| | Molecular Biology A critical role for the loop region of the basic helix–loop–helix/leucine zipper protein Mlx in DNA binding and glucose-regulated transcription Lin Ma, Yuk Y. Sham, Kylie J. Walters, and Howard C. Towle PMCID: PMC1761440 Functional interaction between the homeoprotein CDX1 and the transcriptional machinery containing the TATA-binding protein Alexandre Calon, Isabelle Gross, Irwin Davidson, Michèle Kedinger, Isabelle Duluc, Claire Domon-Dell, and Jean-Noël Freund PMCID: PMC1802564 Exploring membrane-associated NAC transcription factors in Arabidopsis: implications for membrane biology in genome regulation Sun-Young Kim, Sang-Gyu Kim, Youn-Sung Kim, Pil Joon Seo, Mikyoung Bae, Hye-Kyung Yoon, and Chung-Mo Park PMCID: PMC1802569 The p16INK4a tumor suppressor controls p21WAF1 induction in response to ultraviolet light Mai A. Al-Mohanna, Huda H. Al-Khalaf, Nujoud Al-Yousef, and Abdelilah Aboussekhra PMCID: PMC1802571 Transcription factor distribution in Escherichia coli: studies with FNR protein David C. Grainger, Hirofumi Aiba, Douglas Hurd, Douglas F. Browning, and Stephen J. W. Busby PMCID: PMC1802558 Toxin–antitoxin regulation: bimodal interaction of YefM–YoeB with paired DNA palindromes exerts transcriptional autorepression Barbara Kędzierska, Lu-Yun Lian, and Finbarr Hayes PMCID: PMC1802561 p53 and p73 display common and distinct requirements for sequence specific binding to DNA Maria Lokshin, Yingchun Li, Christian Gaiddon, and Carol Prives PMCID: PMC1802567 RNA Different levels of alternative splicing among eukaryotes Eddo Kim, Alon Magen, and Gil Ast PMCID: PMC1802581 Complex splicing control of the human Thrombopoietin gene by intronic G runs Roberto Marcucci, Francisco E. Baralle, and Maurizio Romano PMCID: PMC1802585 Dispersion of the RmInt1 group II intron in the Sinorhizobium meliloti genome upon acquisition by conjugative transfer Rafael Nisa-Martínez, José I. Jiménez-Zurdo, Francisco Martínez-Abarca, Estefanía Muñoz-Adelantado, and Nicolás Toro PMCID: PMC1802570 Use of modified U1 snRNAs to inhibit HIV-1 replication R. Sajic, K. Lee, K. Asai, D. Sakac, D. R. Branch, C. Upton, and A. Cochrane PMCID: PMC1802557 Fragile X related protein 1 isoforms differentially modulate the affinity of fragile X mental retardation protein for G-quartet RNA structure Elias Bechara, Laetitia Davidovic, Mireille Melko, Mounia Bensaid, Sandra Tremblay, Josiane Grosgeorge, Edouard W. Khandjian, Enzo Lalli, and Barbara Bardoni PMCID: PMC1802556 Structural Biology Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor Christian G. Noble, Barbara Beuth, and Ian A. Taylor PMCID: PMC1761425 Structural basis for activation of the therapeutic l-nucleoside analogs 3TC and troxacitabine by human deoxycytidine kinase Elisabetta Sabini, Saugata Hazra, Manfred Konrad, Stephen K. Burley, and Arnon Lavie PMCID: PMC1802566 Survey and Summary An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy Keith Knapp and Yi-Ping Phoebe Chen PMCID: PMC1802560 Genomics Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis M. Thomas P. Gilbert, Jonas Binladen, Webb Miller, Carsten Wiuf, Eske Willerslev, Hendrik Poinar, John E. Carlson, James H. Leebens-Mack, and Stephan C. Schuster PMCID: PMC1802572 Insect small nuclear RNA gene promoters evolve rapidly yet retain conserved features involved in determining promoter activity and RNA polymerase specificity Genaro Hernandez, Jr, Faramarz Valafar, and William E. Stumph PMCID: PMC1761439 Identification of functional, endogenous programmed −1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae Jonathan L. Jacobs, Ashton T. Belew, Rasa Rakauskaite, and Jonathan D. Dinman PMCID: PMC1802563 Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae Arunadevi Yarragudi, Laura Wegener Parfrey, and Randall H. Morse PMCID: PMC1802568 Chemistry The chemical stability of abasic RNA compared to abasic DNA Pascal A. Küpfer and Christian J. Leumann PMCID: PMC1761435 Unanticipated differences between α- and γ-diaminobutyric acid-linked hairpin polyamide-alkylator conjugates Sherry M. Tsai, Michelle E. Farkas, C. James Chou, Joel M. Gottesfeld, and Peter B. Dervan PMCID: PMC1802559 Methods Online CoMoDis: composite motif discovery in mammalian genomes Ian J. Donaldson and Berthold Göttgens PMCID: PMC1702496 Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations Honghai Gao, Jianmin Huang, Francis Barany, and Weiguo Cao PMCID: PMC1702505 Multiple primer extension by DNA polymerase on a novel plastic DNA array coated with a biocompatible polymer Kenji Kinoshita, Kentaro Fujimoto, Toru Yakabe, Shin Saito, Yuzo Hamaguchi, Takayuki Kikuchi, Ken Nonaka, Shigenori Murata, Daisuke Masuda, Wataru Takada, Sohei Funaoka, Susumu Arai, Hisao Nakanishi, Kanehisa Yokoyama, Kazuhiko Fujiwara, and Kenichi Matsubara PMCID: PMC1747182 Control of carry-over contamination for PCR-based DNA methylation quantification using bisulfite treated DNA Reimo Tetzner, Dimo Dietrich, and Juergen Distler PMCID: PMC1747185 An improved method to identify BAC clones using pooled overgos Kavitha Madishetty, Pascal Condamine, Jan T. Svensson, Edmundo Rodriguez, and Timothy J. Close PMCID: PMC1761434 An efficient method for multi-locus molecular haplotyping Bernard A. Konfortov, Alan T. Bankier, and Paul H. Dear PMCID: PMC1802573 Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes Elhanan Borenstein, Tomer Shlomi, Eytan Ruppin, and Roded Sharan PMCID: PMC1802574 Computational Biology Operon prediction in Pyrococcus furiosus Thao T. Tran, Phuongan Dam, Zhengchang Su, Farris L. Poole, II, Michael W. W. Adams, G. Tong Zhou, and Ying Xu PMCID: PMC1761436 Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm Itay Mayrose, Tomer Shlomi, Nimrod D. Rubinstein, Jonathan M. Gershoni, Eytan Ruppin, Roded Sharan, and Tal Pupko PMCID: PMC1761437 Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos Zhenbao Yu, Zhaofeng Jian, Shi-Hsiang Shen, Enrico Purisima, and Edwin Wang PMCID: PMC1802562 Systematic variation in mRNA 3′-processing signals during mouse spermatogenesis Donglin Liu, J. Michael Brockman, Brinda Dass, Lucie N. Hutchins, Priyam Singh, John R. McCarrey, Clinton C. MacDonald, and Joel H. Graber PMCID: PMC1802579 Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae Tra Thi Vu and Jiri Vohradsky PMCID: PMC1802551 Operon prediction using both genome-specific and general genomic information Phuongan Dam, Victor Olman, Kyle Harris, Zhengchang Su, and Ying Xu PMCID: PMC1802555 Nucleic Acid Enzymes Expanding the repertoire of DNA polymerase substrates: template-instructed incorporation of non-nucleoside triphosphate analogues by DNA polymerases β and λ Emmanuele Crespan, Ludmila Alexandrova, Anastasiya Khandazhinskaya, Maxim Jasko, Marina Kukhanova, Giuseppe Villani, Ulrich Hübscher, Silvio Spadari, and Giovanni Maga PMCID: PMC1761426 RecA can stimulate the relaxation activity of topoisomerase I: Molecular basis of topoisomerase-mediated genome-wide transcriptional responses in Escherichia coli Amy R. Reckinger, Kyeong Soo Jeong, Arkady B. Khodursky, and Hiroshi Hiasa PMCID: PMC1761438 Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes Fuyang Li, Monika Papworth, Michal Minczuk, Christian Rohde, Yingying Zhang, Sergei Ragozin, and Albert Jeltsch PMCID: PMC1761428 LEDGF/p75 interacts with divergent lentiviral integrases and modulates their enzymatic activity in vitro Peter Cherepanov PMCID: PMC1802576 Duplex strand joining reactions catalyzed by vaccinia virus DNA polymerase Michael D. Hamilton, Anthony A. Nuara, Don B. Gammon, R. Mark Buller, and David H. Evans PMCID: PMC1802553 Purine analog substitution of the HIV-1 polypurine tract primer defines regions controlling initiation of plus-strand DNA synthesis Jason W. Rausch and Stuart F. J. Le Grice PMCID: PMC1802577 |
