| | Molecular Biology Distinct regions of ATF/CREB proteins Atf1 and Pcr1 control recombination hotspot ade6–M26 and the osmotic stress response Jun Gao, Mari K. Davidson, and Wayne P. Wahls PMCID: PMC2396409 Characterization of Drosophila melanogaster JmjC+N histone demethylases Marta Lloret-Llinares, Clément Carré, Alejandro Vaquero, Natalia de Olano, and Fernando Azorín PMCID: PMC2396428 Minimal components of the RNA polymerase II transcription apparatus determine the consensus TATA box Gudrun Bjornsdottir and Lawrence C. Myers PMCID: PMC2396422 A polycomb group protein, PHF1, is involved in the response to DNA double-strand breaks in human cell Zehui Hong, Jie Jiang, Li Lan, Satoshi Nakajima, Shin-ichiro Kanno, Haruhiko Koseki, and Akira Yasui PMCID: PMC2396414 Transcriptional activation of the tumor suppressor and differentiation gene S100A2 by a novel p63-binding site Ralf D. Kirschner, Katja Sänger, Gerd A. Müller, and Kurt Engeland PMCID: PMC2396407 Transcriptional regulation of chondrogenesis by coactivator Tip60 via chromatin association with Sox9 and Sox5 Takako Hattori, Francoise Coustry, Shelley Stephens, Heidi Eberspaecher, Masaharu Takigawa, Hideyo Yasuda, and Benoit de Crombrugghe PMCID: PMC2396410 Dissection of the regulatory mechanism of a heat-shock responsive promoter in Haloarchaea: a new paradigm for general transcription factor directed archaeal gene regulation Qiuhe Lu, Jing Han, Ligang Zhou, James A. Coker, Priya DasSarma, Shiladitya DasSarma, and Hua Xiang PMCID: PMC2396416 The major form of hepatitis C virus alternate reading frame protein is suppressed by core protein expression Marie Wolf, Maria Dimitrova, Thomas F. Baumert, and Catherine Schuster PMCID: PMC2396417 Overexpression of human mitochondrial valyl tRNA synthetase can partially restore levels of cognate mt-tRNAVal carrying the pathogenic C25U mutation Joanna Rorbach, Abdul Aziz Yusoff, Helen Tuppen, Dyg P. Abg-Kamaludin, Zofia M.A. Chrzanowska-Lightowlers, Robert W. Taylor, Douglass M. Turnbull, Robert McFarland, and Robert N. Lightowlers PMCID: PMC2396425 The three SoxC proteins—Sox4, Sox11 and Sox12—exhibit overlapping expression patterns and molecular properties Peter Dy, Alfredo Penzo-Méndez, Hongzhe Wang, Carlos E. Pedraza, Wendy B. Macklin, and Véronique Lefebvre PMCID: PMC2396431 RNA Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron Ying Poi Liu, Joost Haasnoot, Olivier ter Brake, Ben Berkhout, and Pavlina Konstantinova PMCID: PMC2396423 Apoptotic signals induce specific degradation of ribosomal RNA in yeast Seweryn Mroczek and Joanna Kufel PMCID: PMC2396418 A shared RNA-binding site in the Pet54 protein is required for translational activation and group I intron splicing in yeast mitochondria Benjamin J. Kaspar, Abby L. Bifano, and Mark G. Caprara PMCID: PMC2396411 The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme Abigail L. Brown, Anne T. Perrotta, Timothy S. Wadkins, and Michael D. Been PMCID: PMC2396440 The mRNA encoding the yeast ARE-binding protein Cth2 is generated by a novel 3′ processing pathway Delphine Ciais, Markus T. Bohnsack, and David Tollervey PMCID: PMC2396412 TFIIB aptamers inhibit transcription by perturbing PIC formation at distinct stages Aarti Sevilimedu, Hua Shi, and John T. Lis PMCID: PMC2396426 Structural Biology Mismatched dNTP incorporation by DNA polymerase β does not proceed via globally different conformational pathways Kuo-Hsiang Tang, Marc Niebuhr, Chang-Shung Tung, Hsiu-chien Chan, Chia-Cheng Chou, and Ming-Daw Tsai PMCID: PMC2396427 Copper sensing function of Drosophila metal-responsive transcription factor-1 is mediated by a tetranuclear Cu(I) cluster Xiaohua Chen, Haiqing Hua, Kuppusamy Balamurugan, Xiangming Kong, Limei Zhang, Graham N. George, Oleg Georgiev, Walter Schaffner, and David P. Giedroc PMCID: PMC2396432 Structure and function of the regulatory C-terminal HRDC domain from Deinococcus radiodurans RecQ Michael P. Killoran and James L. Keck PMCID: PMC2396406 Survey and Summary Presence and role of cytosine methylation in DNA viruses of animals Karin Hoelzer, Laura A. Shackelton, and Colin R. Parrish PMCID: PMC2396429 Genomics Lateral transfer of introns in the cryptophyte plastid genome Hameed Khan and John M. Archibald PMCID: PMC2396441 Chemistry Pyrrole-imidazole hairpin polyamides with high affinity at 5′–CGCG–3′ DNA sequence; influence of cytosine methylation on binding Masafumi Minoshima, Toshikazu Bando, Shunta Sasaki, Jun Fujimoto, and Hiroshi Sugiyama PMCID: PMC2396430 Formation of the double helix: a mutational study Mehrdad Majlessi and Michael M. Becker PMCID: PMC2396424 Methods Online Uncovering signal transduction networks from high-throughput data by integer linear programming Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, and Kazuyuki Aihara PMCID: PMC2396433 DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer Gary P. Wang, Alexandrine Garrigue, Angela Ciuffi, Keshet Ronen, Jeremy Leipzig, Charles Berry, Chantal Lagresle-Peyrou, Fatine Benjelloun, Salima Hacein-Bey-Abina, Alain Fischer, Marina Cavazzana-Calvo, and Frederic D. Bushman PMCID: PMC2396413 The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases Hua Wei, Caitlin Therrien, Aine Blanchard, Shengxi Guan, and Zhenyu Zhu PMCID: PMC2396408 Identification of soluble protein fragments by gene fragmentation and genetic selection Michael R. Dyson, Rajika L. Perera, S. Paul Shadbolt, Lynn Biderman, Krystyna Bromek, Natalia V. Murzina, and John McCafferty PMCID: PMC2396403 R-Coffee: a method for multiple alignment of non-coding RNA Andreas Wilm, Desmond G. Higgins, and Cédric Notredame PMCID: PMC2396437 Analysis of siRNA specificity on targets with double-nucleotide mismatches Cecilia Dahlgren, Hong-Yan Zhang, Quan Du, Maria Grahn, Gunnar Norstedt, Claes Wahlestedt, and Zicai Liang PMCID: PMC2396434 Rapid one-step recombinational cloning Changlin Fu, Daniel R. Wehr, Janice Edwards, and Brian Hauge PMCID: PMC2396420 Computational Biology A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets Hairong Wei, Pei Fen Kuan, Shulan Tian, Chuhu Yang, Jeff Nie, Srikumar Sengupta, Victor Ruotti, Gudrun A. Jonsdottir, Sunduz Keles, James A. Thomson, and Ron Stewart PMCID: PMC2396435 Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components Marcela Dávila López, Magnus Alm Rosenblad, and Tore Samuelsson PMCID: PMC2396436 Using support vector machine combined with auto covariance to predict protein–protein interactions from protein sequences Yanzhi Guo, Lezheng Yu, Zhining Wen, and Menglong Li PMCID: PMC2396404 MultiPriDe: automated batch development of quantitative real-time PCR primers A. C. Ziesel, M. A. Chrenek, and P. W. Wong PMCID: PMC2396421 Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation Yingjia Shen, Guoli Ji, Brian J. Haas, Xiaohui Wu, Jianti Zheng, Greg J. Reese, and Qingshun Quinn Li PMCID: PMC2396415 Nucleic Acid Enzymes Understanding how the V(D)J recombinase catalyzes transesterification: distinctions between DNA cleavage and transposition Catherine P. Lu, Jennifer E. Posey, and David B. Roth PMCID: PMC2396405 Tolerance for 8-oxoguanine but not thymine glycol in alignment-based gap filling of partially complementary double-strand break ends by DNA polymerase λ in human nuclear extracts Rui-Zhe Zhou, Luis Blanco, Miguel Garcia-Diaz, Katarzyna Bebenek, Thomas A. Kunkel, and Lawrence F. Povirk PMCID: PMC2396438 Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and fluorescence lifetime studies Ben Youngblood, Eleanor Bonnist, David T.F. Dryden, Anita C. Jones, and Norbert O. Reich PMCID: PMC2396439 End-bridging is required for pol μ to efficiently promote repair of noncomplementary ends by nonhomologous end joining Bryan J. Davis, Jody M. Havener, and Dale A. Ramsden PMCID: PMC2396419 |
