| | Molecular Biology A novel G-quadruplex-forming GGA repeat region in the c-myb promoter is a critical regulator of promoter activity SunMi L. Palumbo, Regan M. Memmott, Diana J. Uribe, Yulia Krotova-Khan, Laurence H. Hurley, and Scot W. Ebbinghaus PMCID: PMC2330228 Apn1 and Apn2 endonucleases prevent accumulation of repair-associated DNA breaks in budding yeast as revealed by direct chromosomal analysis Wenjian Ma, Michael A. Resnick, and Dmitry A. Gordenin PMCID: PMC2346603 p160/SRC/NCoA coactivators form complexes via specific interaction of their PAS-B domain with the CID/AD1 domain Marco Lodrini, Tobias Münz, Nicolas Coudevylle, Christian Griesinger, Stefan Becker, and Edith Pfitzner PMCID: PMC2330239 Identification of CUG-BP1/EDEN-BP target mRNAs in Xenopus tropicalis Antoine Graindorge, Olivier Le Tonquèze, Raphaël Thuret, Nicolas Pollet, H. Beverley Osborne, and Yann Audic PMCID: PMC2330240 C-terminal diversity within the p53 family accounts for differences in DNA binding and transcriptional activity Markus Sauer, Anne Catherine Bretz, Rasa Beinoraviciute-Kellner, Michaela Beitzinger, Christof Burek, Andreas Rosenwald, Gregory S. Harms, and Thorsten Stiewe PMCID: PMC2330244 Angiotensin II induction of PDGF-C expression is mediated by AT1 receptor-dependent Egr-1 transactivation Estella Sanchez-Guerrero, Valerie C. Midgley, and Levon M. Khachigian PMCID: PMC2330232 Secondary DNA structure formation for Hoxb9 promoter and identification of its specific binding protein Takumi Yamagishi, Shigehisa Hirose, and Takashi Kondo PMCID: PMC2330229 Alternative splicing of Alu exons—two arms are better than one Nurit Gal-Mark, Schraga Schwartz, and Gil Ast PMCID: PMC2330237 Oxygen-dependent, alternative promoter controls translation of tco1+ in fission yeast Alfica Sehgal, Bridget T. Hughes, and Peter J. Espenshade PMCID: PMC2330238 Evidence for Ku70/Ku80 association with full-length RAG1 Prafulla Raval, Aleksei N. Kriatchko, Sushil Kumar, and Patrick C. Swanson PMCID: PMC2330247 The effect of sequence context on spontaneous Polζ-dependent mutagenesis in Saccharomyces cerevisiae Amy L. Abdulovic, Brenda K. Minesinger, and Sue Jinks-Robertson PMCID: PMC2330250 RNA Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function Elzbieta Kierzek, Ryszard Kierzek, Walter N. Moss, Shawn M. Christensen, Thomas H. Eickbush, and Douglas H. Turner PMCID: PMC2346776 Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes Tomohiro Miyoshi and Toshio Uchiumi PMCID: PMC2330231 The 3′ processing factor CstF functions in the DNA repair response Nurit Mirkin, Danae Fonseca, Samia Mohammed, Murat A. Cevher, James L. Manley, and Frida E. Kleiman PMCID: PMC2330234 Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence Gilly Padalon-Brauch, Ruth Hershberg, Maya Elgrably-Weiss, Kobi Baruch, Ilan Rosenshine, Hanah Margalit, and Shoshy Altuvia PMCID: PMC2330248 Structural Biology Unexpected A-form formation of 4′-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance Akimasa Matsugami, Takako Ohyama, Masashi Inada, Naonori Inoue, Noriaki Minakawa, Akira Matsuda, and Masato Katahira PMCID: PMC2330235 Structure/function analysis of yeast ribosomal protein L2 Arturas Meskauskas, Johnathan R. Russ, and Jonathan D. Dinman PMCID: PMC2330241 NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops Jan Ferner, Alessandra Villa, Elke Duchardt, Elisabeth Widjajakusuma, Jens Wöhnert, Gerhard Stock, and Harald Schwalbe PMCID: PMC2346598 Genomics Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon Dmitry A. Rodionov, Xiaoqing Li, Irina A. Rodionova, Chen Yang, Leonardo Sorci, Etienne Dervyn, Dariusz Martynowski, Hong Zhang, Mikhail S. Gelfand, and Andrei L. Osterman PMCID: PMC2330245 Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators Dmitry A. Rodionov, Jessica De Ingeniis, Chiara Mancini, Flavio Cimadamore, Hong Zhang, Andrei L. Osterman, and Nadia Raffaelli PMCID: PMC2330246 Chemistry ‘Protected DNA Probes’ capable of strong hybridization without removal of base protecting groups Akihiro Ohkubo, Rintaro Kasuya, Kazushi Sakamoto, Kenichi Miyata, Haruhiko Taguchi, Hiroshi Nagasawa, Toshifumi Tsukahara, Takuma Watanobe, Yoshiyuki Maki, Kohji Seio, and Mitsuo Sekine PMCID: PMC2330233 Methods Online Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays Stuart Macgregor, Zhen Zhen Zhao, Anjali Henders, Martin G. Nicholas, Grant W. Montgomery, and Peter M. Visscher PMCID: PMC2346606 Enzymatic signal amplification of molecular beacons for sensitive DNA detection Jianwei Jeffery Li, Yizhuo Chu, Benjamin Yi-Hung Lee, and Xiaoliang Sunney Xie PMCID: PMC2346604 An optimized split-ubiquitin cDNA-library screening system to identify novel interactors of the human Frizzled 1 receptor Dietmar Dirnberger, Monika Messerschmid, and Ralf Baumeister PMCID: PMC2330230 Computational Biology Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein–protein interaction dataset Jie Guo, Xiaomei Wu, Da-Yong Zhang, and Kui Lin PMCID: PMC2346601 Nucleic Acid Enzymes From one amino acid to another: tRNA-dependent amino acid biosynthesis Kelly Sheppard, Jing Yuan, Michael J. Hohn, Brian Jester, Kevin M. Devine, and Dieter Söll PMCID: PMC2330236 Divergence of selenocysteine tRNA recognition by archaeal and eukaryotic O-phosphoseryl-tRNASec kinase R. Lynn Sherrer, Joanne M. L. Ho, and Dieter Söll PMCID: PMC2330242 Conformational changes of a Swi2/Snf2 ATPase during its mechano-chemical cycle Robert Lewis, Harald Dürr, Karl-Peter Hopfner, and Jens Michaelis PMCID: PMC2346605 A DNA-binding activity in BPV initiator protein E1 required for melting duplex ori DNA but not processive helicase activity initiated on partially single-stranded DNA Cyril M. Sanders PMCID: PMC2330243 Evidence for a functional dimeric form of the PcrA helicase in DNA unwinding Ye Yang, Shuo-Xing Dou, Hua Ren, Peng-Ye Wang, Xing-Dong Zhang, Min Qian, Bing-Yi Pan, and Xu Guang Xi PMCID: PMC2346599 Mechanistic consequences of temperature on DNA polymerization catalyzed by a Y-family DNA polymerase Kevin A. Fiala, Shanen M. Sherrer, Jessica A. Brown, and Zucai Suo PMCID: PMC2346602 Dynamics and consequences of DNA looping by the FokI restriction endonuclease Lucy E. Catto, Stuart R. W. Bellamy, Susan E. Retter, and Stephen E. Halford PMCID: PMC2346600 Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage Vera S. Brok-Volchanskaya, Farid A. Kadyrov, Dmitry E. Sivogrivov, Peter M. Kolosov, Andrey S. Sokolov, Michael G. Shlyapnikov, Valentine M. Kryukov, and Igor E. Granovsky PMCID: PMC2330249 Erratum Identification of cancer genes using a statistical framework for multi-experiment analysis of non-discretized array CGH data Christiaan Klijn, Henne Holstege, Jeroen de Ridder, Xiaoling Liu, Marcel Reinders, Jos Jonkers, and Lodewyk Wessels PMCID: PMC2330251 Corrects: Christiaan Klijn, et al. Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data. Nucleic Acids Res. 2008 February; 36(2): e13. |
