| | Molecular Biology Intracellular expression profiles measured by real-time PCR tomography in the Xenopus laevis oocyte Radek Sindelka, Jiri Jonák, Rebecca Hands, Stephen A. Bustin, and Mikael Kubista PMCID: PMC2241880 DNA tape measurements of AraC Michael E. Rodgers and Robert Schleif PMCID: PMC2241862 Transcription of Satellite III non-coding RNAs is a general stress response in human cells Rut Valgardsdottir, Ilaria Chiodi, Manuela Giordano, Antonio Rossi, Silvia Bazzini, Claudia Ghigna, Silvano Riva, and Giuseppe Biamonti PMCID: PMC2241877 Retinoic acid modulates chromatin to potentiate tumor necrosis factor alpha signaling on the DIF2 promoter Michael Witcher, Filippa Pettersson, Daphne Dupéré-Richer, Alessandra Padovani, Leslie Summers-Deluca, Albert S. Baldwin, and Wilson H. Miller, Jr PMCID: PMC2241879 Structure of discontinuities in kinetoplast DNA-associated minicircles during S phase in Crithidia fasciculata Jane C. Hines and Dan S. Ray PMCID: PMC2241878 Chromatin-associated HMG-17 is a major regulator of homeodomain transcription factor activity modulated by Wnt/β-catenin signaling Melanie Amen, Herbert M. Espinoza, Carol Cox, Xiaowen Liang, Jianbo Wang, Todd M. E. Link, Richard G. Brennan, James F. Martin, and Brad A. Amendt PMCID: PMC2241859 Repair of DNA double-strand breaks within the (GAA•TTC)n sequence results in frequent deletion of the triplet-repeat sequence Laura M. Pollard, Rebecka L. Bourn, and Sanjay I. Bidichandani PMCID: PMC2241870 ATR-dependent pathways control hEXO1 stability in response to stalled forks Mahmoud El-Shemerly, Daniel Hess, Aswin K. Pyakurel, Said Moselhy, and Stefano Ferrari PMCID: PMC2241874 The RNA-dependent RNA polymerase essential for post-transcriptional gene silencing in Neurospora crassa interacts with replication protein A Tony Nolan, Germano Cecere, Carmine Mancone, Tonino Alonzi, Marco Tripodi, Caterina Catalanotto, and Carlo Cogoni PMCID: PMC2241871 The dual control of TFIIB recruitment by NC2 is gene specific Patrick Masson, Elisa Leimgruber, Sandrine Creton, and Martine A. Collart PMCID: PMC2241854 Regulating gene expression in human leukemia cells using light-activated oligodeoxynucleotides XinJing Tang, Jyothishmathi Swaminathan, Alan M. Gewirtz, and Ivan J. Dmochowski PMCID: PMC2241881 Nε-Formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin function Jacek R. Wiśniewski, Alexandre Zougman, and Matthias Mann PMCID: PMC2241850 The interaction of mammalian mitochondrial translational initiation factor 3 with ribosomes: evolution of terminal extensions in IF3mt Md. Emdadul Haque, Domenick Grasso, and Linda L. Spremulli PMCID: PMC2241858 Overlapping activator sequences determined for two oppositely oriented promoters in halophilic Archaea Martina Bauer, Larissa Marschaus, Muriel Reuff, Verena Besche, Simone Sartorius-Neef, and Felicitas Pfeifer PMCID: PMC2241852 Escherichia coli low-copy-number plasmid R1 centromere parC forms a U-shaped complex with its binding protein ParR C. Hoischen, M. Bussiek, J. Langowski, and S. Diekmann PMCID: PMC2241845 Functional endogenous LINE-1 retrotransposons are expressed and mobilized in rat chloroleukemia cells Alexander Kirilyuk, Genrich V. Tolstonog, Annette Damert, Ulrike Held, Silvia Hahn, Roswitha Löwer, Christian Buschmann, Axel V. Horn, Peter Traub, and Gerald G. Schumann PMCID: PMC2241872 RNA Rho-independent transcription terminators inhibit RNase P processing of the secG leuU and metT tRNA polycistronic transcripts in Escherichia coli Bijoy K. Mohanty and Sidney R. Kushner PMCID: PMC2241853 Nuclear RNA export factor 7 is localized in processing bodies and neuronal RNA granules through interactions with shuttling hnRNPs Jun Katahira, Takashi Miki, Keizo Takano, Mitsuji Maruhashi, Masanori Uchikawa, Taro Tachibana, and Yoshihiro Yoneda PMCID: PMC2241847 Epstein–Barr virus-encoded microRNA miR-BART2 down-regulates the viral DNA polymerase BALF5 Stephanie Barth, Thorsten Pfuhl, Alfredo Mamiani, Claudia Ehses, Klaus Roemer, Elisabeth Kremmer, Christoph Jäker, Julia Höck, Gunter Meister, and Friedrich A. Grässer PMCID: PMC2241876 Studies on the mechanism of inhibition of bacterial ribonuclease P by aminoglycoside derivatives Steven A. Kawamoto, Christopher G. Sudhahar, Cynthia L. Hatfield, Jing Sun, Edward J. Behrman, and Venkat Gopalan PMCID: PMC2241863 Structural Biology Interplay of ion binding and attraction in DNA condensed by multivalent cations Brian A. Todd and Donald C. Rau PMCID: PMC2241864 Alternative splicing and protein structure evolution Fabian Birzele, Gergely Csaba, and Ralf Zimmer PMCID: PMC2241867 Chemistry The formation pathway of tetramolecular G-quadruplexes Caroline Bardin and Jean Louis Leroy PMCID: PMC2241855 Methods Online Use of a multi-thermal washer for DNA microarrays simplifies probe design and gives robust genotyping assays Jesper Petersen, Lena Poulsen, Sarunas Petronis, Henrik Birgens, and Martin Dufva PMCID: PMC2241873 Model-based variance-stabilizing transformation for Illumina microarray data Simon M. Lin, Pan Du, Wolfgang Huber, and Warren A. Kibbe PMCID: PMC2241869 Gene Ontology annotation quality analysis in model eukaryotes Teresia J. Buza, Fiona M. McCarthy, Nan Wang, Susan M. Bridges, and Shane C. Burgess PMCID: PMC2241866 Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data Christiaan Klijn, Henne Holstege, Jeroen de Ridder, Xiaoling Liu, Marcel Reinders, Jos Jonkers, and Lodewyk Wessels PMCID: PMC2241875 Computational Biology Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformation Marcos J. Araúzo-Bravo and Akinori Sarai PMCID: PMC2241865 Identifying foldable regions in protein sequence from the hydrophobic signal Chi N.I. Pang, Kuang Lin, Merridee A. Wouters, Jaap Heringa, and Richard A. George PMCID: PMC2241846 Efficient siRNA selection using hybridization thermodynamics Zhi John Lu and David H. Mathews PMCID: PMC2241856 Nucleic Acid Enzymes Cordycepin-hypersensitive growth links elevated polyphosphate levels to inhibition of poly(A) polymerase in Saccharomyces cerevisiae Sandra Holbein, Florian M. Freimoser, Thomas P. Werner, Agnieszka Wengi, and Bernhard Dichtl PMCID: PMC2241851 The N-terminal domain of TWINKLE contributes to single-stranded DNA binding and DNA helicase activities Géraldine Farge, Teresa Holmlund, Julia Khvorostova, Reza Rofougaran, Anders Hofer, and Maria Falkenberg PMCID: PMC2241861 The Leu22Pro tumor-associated variant of DNA polymerase beta is dRP lyase deficient Shibani Dalal, Anna Chikova, Joachim Jaeger, and Joann B. Sweasy PMCID: PMC2241857 Magnesium-binding studies reveal fundamental differences between closely related RNA triphosphatases Marie F. Soulière, Jean-Pierre Perreault, and Martin Bisaillon PMCID: PMC2241848 Mechanisms of covalent self-assembly of the Azoarcus ribozyme from four fragment oligonucleotides Will E. Draper, Eric J. Hayden, and Niles Lehman PMCID: PMC2241849 The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases Nicolas Leulliot, Markus T. Bohnsack, Marc Graille, David Tollervey, and Herman Van Tilbeurgh PMCID: PMC2241868 Structure–function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement Souad Naji, Michela G. Bertero, Patrizia Spitalny, Patrick Cramer, and Michael Thomm PMCID: PMC2241882 DNA polymerase kappa produces interrupted mutations and displays polar pausing within mononucleotide microsatellite sequences Suzanne E. Hile and Kristin A. Eckert PMCID: PMC2241860 |
