Works in Nucleic Acids Research, 2016, Vol 44, Issue 9

Results: 51

Rad18 confers hematopoietic progenitor cell DNA damage tolerance independently of the Fanconi Anemia pathway in vivo.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4174, doi. 10.1093/nar/gkw072

By:

Yang Yang;
Poe, Jonathan C.;
Lisong Yang;
Fedoriw, Andrew;
Desai, Siddhi;
Magnuson, Terry;
Zhiguo Li;
Fedoriw, Yuri;
Araki, Kimi;
Yanzhe Gao;
Satoshi Tateishi;
Sarantopoulos, Stefanie;
Vaziri, Cyrus

Publication type:

Article

Corrigendum.

Published in:: Nucleic Acids Research, 2016, v. 44, n. 9, p. 4486, doi. 10.1093/nar/gkw091
Publication type:: Article

LncDisease: a sequence based bioinformatics tool for predicting lncRNA-disease associations.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 1, doi. 10.1093/nar/gkw093

By:

Junyi Wang;
Ruixia Ma;
Wei Ma;
Ji Chen;
Jichun Yang;
Yaguang Xi;
Qinghua Cui

Publication type:

Article

Using structural-based protein engineering to modulate the differential inhibition effects of SAUGI on human and HSV uracil DNA glycosylase.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4440, doi. 10.1093/nar/gkw185

By:

Hao-Ching Wang;
Chun-Han Ho;
Chia-Cheng Chou;
Tzu-Ping Ko;
Ming-Fen Huang;
Kai-Cheng Hsu;
Wang, Andrew H.-J.

Publication type:

Article

DNA motifs determining the accuracy of repeat duplication during CRISPR adaptation in Haloarcula hispanica.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4266, doi. 10.1093/nar/gkw260

By:

Rui Wang;
Ming Li;
Luyao Gong;
Songnian Hu;
Hua Xiang

Publication type:

Article

Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4067, doi. 10.1093/nar/gkw238

By:

Maojun Wang;
Pengcheng Wang;
Lili Tu;
Sitao Zhu;
Lin Zhang;
Zhonghua Li;
Qinghua Zhang;
Daojun Yuan;
Xianlong Zhang

Publication type:

Article

Is a fully wrapped SSB-DNA complex essential for Escherichia coli survival?

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4817, doi. 10.1093/nar/gkw262

By:

Waldman, Vincent M.;
Weiland, Elizabeth;
Kozlov, Alexander G.;
Lohman, Timothy M.

Publication type:

Article

Identification of a small-molecule ligand of the epigenetic reader protein Spindlin1 via a versatile screening platform.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 1, doi. 10.1093/nar/gkw089

By:

Wagner, Tobias;
Greschik, Holger;
Burgahn, Teresa;
Schmidtkunz, Karin;
Schott, Anne-Kathrin;
McMillan, Joel;
Baranauskienė, Lina;
Yan Xiong;
Fedorov, Oleg;
Jian Jin;
Oppermann, Udo;
Matulis, Daumantas;
Schüle, Roland;
Jung, Manfred

Publication type:

Article

An RNA trapping mechanism in Alphavirus mRNA promotes ribosome stalling and translation initiation.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4368, doi. 10.1093/nar/gkw172

By:

Toribio, René;
Díaz-López, Irene;
Boskovic, Jasminka;
Ventoso, Iván

Publication type:

Article

Rational design of novel N-alkyl-N capped biostable RNA nanostructures for efficient long-term inhibition of gene expression.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4354, doi. 10.1093/nar/gkw169

By:

Terrazas, Montserrat;
Ivani, Ivan;
Villegas, Núria;
Paris, Clément;
Salvans, Cándida;
Brun-Heath, Isabelle;
Orozco, Modesto

Publication type:

Article

Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4123, doi. 10.1093/nar/gkv1530

By:

Yu Gyoung Tak;
Yuli Hung;
Lijing Yao;
Grimmer, Matthew R.;
Do, Albert;
Bhakta, Mital S.;
O'Geen, Henriette;
Segal, David J.;
Farnham, Peggy J.

Publication type:

Article

Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4147, doi. 10.1093/nar/gkw008

By:

Shota Suzuki;
Hiroaki Kato;
Yutaka Suzuki;
Yuji Chikashige;
Yasushi Hiraoka;
Hiroshi Kimura;
Koji Nagao;
Chikashi Obuse;
Shinya Takahata;
Yota Murakami

Publication type:

Article

Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4105, doi. 10.1093/nar/gkv1528

By:

Sunkel, Benjamin;
Dayong Wu;
Zhong Chen;
Chiou-Miin Wang;
Xiangtao Liu;
Zhenqing Ye;
Horning, Aaron M.;
Liu, Joseph;
Mahalingam, Devalingam;
Lopez-Nicora, Horacio;
Chun-Lin Lin;
Goodfellow, Paul J.;
Clinton, Steven K.;
Jin, Victor X.;
Chun-Liang Chen;
Tim H.-M. Huang;
Qianben Wang

Publication type:

Article

Pharmacologic efficacy of PU.1 inhibition by heterocyclic dications: a mechanistic analysis.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4005, doi. 10.1093/nar/gkw229

By:

Stephens, Dominique C.;
Hye Mi Kim;
Kumar, Arvind;
Farahat, Abdelbasset A.;
Boykin, David W.;
Poon, Gregory M. K.

Publication type:

Article

Circular RNA profile in gliomas revealed by identification tool UROBORUS.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 1, doi. 10.1093/nar/gkw075

By:

Xiaofeng Song;
Naibo Zhang;
Ping Han;
Byoung-San Moon;
Lai, Rose K.;
Kai Wang;
Wange Lu

Publication type:

Article

Horizontal transfer of DNA methylation patterns into bacterial chromosomes.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4460, doi. 10.1093/nar/gkw230

By:

Jung-Eun Shin;
Lin, Chris;
Han N. Lim

Publication type:

Article

Long-term dual-color tracking of genomic loci by modified sgRNAs of the CRISPR/Cas9 system.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 1, doi. 10.1093/nar/gkw066

By:

Shipeng Shao;
Weiwei Zhang;
Huan Hu;
Boxin Xue;
Jinshan Qin;
Chaoying Sun;
Yuao Sun;
Wensheng Wei;
Yujie Sun

Publication type:

Article

Epigenome-wide effects of vitamin D and their impact on the transcriptome of human monocytes involve CTCF.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4090, doi. 10.1093/nar/gkv1519

By:

Seuter, Sabine;
Neme, Antonio;
Carlberg, Carsten

Publication type:

Article

Homologous DNA strand exchange activity of the human mitochondrial DNA helicase TWINKLE.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4200, doi. 10.1093/nar/gkw098

By:

Sen, Doyel;
Patel, Gayatri;
Patel, Smita S.

Publication type:

Article

More than 10% of yeast genes are related to genome stability and influence cellular senescence via rDNA maintenance.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4211, doi. 10.1093/nar/gkw110

By:

Kimiko Saka;
Akihiro Takahashi;
Mariko Sasaki;
Takehiko Kobayashi

Publication type:

Article

Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4037, doi. 10.1093/nar/gkw250

By:

Pundhir, Sachin;
Bagger, Frederik O.;
Lauridsen, Felicia B.;
Rapin, Nicolas;
Porse, Bo T.

Publication type:

Article

DHX29 reduces leaky scanning through an upstream AUG codon regardless of its nucleotide context.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4252, doi. 10.1093/nar/gkw240

By:

Pisareva, Vera P.;
Pisarev, Andrey V.

Publication type:

Article

Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4304, doi. 10.1093/nar/gkw244

By:

Meyer, Britta;
Wurm, Jan Philip;
Sharma, Sunny;
Immer, Carina;
Pogoryelov, Denys;
Kötter, Peter;
Lafontaine, Denis L. J.;
Wöhnert, Jens;
Entian, Karl-Dieter

Publication type:

Article

Multifaceted enrichment analysis of RNA-RNA crosstalk reveals cooperating micro-societies in human colorectal cancer.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4025, doi. 10.1093/nar/gkw245

By:

Mazza, Tommaso;
Mazzoccoli, Gianluigi;
Fusilli, Caterina;
Capocefalo, Daniele;
Panza, Anna;
Biagini, Tommaso;
Castellana, Stefano;
Gentile, Annamaria;
De Cata, Angelo;
Palumbo, Orazio;
Stallone, Raffaella;
Rubino, Rosa;
Carella, Massimo;
Piepoli, Ada

Publication type:

Article

Diverse CRISPR-Cas responses and dramatic cellular DNA changes and cell death in pKEF9-conjugated Sulfolobus species.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4233, doi. 10.1093/nar/gkw286

By:

Guannan Liu;
Qunxin She;
Garrett, Roger A.

Publication type:

Article

Pif1 is a force-regulated helicase.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4330, doi. 10.1093/nar/gkw295

By:

Jing-Hua Li;
Wen-Xia Lin;
Bo Zhang;
Da-Guan Nong;
Hai-Peng Ju;
Jian-Bing Ma;
Chun-Hua Xu;
Fang-Fu Ye;
Xu Guang Xi;
Ming Li;
Ying Lu;
Shuo-Xing Dou

Publication type:

Article

A structural view of microRNA-target recognition.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 1, doi. 10.1093/nar/gkw043

By:

Leoni, Guido;
Tramontano, Anna

Publication type:

Article

Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4396, doi. 10.1093/nar/gkw154

By:

Kulkarni, Manasi;
Nirwan, Neha;
van Aelst, Kara;
Szczelkun, Mark D.;
Saikrishnan, Kayarat

Publication type:

Article

The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 3989, doi. 10.1093/nar/gkw271

By:

Knott, Gavin J.;
Bond, Charles S.;
Fox, Archa H.

Publication type:

Article

Insertion of oxidized nucleotide triggers rapid DNA polymerase opening.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4409, doi. 10.1093/nar/gkw174

By:

Taejin Kim;
Freudenthal, Bret D.;
Beard, William A.;
Wilson, Samuel H.;
Schlick, Tamar

Publication type:

Article

The mutation spectrum in genomic late replication domains shapes mammalian GC content.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4222, doi. 10.1093/nar/gkw268

By:

Kenigsberg, Ephraim;
Yishai Yehuda;
Marjavaara, Lisette;
Keszthelyi, Andrea;
Chabes, Andrei;
Tanay, Amos;
Simon, Itamar

Publication type:

Article

Using intron position conservation for homology-based gene prediction.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 1, doi. 10.1093/nar/gkw092

By:

Keilwagen, Jens;
Wenk, Michael;
Erickson, Jessica L.;
Schattat, Martin H.;
Grau, Jan;
Hartung, Frank

Publication type:

Article

A PPR protein in the PLS subfamily stabilizes the 5'-end of processed rpl16 mRNAs in maize chloroplasts.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4278, doi. 10.1093/nar/gkw270

By:

Hammani, Kamel;
Mizuki Takenaka;
Miranda, Rafael;
Barkan, Alice

Publication type:

Article

The evolutionary pathway from a biologically inactive polypeptide sequence to a folded, active structural mimic of DNA.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4289, doi. 10.1093/nar/gkw234

By:

Kanwar, Nisha;
Roberts, Gareth A.;
Cooper, Laurie P.;
Stephanou, Augoustinos S.;
Dryden, David T. F.

Publication type:

Article

Targeting BRCA1- and BRCA2-deficient cells with RAD52 small molecule inhibitors.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4189, doi. 10.1093/nar/gkw087

By:

Fei Huang;
Goyal, Nadish;
Sullivan, Katherine;
Hanamshet, Kritika;
Patel, Mikir;
Mazina, Olga M.;
Wang, Charles X.;
An, W. Frank;
Spoonamore, James;
Metkar, Shailesh;
Emmitte, Kyle A.;
Cocklin, Simon;
Skorski, Tomasz;
Mazin, Alexander V.

Publication type:

Article

Effective knockdown of Drosophila long non-coding RNAs by CRISPR interference.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 1, doi. 10.1093/nar/gkw063

By:

Ghosh, Sanjay;
Tibbit, Charlotte;
Ji-Long Liu

Publication type:

Article

Quantification of read species behavior within whole genome sequencing of cancer genomes for the stratification and visualization of genomic variation.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 1, doi. 10.1093/nar/gkw031

By:

Hibsh, Dror;
Buetow, Kenneth H.;
Yaari, Gur;
Efroni, Sol

Publication type:

Article

Knock-in of large reporter genes in human cells via CRISPR/Cas9-induced homology-dependent and independent DNA repair.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 1, doi. 10.1093/nar/gkw064

By:

Xiangjun He;
Chunlai Tan;
Feng Wang;
Yaofeng Wang;
Rui Zhou;
Dexuan Cui;
Wenxing You;
Hui Zhao;
Jianwei Ren;
Bo Feng

Publication type:

Article

Shwachman-Bodian-Diamond syndrome (SBDS) protein deficiency impairs translation re-initiation from C/EBPα and C/EBPβ mRNAs.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4134, doi. 10.1093/nar/gkw005

By:

Kyungmin In;
Zaini, Mohamad A.;
Müller, Christine;
Warren, Alan J.;
von Lindern, Marieke;
Calkhoven, Cornelis F.

Publication type:

Article

Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 1, doi. 10.1093/nar/gkw048

By:

HafezQorani, Saber;
Lafzi, Atefeh;
de Bruin, Ruben G.;
van Zonneveld, Anton Jan;
van der Veer, Eric P.;
Son, Yeşim Aydın;
Kazan, Hilal

Publication type:

Article

Exclusion of small terminase mediated DNA threading models for genome packaging in bacteriophage T4.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4425, doi. 10.1093/nar/gkw184

By:

Song Gao;
Liang Zhang;
Rao, Venigalla B.

Publication type:

Article

Tat-dependent production of an HIV-1 TAR-encoded miRNA-like small RNA.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4340, doi. 10.1093/nar/gkw167

By:

Harwig, Alex;
Jongejan, Aldo;
van Kampen, Antoine H. C.;
Berkhout, Ben;
Das, Atze T.

Publication type:

Article

A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4450, doi. 10.1093/nar/gkw206

By:

Durand, Guillaume;
Dausse, Eric;
Goux, Emma;
Fiore, Emmanuelle;
Peyrin, Eric;
Ravelet, Corinne;
Toulmé, Jean-Jacques

Publication type:

Article

G-quadruplexes as novel cis-elements controlling transcription during embryonic development.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4163, doi. 10.1093/nar/gkw011

By:

David, Aldana P.;
Margarit, Ezequiel;
Domizi, Pablo;
Banchio, Claudia;
Armas, Pablo;
Calcaterra, Nora B.

Publication type:

Article

Long-timescale dynamics of the Drew-Dickerson dodecamer.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4052, doi. 10.1093/nar/gkw264

By:

Dans, Pablo D.;
Danilāne, Linda;
Ivani, Ivan;
Dršata, Tomáš;
Lankaš, Filip;
Hospital, Adam;
Walther, Jürgen;
Pujagut, Ricard Illa;
Battistini, Federica;
Gelpí, Josep Lluis;
Lavery, Richard;
Orozco, Modesto

Publication type:

Article

Consequences of Cas9 cleavage in the chromosome of Escherichia coli.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4243, doi. 10.1093/nar/gkw223

By:

Lun Cui;
Bikard, David

Publication type:

Article

Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4472, doi. 10.1093/nar/gkw231

By:

Cress, Brady F.;
Jones, J. Andrew;
Kim, Daniel C.;
Leitz, Quentin D.;
Englaender, Jacob A.;
Collins, Shannon M.;
Linhardt, Robert J.;
Koffas, Mattheos A. G.

Publication type:

Article

Rbfox proteins regulate microRNA biogenesis by sequence-specific binding to their precursors and target downstream Dicer.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4381, doi. 10.1093/nar/gkw177

By:

Yu Chen;
Zubovic, Lorena;
Fan Yang;
Godin, Katherine;
Pavelitz, Tom;
Castellanos, Javier;
Macchi, Paolo;
Varani, Gabriele

Publication type:

Article

Deciphering the genomic targets of alkylating polyamide conjugates using high-throughput sequencing.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4014, doi. 10.1093/nar/gkw283

By:

Chandran, Anandhakumar;
Syed, Junetha;
Taylor, Rhys D.;
Gengo Kashiwazaki;
Shinsuke Sato;
Kaori Hashiya;
Toshikazu Bando;
Hiroshi Sugiyama

Publication type:

Article

Mechanisms of small molecule-DNA interactions probed by single-molecule force spectroscopy.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 3971, doi. 10.1093/nar/gkw237

By:

Almaqwashi, Ali A.;
Thayaparan Paramanathan;
Rouzina, Ioulia;
Williams, Mark C.

Publication type:

Article