;
Severinov, Konstantin

Publication type:

Article

Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 29, doi. 10.1093/nar/gky1118

By:

Yamagami, Ryota;
Kayedkhordeh, Mohammad;
Mathews, David H;
Bevilacqua, Philip C

Publication type:

Article

Binding of cellular nucleolin with the viral core RNA G-quadruplex structure suppresses HCV replication.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 56, doi. 10.1093/nar/gky1177

By:

Bian, Wen-Xiu;
Xie, Yan;
Wang, Xiao-Ning;
Xu, Guo-Hua;
Fu, Bo-Shi;
Li, Shu;
Long, Gang;
Zhou, Xiang;
Zhang, Xiao-Lian

Publication type:

Article

Assaying RNA structure with LASER-Seq.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 43, doi. 10.1093/nar/gky1172

By:

Zinshteyn, Boris;
Chan, Dalen;
England, Whitney;
Feng, Chao;
Green, Rachel;
Spitale, Robert C

Publication type:

Article

Alu insertion variants alter mRNA splicing.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 421, doi. 10.1093/nar/gky1086

By:

Payer, Lindsay M;
Steranka, Jared P;
Ardeljan, Daniel;
Walker, JaNiece;
Fitzgerald, Kathryn C;
Calabresi, Peter A;
Cooper, Thomas A;
Burns, Kathleen H

Publication type:

Article

Activation of the oncogenic transcription factor B-Myb via multisite phosphorylation and prolyl cis/trans isomerization.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 1, p. 103, doi. 10.1093/nar/gky935

By:

Werwein, Eugen;
Cibis, Hannah;
Hess, Daniel;
Klempnauer, Karl-Heinz

Publication type:

Article