| | Molecular Biology Two conserved modules of Schizosaccharomyces pombe Mediator regulate distinct cellular pathways Tomas Linder, Nina N. Rasmussen, Camilla O. Samuelsen, Emmanouella Chatzidaki, Vera Baraznenok, Jenny Beve, Peter Henriksen, Claes M. Gustafsson, and Steen Holmberg PMCID: PMC2377428 Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping Davide Normanno, Francesco Vanzi, and Francesco Saverio Pavone PMCID: PMC2377426 Molecular dissection of Penelope transposable element regulatory machinery Nataliya Schostak, Konstantin Pyatkov, Elena Zelentsova, Irina Arkhipova, Dmitrii Shagin, Irina Shagina, Elena Mudrik, Anatolii Blintsov, Ivan Clark, David J. Finnegan, and Michael Evgen’ev PMCID: PMC2377424 Distinct roles of XRCC4 and Ku80 in non-homologous end-joining of endonuclease- and ionizing radiation-induced DNA double-strand breaks Leonie Schulte-Uentrop, Raafat A. El-Awady, Lena Schliecker, Henning Willers, and Jochen Dahm-Daphi PMCID: PMC2377445 Mitogen-induced recruitment of ERK and MSK to SRE promoter complexes by ternary complex factor Elk-1 Hong-Mei Zhang, Li Li, Nektaria Papadopoulou, Glenn Hodgson, Emma Evans, Matthew Galbraith, Mark Dear, Stéphanie Vougier, Janice Saxton, and Peter E. Shaw PMCID: PMC2377423 Sequence homology and microhomology dominate chromosomal double-strand break repair in African trypanosomes Lucy Glover, Richard McCulloch, and David Horn PMCID: PMC2377438 Determinants of a transcriptionally competent environment at the GM-CSF promoter K. H. Brettingham-Moore, O. R. Sprod, X. Chen, P. Oakford, M. F. Shannon, and A. F. Holloway PMCID: PMC2377420 Autoregulation of the Escherichia coli melR promoter: repression involves four molecules of MelR Shivanthi Samarasinghe, Mohamed Samir El-Robh, David C. Grainger, Wenke Zhang, Panos Soultanas, and Stephen J. W. Busby PMCID: PMC2377442 Transforming growth factor-β-regulated miR-24 promotes skeletal muscle differentiation Qiang Sun, Yan Zhang, Guang Yang, Xiaoping Chen, Yingai Zhang, Guojun Cao, Jian Wang, Yanxun Sun, Peng Zhang, Ming Fan, Ningsheng Shao, and Xiao Yang PMCID: PMC2377434 Intracellular delivery of an anionic antisense oligonucleotide via receptor-mediated endocytosis Md Rowshon Alam, Vidula Dixit, Hyunmin Kang, Zi-Bo Li, Xiaoyuan Chen, JoAnn Trejo, Michael Fisher, and Rudy L. Juliano PMCID: PMC2377441 A BBP–Mud2p heterodimer mediates branchpoint recognition and influences splicing substrate abundance in budding yeast Qiang Wang, Li Zhang, Bert Lynn, and Brian C. Rymond PMCID: PMC2377449 RNA Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in ribosomal RNAs Sébastien Muller, Fabrice Leclerc, Isabelle Behm-Ansmant, Jean-Baptiste Fourmann, Bruno Charpentier, and Christiane Branlant PMCID: PMC2377435 Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA Gelina S. Kopeina, Zhanna A. Afonina, Kira V. Gromova, Vladimir A. Shirokov, Victor D. Vasiliev, and Alexander S. Spirin PMCID: PMC2377419 Evolution of acceptor stem tRNA recognition by class II prolyl-tRNA synthetase Songon An, George Barany, and Karin Musier-Forsyth PMCID: PMC2377447 Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses Peter Simmonds, Ioannis Karakasiliotis, Dalan Bailey, Yasmin Chaudhry, David J. Evans, and Ian G. Goodfellow PMCID: PMC2377429 The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli Birte Reichenbach, Alexandre Maes, Falk Kalamorz, Eliane Hajnsdorf, and Boris Görke PMCID: PMC2377431 A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting Pei-Yu Liao, Prateek Gupta, Alexey N. Petrov, Jonathan D. Dinman, and Kelvin H. Lee PMCID: PMC2377451 The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates Jiro Kondo and Eric Westhof PMCID: PMC2377432 Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis Christoph Jöchl, Mathieu Rederstorff, Jana Hertel, Peter F. Stadler, Ivo L. Hofacker, Markus Schrettl, Hubertus Haas, and Alexander Hüttenhofer PMCID: PMC2377427 Dissecting protein–RNA recognition sites Ranjit Prasad Bahadur, Martin Zacharias, and Joël Janin PMCID: PMC2377425 Recognition of tRNALeu by Aquifex aeolicus leucyl-tRNA synthetase during the aminoacylation and editing steps Peng Yao, Bin Zhu, Sophie Jaeger, Gilbert Eriani, and En-Duo Wang PMCID: PMC2377443 Structural Biology Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins Sunggeon Ko, Sung-Hoon Jun, Hansol Bae, Jung-Sue Byun, Woong Han, Heeyoung Park, Seong Wook Yang, Sam-Yong Park, Young Ho Jeon, Chaejoon Cheong, Woo Taek Kim, Weontae Lee, and Hyun-Soo Cho PMCID: PMC2377444 Structural probing of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands Kevin B. Turner, Robert G. Brinson, Hye Young Yi-Brunozzi, Jason W. Rausch, Jennifer T. Miller, Stuart F.J. Le Grice, John P. Marino, and Daniele Fabris PMCID: PMC2377446 Genomics A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system Marcus B. Noyes, Xiangdong Meng, Atsuya Wakabayashi, Saurabh Sinha, Michael H. Brodsky, and Scot A. Wolfe PMCID: PMC2377422 The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements Alan K. Todd and Stephen Neidle PMCID: PMC2377421 Spontaneous symmetry breaking in genome evolution Yaroslav Ryabov and Michael Gribskov PMCID: PMC2377439 Methods Online A dual-tag microarray platform for high-performance nucleic acid and protein analyses Olle Ericsson, Jonas Jarvius, Edith Schallmeiner, Mathias Howell, Rachel Yuan Nong, Hendrik Reuter, Meinhard Hahn, Johan Stenberg, Mats Nilsson, and Ulf Landegren PMCID: PMC2377440 Detecting cis-regulatory binding sites for cooperatively binding proteins Liesbeth van Oeffelen, Pierre Cornelis, Wouter Van Delm, Fedor De Ridder, Bart De Moor, and Yves Moreau PMCID: PMC2377448 Exalign: a new method for comparative analysis of exon–intron gene structures Giulio Pavesi, Federico Zambelli, Corrado Caggese, and Graziano Pesole PMCID: PMC2377436 Computational Biology A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence Osamu Gotoh PMCID: PMC2377433 The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site Kannan Tharakaraman, Olivier Bodenreider, David Landsman, John L. Spouge, and Leonardo Mariño-Ramírez PMCID: PMC2377430 Nucleic Acid Enzymes Real-time kinetics of restriction–modification gene expression after entry into a new host cell Iwona Mruk and Robert M. Blumenthal PMCID: PMC2377437 Human abasic endonuclease action on multilesion abasic clusters: implications for radiation-induced biological damage Brigitte Paap, David M. Wilson, III, and Betsy M. Sutherland PMCID: PMC2377450 |
