Works in Nucleic Acids Research, 2019, Vol 47, Issue 21

Results: 47

Biogenesis of RNase P RNA from an intron requires co-assembly with cognate protein subunits.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11480, doi. 10.1093/nar/gkz983

By:

Palsule, Geeta;
Gopalan, Venkat;
Simcox, Amanda

Publication type:

Article

Characterization of the Type III restriction endonuclease PstII from Providencia stuartii.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11477, doi. 10.1093/nar/gkz971

By:

Sears, Alice;
Peakman, Luke J;
Wilson, Geoffrey G;
Szczelkun, Mark D

Publication type:

Article

Control of ϕC31 integrase-mediated site-specific recombination by protein trans-splicing.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11452, doi. 10.1093/nar/gkz936

By:

Olorunniji, Femi J;
Lawson-Williams, Makeba;
McPherson, Arlene L;
Paget, Jane E;
Stark, W Marshall;
Rosser, Susan J

Publication type:

Article

New insights into protein–DNA binding specificity from hydrogen bond based comparative study.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11103, doi. 10.1093/nar/gkz963

By:

Lin, Maoxuan;
Guo, Jun-tao

Publication type:

Article

RB, p130 and p107 differentially repress G1/S and G2/M genes after p53 activation.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11197, doi. 10.1093/nar/gkz961

By:

Schade, Amy E;
Fischer, Martin;
DeCaprio, James A

Publication type:

Article

Characterization and repurposing of the endogenous Type I-F CRISPR–Cas system of Zymomonas mobilis for genome engineering.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11461, doi. 10.1093/nar/gkz940

By:

Zheng, Yanli;
Han, Jiamei;
Wang, Baiyang;
Hu, Xiaoyun;
Li, Runxia;
Shen, Wei;
Ma, Xiangdong;
Ma, Lixin;
Yi, Li;
Yang, Shihui;
Peng, Wenfang

Publication type:

Article

A dynamic i-motif with a duplex stem-loop in the long terminal repeat promoter of the HIV-1 proviral genome modulates viral transcription.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11057, doi. 10.1093/nar/gkz937

By:

Ruggiero, Emanuela;
Lago, Sara;
Šket, Primož;
Nadai, Matteo;
Frasson, Ilaria;
Plavec, Janez;
Richter, Sara N

Publication type:

Article

Branch site bulge conformations in domain 6 determine functional sugar puckers in group II intron splicing.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11430, doi. 10.1093/nar/gkz965

By:

Plangger, Raphael;
Juen, Michael Andreas;
Hoernes, Thomas Philipp;
Nußbaumer, Felix;
Kremser, Johannes;
Strebitzer, Elisabeth;
Klingler, David;
Erharter, Kevin;
Tollinger, Martin;
Erlacher, Matthias David;
Kreutz, Christoph

Publication type:

Article

uS3/Rps3 controls fidelity of translation termination and programmed stop codon readthrough in co-operation with eIF3.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11326, doi. 10.1093/nar/gkz929

By:

Poncová, Kristýna;
Wagner, Susan;
Jansen, Myrte Esmeralda;
Beznosková, Petra;
Gunišová, Stanislava;
Herrmannová, Anna;
Zeman, Jakub;
Dong, Jinsheng;
Valášek, Leoš Shivaya

Publication type:

Article

Assembly and annotation of the mitochondrial minicircle genome of a differentiation-competent strain of Trypanosoma brucei.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11304, doi. 10.1093/nar/gkz928

By:

Cooper, Sinclair;
Wadsworth, Elizabeth S;
Ochsenreiter, Torsten;
Ivens, Alasdair;
Savill, Nicholas J;
Schnaufer, Achim

Publication type:

Article

Controlling aggregation of cholesterol-modified DNA nanostructures.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11441, doi. 10.1093/nar/gkz914

By:

Ohmann, Alexander;
Göpfrich, Kerstin;
Joshi, Himanshu;
Thompson, Rebecca F;
Sobota, Diana;
Ranson, Neil A;
Aksimentiev, Aleksei;
Keyser, Ulrich F

Publication type:

Article

Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11355, doi. 10.1093/nar/gkz911

By:

Emperle, Max;
Adam, Sabrina;
Kunert, Stefan;
Dukatz, Michael;
Baude, Annika;
Plass, Christoph;
Rathert, Philipp;
Bashtrykov, Pavel;
Jeltsch, Albert

Publication type:

Article

CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11181, doi. 10.1093/nar/gkz908

By:

Clarkson, Christopher T;
Deeks, Emma A;
Samarista, Ralph;
Mamayusupova, Hulkar;
Zhurkin, Victor B;
Teif, Vladimir B

Publication type:

Article

Streamlining effects of extra telomeric repeat on telomeric DNA folding revealed by fluorescence-force spectroscopy.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11044, doi. 10.1093/nar/gkz906

By:

Mitra, Jaba;
Ha, Taekjip

Publication type:

Article

The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11090, doi. 10.1093/nar/gkz905

By:

Dans, Pablo D;
Balaceanu, Alexandra;
Pasi, Marco;
Patelli, Alessandro S;
Petkevičiūtė, Daiva;
Walther, Jürgen;
Hospital, Adam;
Bayarri, Genís;
Lavery, Richard;
Maddocks, John H;
Orozco, Modesto

Publication type:

Article

Direct interplay between stereochemistry and conformational preferences in aminoacylated oligoribonucleotides.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11077, doi. 10.1093/nar/gkz902

By:

Polyansky, Anton A;
Kreuter, Mathias;
Sutherland, John D;
Zagrovic, Bojan

Publication type:

Article

A novel and translational role for autophagy in antisense oligonucleotide trafficking and activity.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11284, doi. 10.1093/nar/gkz901

By:

Ochaba, Joseph;
Powers, Andrew F;
Tremble, Kaitlyn A;
Greenlee, Sarah;
Post, Noah M;
Matson, John E;
MacLeod, A Robert;
Guo, Shuling;
Aghajan, Mariam

Publication type:

Article

HER3-targeted protein chimera forms endosomolytic capsomeres and self-assembles into stealth nucleocapsids for systemic tumor homing of RNA interference in vivo.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11020, doi. 10.1093/nar/gkz900

By:

Alonso-Valenteen, Felix;
Pacheco, Sayuri;
Srinivas, Dustin;
Rentsendorj, Altan;
Chu, David;
Lubow, Jay;
Sims, Jessica;
Miao, Tianxin;
Mikhael, Simoun;
Hwang, Jae Youn;
Abrol, Ravinder;
Medina Kauwe, Lali K

Publication type:

Article

GLP-catalyzed H4K16me1 promotes 53BP1 recruitment to permit DNA damage repair and cell survival.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 10977, doi. 10.1093/nar/gkz897

By:

Lu, Xiaopeng;
Tang, Ming;
Zhu, Qian;
Yang, Qiaoyan;
Li, Zhiming;
Bao, Yantao;
Liu, Ge;
Hou, Tianyun;
Lv, Yafei;
Zhao, Ying;
Wang, Haiying;
Yang, Yang;
Cheng, Zhongyi;
Wen, He;
Liu, Baohua;
Xu, Xingzhi;
Gu, Luo;
Zhu, Wei-Guo

Publication type:

Article

Ring-shaped replicative helicase encircles double-stranded DNA during unwinding.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11344, doi. 10.1093/nar/gkz893

By:

Joo, Sihwa;
Chung, Bong H;
Lee, Mina;
Ha, Tai H

Publication type:

Article

Deciphering the activation and recognition mechanisms of Staphylococcus aureus response regulator ArlR.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11418, doi. 10.1093/nar/gkz891

By:

Ouyang, Zhenlin;
Zheng, Fang;
Chew, Jared Y;
Pei, Yingmei;
Zhou, Jinhong;
Wen, Keqing;
Han, Miao;
Lemieux, M Joanne;
Hwang, Peter M;
Wen, Yurong

Publication type:

Article

Crystal structure of the transcriptional repressor DdrO: insight into the metalloprotease/repressor-controlled radiation response in Deinococcus.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11403, doi. 10.1093/nar/gkz883

By:

de Groot, Arjan;
Siponen, Marina I;
Magerand, Romaric;
Eugénie, Nicolas;
Martin-Arevalillo, Raquel;
Doloy, Jade;
Lemaire, David;
Brandelet, Géraldine;
Parcy, François;
Dumas, Renaud;
Roche, Philippe;
Servant, Pascale;
Confalonieri, Fabrice;
Arnoux, Pascal;
Pignol, David;
Blanchard, Laurence

Publication type:

Article

Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3S HDAC complex in C. elegans.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11164, doi. 10.1093/nar/gkz880

By:

Beurton, Flore;
Stempor, Przemyslaw;
Caron, Matthieu;
Appert, Alex;
Dong, Yan;
Chen, Ron A-j;
Cluet, David;
Couté, Yohann;
Herbette, Marion;
Huang, Ni;
Polveche, Hélène;
Spichty, Martin;
Bedet, Cécile;
Ahringer, Julie;
Palladino, Francesca

Publication type:

Article

Transcriptome signature of cellular senescence.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11476, doi. 10.1093/nar/gkz879

By:

Casella, Gabriel;
Munk, Rachel;
Kim, Kyoung Mi;
Piao, Yulan;
De, Supriyo;
Abdelmohsen, Kotb;
Gorospe, Myriam

Publication type:

Article

The regulation of sequence specific NF-κB DNA binding and transcription by IKKβ phosphorylation of NF-κB p50 at serine 80.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11151, doi. 10.1093/nar/gkz873

By:

Smith, Emma L;
Somma, Domenico;
Kerrigan, David;
McIntyre, Zoe;
Cole, John J;
Liang, Kai Ling;
Kiely, Patrick A;
Keeshan, Karen;
Carmody, Ruaidhrí J

Publication type:

Article

Retrons and their applications in genome engineering.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11007, doi. 10.1093/nar/gkz865

By:

Simon, Anna J;
Ellington, Andrew D;
Finkelstein, Ilya J

Publication type:

Article

Exogenous pyruvate represses histone gene expression and inhibits cancer cell proliferation via the NAMPT–NAD<sup>+</sup>–SIRT1 pathway.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11132, doi. 10.1093/nar/gkz864

By:

Ma, Rui;
Wu, Yinsheng;
Zhai, Yansheng;
Hu, Bicheng;
Ma, Wei;
Yang, Wenqiang;
Yu, Qi;
Chen, Zhen;
Workman, Jerry L;
Yu, Xilan;
Li, Shanshan

Publication type:

Article

ZAR1 and ZAR2 are required for oocyte meiotic maturation by regulating the maternal transcriptome and mRNA translational activation.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11387, doi. 10.1093/nar/gkz863

By:

Rong, Yan;
Ji, Shu-Yan;
Zhu, Ye-Zhang;
Wu, Yun-Wen;
Shen, Li;
Fan, Heng-Yu

Publication type:

Article

Chromatin Assembly Factor 1 (CAF-1) facilitates the establishment of facultative heterochromatin during pluripotency exit.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11114, doi. 10.1093/nar/gkz858

By:

Cheng, Liang;
Zhang, Xu;
Wang, Yan;
Gan, Haiyun;
Xu, Xiaowei;
Lv, Xiangdong;
Hua, Xu;
Que, Jianwen;
Ordog, Tamas;
Zhang, Zhiguo

Publication type:

Article

Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 10994, doi. 10.1093/nar/gkz841

By:

Tørresen, Ole K;
Star, Bastiaan;
Mier, Pablo;
Andrade-Navarro, Miguel A;
Bateman, Alex;
Jarnot, Patryk;
Gruca, Aleksandra;
Grynberg, Marcin;
Kajava, Andrey V;
Promponas, Vasilis J;
Anisimova, Maria;
Jakobsen, Kjetill S;
Linke, Dirk

Publication type:

Article

Atomistic insight into the kinetic pathways for Watson–Crick to Hoogsteen transitions in DNA.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11069, doi. 10.1093/nar/gkz837

By:

Vreede, Jocelyne;
Pérez de Alba Ortíz, Alberto;
Bolhuis, Peter G;
Swenson, David W H

Publication type:

Article

Ribosome assembly defects subvert initiation Factor3 mediated scrutiny of bona fide start signal.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11368, doi. 10.1093/nar/gkz825

By:

Sharma, Himanshu;
Anand, B

Publication type:

Article

UBR5 interacts with the replication fork and protects DNA replication from DNA polymerase η toxicity.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11268, doi. 10.1093/nar/gkz824

By:

Cipolla, Lina;
Bertoletti, Federica;
Maffia, Antonio;
Liang, Chih-Chao;
Lehmann, Alan R;
Cohn, Martin A;
Sabbioneda, Simone

Publication type:

Article

Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11250, doi. 10.1093/nar/gkz820

By:

Smith, Rebecca;
Lebeaupin, Théo;
Juhász, Szilvia;
Chapuis, Catherine;
D'Augustin, Ostiane;
Dutertre, Stéphanie;
Burkovics, Peter;
Biertümpfel, Christian;
Timinszky, Gyula;
Huet, Sébastien

Publication type:

Article

funtrp: identifying protein positions for variation driven functional tuning.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. e142, doi. 10.1093/nar/gkz818

By:

Miller, Maximilian;
Vitale, Daniel;
Kahn, Peter C;
Rost, Burkhard;
Bromberg, Yana

Publication type:

Article

CDK and Mec1/Tel1-catalyzed phosphorylation of Sae2 regulate different responses to DNA damage.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11238, doi. 10.1093/nar/gkz814

By:

Yu, Tai-Yuan;
Garcia, Valerie E;
Symington, Lorraine S

Publication type:

Article

Low temperature isothermal amplification of microsatellites drastically reduces stutter artifact formation and improves microsatellite instability detection in cancer.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. e141, doi. 10.1093/nar/gkz811

By:

Daunay, Antoine;
Duval, Alex;
Baudrin, Laura G;
Buhard, Olivier;
Renault, Victor;
Deleuze, Jean-François;
How-Kit, Alexandre

Publication type:

Article

Single-molecule visualization of human BLM helicase as it acts upon double- and single-stranded DNA substrates.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11225, doi. 10.1093/nar/gkz810

By:

Xue, Chaoyou;
Daley, James M;
Xue, Xiaoyu;
Steinfeld, Justin;
Kwon, Youngho;
Sung, Patrick;
Greene, Eric C

Publication type:

Article

Next-generation forward genetic screens: using simulated data to improve the design of mapping-by-sequencing experiments in Arabidopsis.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. e140, doi. 10.1093/nar/gkz806

By:

Wilson-Sánchez, David;
Lup, Samuel Daniel;
Sarmiento-Mañús, Raquel;
Ponce, María Rosa;
Micol, José Luis

Publication type:

Article

A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. e139, doi. 10.1093/nar/gkz800

By:

Levitsky, Victor;
Zemlyanskaya, Elena;
Oshchepkov, Dmitry;
Podkolodnaya, Olga;
Ignatieva, Elena;
Grosse, Ivo;
Mironova, Victoria;
Merkulova, Tatyana

Publication type:

Article

A novel mode of DnaA–DnaA interaction promotes ADP dissociation for reactivation of replication initiation activity.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. 11209, doi. 10.1093/nar/gkz795

By:

Sugiyama, Ryo;
Kasho, Kazutoshi;
Miyoshi, Kenya;
Ozaki, Shogo;
Kagawa, Wataru;
Kurumizaka, Hitoshi;
Katayama, Tsutomu

Publication type:

Article

cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. e138, doi. 10.1093/nar/gkz789

By:

DePasquale, Erica A K;
Schnell, Daniel;
Dexheimer, Phillip;
Ferchen, Kyle;
Hay, Stuart;
Chetal, Kashish;
Valiente-Alandí, Íñigo;
Blaxall, Burns C;
Grimes, H Leighton;
Salomonis, Nathan

Publication type:

Article

A tight cold-inducible switch built by coupling thermosensitive transcriptional and proteolytic regulatory parts.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. e137, doi. 10.1093/nar/gkz785

By:

Zheng, Yang;
Meng, Fankang;
Zhu, Zihui;
Wei, Weijia;
Sun, Zhi;
Chen, Jinchun;
Yu, Bo;
Lou, Chunbo;
Chen, Guo-Qiang

Publication type:

Article

Assessment of kinship detection using RNA-seq data.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. e136, doi. 10.1093/nar/gkz776

By:

Blay, Natalia;
Casas, Eduard;
Galván-Femenía, Iván;
Graffelman, Jan;
de Cid, Rafael;
Vavouri, Tanya

Publication type:

Article

Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. e135, doi. 10.1093/nar/gkz775

By:

Ivanov, Maxim;
Ivanov, Mikhail;
Kasianov, Artem;
Rozhavskaya, Ekaterina;
Musienko, Sergey;
Baranova, Ancha;
Mileyko, Vladislav

Publication type:

Article

Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. e133, doi. 10.1093/nar/gkz601

By:

Pont, Frédéric;
Tosolini, Marie;
Fournié, Jean J

Publication type:

Article

regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 21, p. e134, doi. 10.1093/nar/gkz774

By:

Zhang, Shijie;
He, Yukun;
Liu, Huanhuan;
Zhai, Haoyu;
Huang, Dandan;
Yi, Xianfu;
Dong, Xiaobao;
Wang, Zhao;
Zhao, Ke;
Zhou, Yao;
Wang, Jianhua;
Yao, Hongcheng;
Xu, Hang;
Yang, Zhenglu;
Sham, Pak Chung;
Chen, Kexin;
Li, Mulin Jun

Publication type:

Article