| | Molecular Biology siRNA-dependent and -independent post-transcriptional cosuppression of the LTR-retrotransposon MAGGY in the phytopathogenic fungus Magnaporthe oryzae Toshiki Murata, Naoki Kadotani, Miki Yamaguchi, Yukio Tosa, Shigeyuki Mayama, and Hitoshi Nakayashiki PMCID: PMC2094067 Tip60 functions as a potential corepressor of KLF4 in regulation of HDC promoter activity Walden Ai, Hai Zheng, Xiangdong Yang, Ying Liu, and Timothy C. Wang PMCID: PMC2094084 The Mediator subunit MED1/TRAP220 is required for optimal glucocorticoid receptor-mediated transcription activation Wei Chen and Robert G. Roeder PMCID: PMC2094069 Tryptophane-205 of human topoisomerase I is essential for camptothecin inhibition of negative but not positive supercoil removal Rikke From Frøhlich, Christopher Veigaard, Félicie Faucon Andersen, A. Kathleen McClendon, Amanda C. Gentry, Anni Hangaard Andersen, Neil Osheroff, Tinna Stevnsner, and Birgitta Ruth Knudsen PMCID: PMC2094083 Dynamic interactions within sub-complexes of the H/ACA pseudouridylation guide RNP Osama A. Youssef, Rebecca M. Terns, and Michael P. Terns PMCID: PMC2094053 The Arabidopsis homologs of trithorax (ATX1) and enhancer of zeste (CLF) establish ‘bivalent chromatin marks’ at the silent AGAMOUS locus Abdelaty Saleh, Ayed Al-Abdallat, Ivan Ndamukong, Raul Alvarez-Venegas, and Zoya Avramova PMCID: PMC2094062 Acetylation increases access of remodelling complexes to their nucleosome targets to enhance initiation of V(D)J recombination Karl P. Nightingale, Matthias Baumann, Anton Eberharter, Adamantios Mamais, Peter B. Becker, and Joan Boyes PMCID: PMC2094086 RNA In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5′ splice sites Kentaro Sahashi, Akio Masuda, Tohru Matsuura, Jun Shinmi, Zhujun Zhang, Yasuhiro Takeshima, Masafumi Matsuo, Gen Sobue, and Kinji Ohno PMCID: PMC2094079 Stabilization of SMAR1 mRNA by PGA2 involves a stem–loop structure in the 5′ UTR Lakshminarasimhan Pavithra, Shravanti Rampalli, Surajit Sinha, Kadreppa Sreenath, Richard G. Pestell, and Samit Chattopadhyay PMCID: PMC2094063 A specific role for the C-terminal region of the Poly(A)-binding protein in mRNA decay Ernesto Simón and Bertrand Séraphin PMCID: PMC2094065 Engineering the rRNA decoding site of eukaryotic cytosolic ribosomes in bacteria Sven N. Hobbie, Sarath K. Kalapala, Subramanian Akshay, Christian Bruell, Sebastian Schmidt, Sabine Dabow, Andrea Vasella, Peter Sander, and Erik C. Böttger PMCID: PMC2094070 Pseudoknot structures with conserved base triples in telomerase RNAs of ciliates Nikolai B. Ulyanov, Kinneret Shefer, Thomas L. James, and Yehuda Tzfati PMCID: PMC2094054 Novel rapidly evolving hominid RNAs bind nuclear factor 90 and display tissue-restricted distribution Andrew M. Parrott and Michael B. Mathews PMCID: PMC2094060 Deletion of the nuclear exosome component RRP6 leads to continued accumulation of the histone mRNA HTB1 in S-phase of the cell cycle in Saccharomyces cerevisiae Ruth Canavan and Ursula Bond PMCID: PMC2094057 A critical three-way junction is conserved in budding yeast and vertebrate telomerase RNAs Yogev Brown, Mira Abraham, Sivan Pearl, Majdi M. Kabaha, Elhanan Elboher, and Yehuda Tzfati PMCID: PMC2094081 Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine Qing Dai, Robert Fong, Mridusmita Saikia, David Stephenson, Yi-tao Yu, Tao Pan, and Joseph A. Piccirilli PMCID: PMC2094055 Structural Biology The arginine finger of the Bloom syndrome protein: its structural organization and its role in energy coupling Hua Ren, Shuo-Xing Dou, Pascal Rigolet, Ye Yang, Peng-Ye Wang, Mounira Amor-Gueret, and Xu Guang Xi PMCID: PMC2094072 Sequence-dependent DNA deformability studied using molecular dynamics simulations Satoshi Fujii, Hidetoshi Kono, Shigeori Takenaka, Nobuhiro Go, and Akinori Sarai PMCID: PMC2094071 NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA-modified aptamer Isabelle Lebars, Tristan Richard, Carmelo Di Primo, and Jean-Jacques Toulmé PMCID: PMC2094059 A study of 7-deaza-2′-deoxyguanosine–2′-deoxycytidine base pairing in DNA Manjori Ganguly, Feng Wang, Mahima Kaushik, Michael P. Stone, Luis A. Marky, and Barry Gold PMCID: PMC2094092 Survey and Summary DNA sequencing: bench to bedside and beyond Clyde A. Hutchison, III PMCID: PMC2094077 Genomics Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis Yoshiharu Y. Yamamoto, Hiroyuki Ichida, Tomoko Abe, Yutaka Suzuki, Sumio Sugano, and Junichi Obokata PMCID: PMC2094075 High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes Benjamin Lang, Nicolas Blot, Emeline Bouffartigues, Malcolm Buckle, Marcel Geertz, Claudio O. Gualerzi, Ramesh Mavathur, Georgi Muskhelishvili, Cynthia L. Pon, Sylvie Rimsky, Stefano Stella, M. Madan Babu, and Andrew Travers PMCID: PMC2094087 Methods Online Sequence specific detection of DNA using nicking endonuclease signal amplification (NESA) Traci Kiesling, Kendra Cox, Eugene A. Davidson, Kenneth Dretchen, Guy Grater, Shannon Hibbard, Roger S. Lasken, Jonathan Leshin, Evan Skowronski, and Mark Danielsen PMCID: PMC2094061 A UTF1-based selection system for stable homogeneously pluripotent human embryonic stem cell cultures Shen Mynn Tan, Siew Tein Wang, Hannes Hentze, and Peter Dröge PMCID: PMC2094078 Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements Marcel W. Coolen, Aaron L. Statham, Margaret Gardiner-Garden, and Susan J. Clark PMCID: PMC2094090 Short pyrosequencing reads suffice for accurate microbial community analysis Zongzhi Liu, Catherine Lozupone, Micah Hamady, Frederic D. Bushman, and Rob Knight PMCID: PMC2094085 Back to basics: the untreated rabbit reticulocyte lysate as a competitive system to recapitulate cap/poly(A) synergy and the selective advantage of IRES-driven translation Ricardo Soto Rifo, Emiliano P. Ricci, Didier Décimo, Olivier Moncorgé, and Théophile Ohlmann PMCID: PMC2094066 SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages Laurent Bianchetti, Yan Wu, Eric Guerin, Frédéric Plewniak, and Olivier Poch PMCID: PMC2094080 Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities Masatoshi Ichihara, Yoshiki Murakumo, Akio Masuda, Toru Matsuura, Naoya Asai, Mayumi Jijiwa, Maki Ishida, Jun Shinmi, Hiroshi Yatsuya, Shanlou Qiao, Masahide Takahashi, and Kinji Ohno PMCID: PMC2094068 Surveillance of siRNA integrity by FRET imaging Anne Järve, Julius Müller, Il-Han Kim, Karl Rohr, Caroline MacLean, Gert Fricker, Ulrich Massing, Florian Eberle, Alexander Dalpke, Roger Fischer, Michael F. Trendelenburg, and Mark Helm PMCID: PMC2094076 Nucleic Acid Enzymes An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro Arnaud Hecker, Nicolas Leulliot, Danièle Gadelle, Marc Graille, Anthony Justome, Pierre Dorlet, Céline Brochier, Sophie Quevillon-Cheruel, Eric Le Cam, Herman van Tilbeurgh, and Patrick Forterre PMCID: PMC2094082 Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/template complexes upon binding and incorporation of matched deoxynucleoside triphosphates H. Zhang, W. Cao, E. Zakharova, W. Konigsberg, and E. M. De La Cruz PMCID: PMC2094073 Hot-spot consensus of fluoroquinolone-mediated DNA cleavage by Gram-negative and Gram-positive type II DNA topoisomerases Sara N. Richter, Giulia Giaretta, Valentina Comuzzi, Elisabetta Leo, Lesley A. Mitchenall, L. Mark Fisher, Anthony Maxwell, and Manlio Palumbo PMCID: PMC2094056 An aminoacyl-tRNA synthetase:elongation factor complex for substrate channeling in archaeal translation Corinne D. Hausmann, Mette Prætorius-Ibba, and Michael Ibba PMCID: PMC2094089 The hSNM1 protein is a DNA 5′-exonuclease James Hejna, Sahaayaruban Philip, Jesse Ott, Craig Faulkner, and Robb Moses PMCID: PMC2094091 Chaperone activation of the hepadnaviral reverse transcriptase for template RNA binding is established by the Hsp70 and stimulated by the Hsp90 system Michael Stahl, Marco Retzlaff, Michael Nassal, and Jürgen Beck PMCID: PMC2094093 The human checkpoint sensor Rad9–Rad1–Hus1 interacts with and stimulates DNA repair enzyme TDG glycosylase Xin Guan, Amrita Madabushi, Dau-Yin Chang, Megan E. Fitzgerald, Gouli Shi, Alexander C. Drohat, and A-Lien Lu PMCID: PMC2094074 Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities Siu-hong Chan, Yongming Bao, Ewa Ciszak, Sophie Laget, and Shuang-yong Xu PMCID: PMC2094064 Structure-function study of maize ribosome-inactivating protein: implications for the internal inactivation region and the sole glutamate in the active site Amanda Nga-Sze Mak, Yuen-Ting Wong, Young-Jun An, Sun-Shin Cha, Kong-Hung Sze, Shannon Wing-Ngor Au, Kam-Bo Wong, and Pang-Chui Shaw PMCID: PMC2094058 Structural and functional analyses of disease-causing missense mutations in Bloom syndrome protein Rong-Bing Guo, Pascal Rigolet, Hua Ren, Bo Zhang, Xing-Dong Zhang, Shuo-Xing Dou, Peng-Ye Wang, Mounira Amor-Gueret, and Xu Guang Xi PMCID: PMC2094094 Corrigendum T1DBase: integration and presentation of complex data for type 1 diabetes research PMCID: PMC2094088 Corrects: Erin M. Hulbert, et al. T1DBase: integration and presentation of complex data for type 1 diabetes research. Nucleic Acids Res. 2007 January; 35(Database issue): D742–D746. |
