Nucleic Acids Research

Survey and Summary:

Petr V. Sergiev, Alexey A. Bogdanov, and Olga A. Dontsova

Ribosomal RNA guanine-(N2)-methyltransferases and their targets
Nucleic Acids Research Advance Access published on March 27, 2007
Nucl. Acids Res. 2007 35: 2295-2301; doi:10.1093/nar/gkm104 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Computational Biology:

Hongwei Wu, Fenglou Mao, Victor Olman, and Ying Xu

Hierarchical classification of functionally equivalent genes in prokaryotes
Nucleic Acids Research Advance Access published on March 11, 2007
Nucl. Acids Res. 2007 35: 2125-2140; doi:10.1093/nar/gkl1114 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Raquel Quatrini, Claudia Lefimil, Felipe A. Veloso, Inti Pedroso, David S. Holmes, and Eugenia Jedlicki

Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans
Nucleic Acids Research Advance Access published on March 13, 2007
Nucl. Acids Res. 2007 35: 2153-2166; doi:10.1093/nar/gkm068 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Dariusz Przybylski and Burkhard Rost

Consensus sequences improve PSI-BLAST through mimicking profile–profile alignments
Nucleic Acids Research Advance Access published on March 16, 2007
Nucl. Acids Res. 2007 35: 2238-2246; doi:10.1093/nar/gkm107 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Giacomo Finocchiaro, Francesco Mattia Mancuso, Davide Cittaro, and Heiko Muller

Graph-based identification of cancer signaling pathways from published gene expression signatures using PubLiME
Nucleic Acids Research Advance Access published on March 27, 2007
Nucl. Acids Res. 2007 35: 2343-2355; doi:10.1093/nar/gkm119 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Genomics:

Jason A. Hackney, Gretchen M. Ehrenkaufer, and Upinder Singh

Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference
Nucleic Acids Research Advance Access published on March 13, 2007
Nucl. Acids Res. 2007 35: 2141-2152; doi:10.1093/nar/gkm028 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Yanglong Zhu, Dileep K. Pulukkunat, and Yong Li

Deciphering RNA structural diversity and systematic phylogeny from microbial metagenomes
Nucleic Acids Research Advance Access published on March 27, 2007
Nucl. Acids Res. 2007 35: 2283-2294; doi:10.1093/nar/gkm057 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Molecular Biology:

Zhong Yu, Paul-André Genest, Bas ter Riet, Kate Sweeney, Courtney DiPaolo, Rudo Kieft, Evangelos Christodoulou, Anastassis Perrakis, Jana M. Simmons, Robert P. Hausinger, Henri G.A.M. van Luenen, Daniel J. Rigden, Robert Sabatini, and Piet Borst

The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase
Nucleic Acids Research Advance Access published on March 27, 2007
Nucl. Acids Res. 2007 35: 2107-2115; doi:10.1093/nar/gkm049 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Paul-André Genest, Bas ter Riet, Tony Cijsouw, Henri G.A.M. van Luenen, and Piet Borst

Telomeric localization of the modified DNA base J in the genome of the protozoan parasite Leishmania
Nucleic Acids Research Advance Access published on February 28, 2007
Nucl. Acids Res. 2007 35: 2116-2124; doi:10.1093/nar/gkm050 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Matthew A. Stoner, Scott S. Auerbach, Stephanie M. Zamule, Stephen C. Strom, and Curtis J. Omiecinski

Transactivation of a DR-1 PPRE by a human constitutive androstane receptor variant expressed from internal protein translation start sites
Nucleic Acids Research Advance Access published on March 13, 2007
Nucl. Acids Res. 2007 35: 2177-2190; doi:10.1093/nar/gkm090 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Sara R. Heras, Manuel C. López, Mónica Olivares, and M. Carmen Thomas

The L1Tc non-LTR retrotransposon of Trypanosoma cruzi contains an internal RNA-pol II-dependent promoter that strongly activates gene transcription and generates unspliced transcripts
Nucleic Acids Research Advance Access published on March 16, 2007
Nucl. Acids Res. 2007 35: 2199-2214; doi:10.1093/nar/gkl1137 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Pierpaolo Ceci, Laura Mangiarotti, Claudio Rivetti, and Emilia Chiancone

The neutrophil-activating Dps protein of Helicobacter pylori, HP-NAP, adopts a mechanism different from Escherichia coli Dps to bind and condense DNA
Nucleic Acids Research Advance Access published on March 19, 2007
Nucl. Acids Res. 2007 35: 2247-2256; doi:10.1093/nar/gkm077 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Pawan Gupta, Sung Wook Park, Mariya Farooqui, and L.-N. Wei

Orphan nuclear receptor TR2, a mediator of preadipocyte proliferation, is differentially regulated by RA through exchange of coactivator PCAF with corepressor RIP140 on a platform molecule GRIP1
Nucleic Acids Research Advance Access published on March 27, 2007
Nucl. Acids Res. 2007 35: 2269-2282; doi:10.1093/nar/gkl1147 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lingfang Shi, Daoming Qiu, Guohua Zhao, Blaise Corthesy, Susan Lees-Miller, Westley H. Reeves, and Peter N. Kao

Dynamic binding of Ku80, Ku70 and NF90 to the IL-2 promoter in vivo in activated T-cells
Nucleic Acids Research Advance Access published on March 27, 2007
Nucl. Acids Res. 2007 35: 2302-2310; doi:10.1093/nar/gkm117 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Barbara Kedzierska, Anna Szambowska, Anna Herman-Antosiewicz, David J. Lee, Stephen J.W. Busby, Grzegorz Wegrzyn, and Mark S. Thomas

The C-terminal domain of the Escherichia coli RNA polymerase subunit plays a role in the CI-dependent activation of the bacteriophage p_M promoter
Nucleic Acids Research Advance Access published on March 27, 2007
Nucl. Acids Res. 2007 35: 2311-2320; doi:10.1093/nar/gkm123 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gernot Herrmann, Sanja Kais, Jan Hoffbauer, Kijwasch Shah-Hosseini, Nicole Brüggenolte, Heiko Schober, Margaret Fäsi, and Primo Schär

Conserved interactions of the splicing factor Ntr1/Spp382 with proteins involved in DNA double-strand break repair and telomere metabolism
Nucleic Acids Research Advance Access published on March 27, 2007
Nucl. Acids Res. 2007 35: 2321-2332; doi:10.1093/nar/gkm127 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jianguo Wu, Pasha Apontes, Lei Song, Ping Liang, Lily Yang, and Fengzhi Li

Molecular mechanism of upregulation of survivin transcription by the AT-rich DNA-binding ligand, Hoechst33342: evidence for survivin involvement in drug resistance
Nucleic Acids Research Advance Access published on March 28, 2007
Nucl. Acids Res. 2007 35: 2390-2402; doi:10.1093/nar/gkm149 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ai Takemoto, Akiko Murayama, Miyuki Katano, Takeshi Urano, Koichi Furukawa, Shigeyuki Yokoyama, Junn Yanagisawa, Fumio Hanaoka, and Keiji Kimura

Analysis of the role of Aurora B on the chromosomal targeting of condensin I
Nucleic Acids Research Advance Access published on March 28, 2007
Nucl. Acids Res. 2007 35: 2403-2412; doi:10.1093/nar/gkm157 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Klaas W. Mulder, Arjan B. Brenkman, Akiko Inagaki, Niels J. F. van den Broek, and H. Th. Marc Timmers

Regulation of histone H3K4 tri-methylation and PAF complex recruitment by the Ccr4-Not complex
Nucleic Acids Research Advance Access published on March 28, 2007
Nucl. Acids Res. 2007 35: 2428-2439; doi:10.1093/nar/gkm175 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acid Enzymes:

Jesús Espada, Esteban Ballestar, Raffaella Santoro, Mario F. Fraga, Ana Villar-Garea, Attila Németh, Lidia Lopez-Serra, Santiago Ropero, Agustin Aranda, Helena Orozco, Vanessa Moreno, Angeles Juarranz, Juan Carlos Stockert, Gernot Längst, Ingrid Grummt, Wendy Bickmore, and Manel Esteller

Epigenetic disruption of ribosomal RNA genes and nucleolar architecture in DNA methyltransferase 1 (Dnmt1) deficient cells
Nucleic Acids Research Advance Access published on March 13, 2007
Nucl. Acids Res. 2007 35: 2191-2198; doi:10.1093/nar/gkm118 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Masha Y. Niv, Daniel R. Ripoll, Jorge A. Vila, Adam Liwo, Éva S. Vanamee, Aneel K. Aggarwal, Harel Weinstein, and Harold A. Scheraga

Topology of Type II REases revisited; structural classes and the common conserved core
Nucleic Acids Research Advance Access published on March 16, 2007
Nucl. Acids Res. 2007 35: 2227-2237; doi:10.1093/nar/gkm045 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Rasa Sukackaite, Arunas Lagunavicius, Kornelijus Stankevicius, Claus Urbanke, Ceslovas Venclovas, and Virginijus Siksnys

Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday junction resolvase family
Nucleic Acids Research Advance Access published on March 28, 2007
Nucl. Acids Res. 2007 35: 2377-2389; doi:10.1093/nar/gkm164 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material][Supplementary Material] [Request Permissions]  

Paola Loguercio Polosa, Stefania Deceglie, Maria Falkenberg, Marina Roberti, Barbara Di Ponzio, Maria Nicola Gadaleta, and Palmiro Cantatore

Cloning of the sea urchin mitochondrial RNA polymerase and reconstitution of the transcription termination system
Nucleic Acids Research Advance Access published on March 28, 2007
Nucl. Acids Res. 2007 35: 2413-2427; doi:10.1093/nar/gkm159 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

RNA:

Michael K. Slevin, Francoise Gourronc, and Rebecca S. Hartley

ElrA binding to the 3'UTR of cyclin E1 mRNA requires polyadenylation elements
Nucleic Acids Research Advance Access published on March 13, 2007
Nucl. Acids Res. 2007 35: 2167-2176; doi:10.1093/nar/gkm084 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Kamila Belhocine, Anthony B. Mak, and Benoit Cousineau

Trans-splicing of the Ll.LtrB group II intron in Lactococcus lactis
Nucleic Acids Research Advance Access published on March 27, 2007
Nucl. Acids Res. 2007 35: 2257-2268; doi:10.1093/nar/gkl1146 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Pål Sætrom, Bret S.E. Heale, Ola Snøve, Jr, Lars Aagaard, Jessica Alluin, and John J. Rossi

Distance constraints between microRNA target sites dictate efficacy and cooperativity
Nucleic Acids Research Advance Access published on March 27, 2007
Nucl. Acids Res. 2007 35: 2333-2342; doi:10.1093/nar/gkm133 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

N. L. Mironova, D. V. Pyshnyi, D. V. Shtadler, A. A. Fedorova, V. V. Vlassov, and M. A. Zenkova

RNase T1 mimicking artificial ribonuclease
Nucleic Acids Research Advance Access published on March 27, 2007
Nucl. Acids Res. 2007 35: 2356-2367; doi:10.1093/nar/gkm143 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Matthieu Saguy, Reynald Gillet, Patricia Skorski, Sylvie Hermann-Le Denmat, and Brice Felden

Ribosomal protein S1 influences trans-translation in vitro and in vivo
Nucleic Acids Research Advance Access published on March 28, 2007
Nucl. Acids Res. 2007 35: 2368-2376; doi:10.1093/nar/gkm100 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Structural Biology:

Francisca Barceló, Claudia Scotta, Miguel Ortiz-Lombardía, Carmen Méndez, José A. Salas, and José Portugal

Entropically-driven binding of mithramycin in the minor groove of C/G-rich DNA sequences
Nucleic Acids Research Advance Access published on March 16, 2007
Nucl. Acids Res. 2007 35: 2215-2226; doi:10.1093/nar/gkm037 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jixun Dai, Chandanamali Punchihewa, Attila Ambrus, Ding Chen, Roger A. Jones, and Danzhou Yang

Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation
Nucleic Acids Research Advance Access published on March 29, 2007
Nucl. Acids Res. 2007 35: 2440-2450; doi:10.1093/nar/gkm009 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Bjørn Dalhus, Ina Høydal Helle, Paul H. Backe, Ingrun Alseth, Torbjørn Rognes, Magnar Bjørås, and Jon K. Laerdahl

Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats
Nucleic Acids Research Advance Access published on March 29, 2007
Nucl. Acids Res. 2007 35: 2451-2459; doi:10.1093/nar/gkm039 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Methods Online:

Simon Fredriksson, Johan Banér, Fredrik Dahl, Angela Chu, Hanlee Ji, Katrina Welch, and Ronald W. Davis

Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector
Nucleic Acids Research Advance Access published on February 22, 2007
Nucl. Acids Res. 2007 35: e47; doi:10.1093/nar/gkm078 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Georg M. Bruun, Rasmus Wernersson, Agnieszka S. Juncker, Hanni Willenbrock, and Henrik Bjørn Nielsen

Improving comparability between microarray probe signals by thermodynamic intensity correction
Nucleic Acids Research Advance Access published on March 2, 2007
Nucl. Acids Res. 2007 35: e48; doi:10.1093/nar/gkl1098 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

May C. Morris, Edwige Gros, Gudrun Aldrian-Herrada, Michael Choob, John Archdeacon, Frederic Heitz, and Gilles Divita

A non-covalent peptide-based carrier for in vivo delivery of DNA mimics
Nucleic Acids Research Advance Access published on March 5, 2007
Nucl. Acids Res. 2007 35: e49; doi:10.1093/nar/gkm053 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Stephen R. Yant, Yong Huang, Bassel Akache, and Mark A. Kay

Site-directed transposon integration in human cells
Nucleic Acids Research Advance Access published on March 7, 2007
Nucl. Acids Res. 2007 35: e50; doi:10.1093/nar/gkm089 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Stefan Pfister, Christof Schlaeger, Frank Mendrzyk, Andrea Wittmann, Axel Benner, Andreas Kulozik, Wolfram Scheurlen, Bernhard Radlwimmer, and Peter Lichter

Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma
Nucleic Acids Research Advance Access published on March 7, 2007
Nucl. Acids Res. 2007 35: e51; doi:10.1093/nar/gkm094 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Iwan Beuvink, Fabrice A. Kolb, Wolfgang Budach, Arlette Garnier, Joerg Lange, Francois Natt, Uwe Dengler, Jonathan Hall, Witold Filipowicz, and Jan Weiler

A novel microarray approach reveals new tissue-specific signatures of known and predicted mammalian microRNAs
Nucleic Acids Research Advance Access published on March 13, 2007
Nucl. Acids Res. 2007 35: e52; doi:10.1093/nar/gkl1118 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Yoji Yamamoto, Masao Mori, Yuichiro Aiba, Takafumi Tomita, Wen Chen, Jing-Min Zhou, Akihiko Uehara, Yi Ren, Yoshihito Kitamura, and Makoto Komiyama

Chemical modification of Ce(IV)/EDTA-based artificial restriction DNA cutter for versatile manipulation of double-stranded DNA
Nucleic Acids Research Advance Access published on March 21, 2007
Nucl. Acids Res. 2007 35: e53; doi:10.1093/nar/gkm052 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jost Seibler, Andre Kleinridders, Birgit Küter-Luks, Sandra Niehaves, Jens C. Brüning, and Frieder Schwenk

Reversible gene knockdown in mice using a tight, inducible shRNA expression system
Nucleic Acids Research Advance Access published on March 21, 2007
Nucl. Acids Res. 2007 35: e54; doi:10.1093/nar/gkm122 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fernando Geu-Flores, Hussam H. Nour-Eldin, Morten T. Nielsen, and Barbara A. Halkier

USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products
Nucleic Acids Research Advance Access published on March 27, 2007
Nucl. Acids Res. 2007 35: e55; doi:10.1093/nar/gkm106 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erratum:

Lata I. Shukla, Amitava Adhikary, Robert Pazdro, David Becker, and Michael D. Sevilla

Formation of 8-oxo-7,8-dihydroguanine-radicals in -irradiated DNA by multiple one-electron oxidations
Nucleic Acids Research Advance Access published on March 27, 2007
Nucl. Acids Res. 2007 35: 2460-2461; doi:10.1093/nar/gkm083 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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