| | Molecular Biology The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase 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 PMCID: PMC1874643 Telomeric localization of the modified DNA base J in the genome of the protozoan parasite Leishmania Paul-André Genest, Bas ter Riet, Tony Cijsouw, Henri G.A.M. van Luenen, and Piet Borst PMCID: PMC1874636 Transactivation of a DR-1 PPRE by a human constitutive androstane receptor variant expressed from internal protein translation start sites Matthew A. Stoner, Scott S. Auerbach, Stephanie M. Zamule, Stephen C. Strom, and Curtis J. Omiecinski PMCID: PMC1874654 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 Sara R. Heras, Manuel C. López, Mónica Olivares, and M. Carmen Thomas PMCID: PMC1874656 The neutrophil-activating Dps protein of Helicobacter pylori, HP-NAP, adopts a mechanism different from Escherichia coli Dps to bind and condense DNA Pierpaolo Ceci, Laura Mangiarotti, Claudio Rivetti, and Emilia Chiancone PMCID: PMC1874666 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 Pawan Gupta, Sung Wook Park, Mariya Farooqui, and L.-N. Wei PMCID: PMC1874640 Dynamic binding of Ku80, Ku70 and NF90 to the IL-2 promoter in vivo in activated T-cells Lingfang Shi, Daoming Qiu, Guohua Zhao, Blaise Corthesy, Susan Lees-Miller, Westley H. Reeves, and Peter N. Kao PMCID: PMC1874627 The C-terminal domain of the Escherichia coli RNA polymerase α subunit plays a role in the CI-dependent activation of the bacteriophage λ pM promoter Barbara Kedzierska, Anna Szambowska, Anna Herman-Antosiewicz, David J. Lee, Stephen J.W. Busby, Grzegorz Wegrzyn, and Mark S. Thomas PMCID: PMC1874639 Conserved interactions of the splicing factor Ntr1/Spp382 with proteins involved in DNA double-strand break repair and telomere metabolism Gernot Herrmann, Sanja Kais, Jan Hoffbauer, Kijwasch Shah-Hosseini, Nicole Brüggenolte, Heiko Schober, Margaret Fäsi, and Primo Schär PMCID: PMC1874655 Molecular mechanism of upregulation of survivin transcription by the AT-rich DNA-binding ligand, Hoechst33342: evidence for survivin involvement in drug resistance Jianguo Wu, Pasha Apontes, Lei Song, Ping Liang, Lily Yang, and Fengzhi Li PMCID: PMC1874665 Analysis of the role of Aurora B on the chromosomal targeting of condensin I Ai Takemoto, Akiko Murayama, Miyuki Katano, Takeshi Urano, Koichi Furukawa, Shigeyuki Yokoyama, Junn Yanagisawa, Fumio Hanaoka, and Keiji Kimura PMCID: PMC1874644 Regulation of histone H3K4 tri-methylation and PAF complex recruitment by the Ccr4-Not complex Klaas W. Mulder, Arjan B. Brenkman, Akiko Inagaki, Niels J. F. van den Broek, and H. Th. Marc Timmers PMCID: PMC1874646 RNA ElrA binding to the 3′UTR of cyclin E1 mRNA requires polyadenylation elements Michael K. Slevin, Francoise Gourronc, and Rebecca S. Hartley PMCID: PMC1874641 Trans-splicing of the Ll.LtrB group II intron in Lactococcus lactis Kamila Belhocine, Anthony B. Mak, and Benoit Cousineau PMCID: PMC1874635 Distance constraints between microRNA target sites dictate efficacy and cooperativity Pål Sætrom, Bret S.E. Heale, Ola Snøve, Jr, Lars Aagaard, Jessica Alluin, and John J. Rossi PMCID: PMC1874663 RNase T1 mimicking artificial ribonuclease N. L. Mironova, D. V. Pyshnyi, D. V. Shtadler, A. A. Fedorova, V. V. Vlassov, and M. A. Zenkova PMCID: PMC1874650 Ribosomal protein S1 influences trans-translation in vitro and in vivo Matthieu Saguy, Reynald Gillet, Patricia Skorski, Sylvie Hermann-Le Denmat, and Brice Felden PMCID: PMC1874662 Structural Biology Entropically-driven binding of mithramycin in the minor groove of C/G-rich DNA sequences Francisca Barceló, Claudia Scotta, Miguel Ortiz-Lombardía, Carmen Méndez, José A. Salas, and José Portugal PMCID: PMC1874653 Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation Jixun Dai, Chandanamali Punchihewa, Attila Ambrus, Ding Chen, Roger A. Jones, and Danzhou Yang PMCID: PMC1874667 Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats Bjørn Dalhus, Ina Høydal Helle, Paul H. Backe, Ingrun Alseth, Torbjørn Rognes, Magnar Bjørås, and Jon K. Laerdahl PMCID: PMC1874660 Survey and Summary Ribosomal RNA guanine-(N2)-methyltransferases and their targets Petr V. Sergiev, Alexey A. Bogdanov, and Olga A. Dontsova PMCID: PMC1874633 Genomics Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference Jason A. Hackney, Gretchen M. Ehrenkaufer, and Upinder Singh PMCID: PMC1874630 Deciphering RNA structural diversity and systematic phylogeny from microbial metagenomes Yanglong Zhu, Dileep K. Pulukkunat, and Yong Li PMCID: PMC1874661 Methods Online Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector Simon Fredriksson, Johan Banér, Fredrik Dahl, Angela Chu, Hanlee Ji, Katrina Welch, and Ronald W. Davis PMCID: PMC1874629 Improving comparability between microarray probe signals by thermodynamic intensity correction Georg M. Bruun, Rasmus Wernersson, Agnieszka S. Juncker, Hanni Willenbrock, and Henrik Bjørn Nielsen PMCID: PMC1874658 A non-covalent peptide-based carrier for in vivo delivery of DNA mimics May C. Morris, Edwige Gros, Gudrun Aldrian-Herrada, Michael Choob, John Archdeacon, Frederic Heitz, and Gilles Divita PMCID: PMC1874649 Site-directed transposon integration in human cells Stephen R. Yant, Yong Huang, Bassel Akache, and Mark A. Kay PMCID: PMC1874657 Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma Stefan Pfister, Christof Schlaeger, Frank Mendrzyk, Andrea Wittmann, Axel Benner, Andreas Kulozik, Wolfram Scheurlen, Bernhard Radlwimmer, and Peter Lichter PMCID: PMC1874664 A novel microarray approach reveals new tissue-specific signatures of known and predicted mammalian microRNAs Iwan Beuvink, Fabrice A. Kolb, Wolfgang Budach, Arlette Garnier, Joerg Lange, Francois Natt, Uwe Dengler, Jonathan Hall, Witold Filipowicz, and Jan Weiler PMCID: PMC1874652 Chemical modification of Ce(IV)/EDTA-based artificial restriction DNA cutter for versatile manipulation of double-stranded DNA Yoji Yamamoto, Masao Mori, Yuichiro Aiba, Takafumi Tomita, Wen Chen, Jing-Min Zhou, Akihiko Uehara, Yi Ren, Yoshihito Kitamura, and Makoto Komiyama PMCID: PMC1874645 Reversible gene knockdown in mice using a tight, inducible shRNA expression system Jost Seibler, Andre Kleinridders, Birgit Küter-Luks, Sandra Niehaves, Jens C. Brüning, and Frieder Schwenk PMCID: PMC1874634 USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products Fernando Geu-Flores, Hussam H. Nour-Eldin, Morten T. Nielsen, and Barbara A. Halkier PMCID: PMC1874642 Computational Biology Hierarchical classification of functionally equivalent genes in prokaryotes Hongwei Wu, Fenglou Mao, Victor Olman, and Ying Xu PMCID: PMC1874638 Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans Raquel Quatrini, Claudia Lefimil, Felipe A. Veloso, Inti Pedroso, David S. Holmes, and Eugenia Jedlicki PMCID: PMC1874648 Consensus sequences improve PSI-BLAST through mimicking profile–profile alignments Dariusz Przybylski and Burkhard Rost PMCID: PMC1874647 Graph-based identification of cancer signaling pathways from published gene expression signatures using PubLiME Giacomo Finocchiaro, Francesco Mattia Mancuso, Davide Cittaro, and Heiko Muller PMCID: PMC1874632 Nucleic Acid Enzymes Epigenetic disruption of ribosomal RNA genes and nucleolar architecture in DNA methyltransferase 1 (Dnmt1) deficient cells 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 PMCID: PMC1874631 Topology of Type II REases revisited; structural classes and the common conserved core Masha Y. Niv, Daniel R. Ripoll, Jorge A. Vila, Adam Liwo, Éva S. Vanamee, Aneel K. Aggarwal, Harel Weinstein, and Harold A. Scheraga PMCID: PMC1874628 Restriction endonuclease BpuJI specific for the 5′-CCCGT sequence is related to the archaeal Holliday junction resolvase family Rasa Sukackaite, Arunas Lagunavicius, Kornelijus Stankevicius, Claus Urbanke, Česlovas Venclovas, and Virginijus Siksnys PMCID: PMC1874659 Cloning of the sea urchin mitochondrial RNA polymerase and reconstitution of the transcription termination system Paola Loguercio Polosa, Stefania Deceglie, Maria Falkenberg, Marina Roberti, Barbara Di Ponzio, Maria Nicola Gadaleta, and Palmiro Cantatore PMCID: PMC1874651 Erratum Formation of 8-oxo-7,8-dihydroguanine-radicals in γ-irradiated DNA by multiple one-electron oxidations Lata I. Shukla, Amitava Adhikary, Robert Pazdro, David Becker, and Michael D. Sevilla PMCID: PMC1874637 Corrects: Lata I. Shukla, et al. Formation of 8-oxo-7,8-dihydroguanine-radicals in γ-irradiated DNA by multiple one-electron oxidations. Nucleic Acids Res. 2004; 32(22): 6565–6574. |
