| | Gene Regulation, Chromatin and Epigenetics Phosphorylation of the carboxy-terminal domain of histone H1: effects on secondary structure and DNA condensation Alicia Roque, Inma Ponte, José Luis R. Arrondo, and Pedro Suau PMCID: PMC2504289 Molecular Biology The role of transcriptional activator GATA-1 at human β-globin HS2 Youngran Cho, Sang-Hyun Song, Jong Joo Lee, Narae Choi, Chul Geun Kim, Ann Dean, and AeRi Kim PMCID: PMC2504316 Development of an isoform-specific gene suppression system: the study of the human Pax-5B transcriptional element Gilles A. Robichaud, Jean-Pierre Perreault, and Rodney J. Ouellette PMCID: PMC2504290 Processing of triplex-directed psoralen DNA interstrand crosslinks by recombination mechanisms Yaobin Liu, Rodney S. Nairn, and Karen M. Vasquez PMCID: PMC2504320 DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight Daniel J. Weisenberger, Binh N. Trinh, Mihaela Campan, Shikhar Sharma, Tiffany I. Long, Suchitra Ananthnarayan, Gangning Liang, Francisco J. Esteva, Gabriel N. Hortobagyi, Frank McCormick, Peter A. Jones, and Peter W. Laird PMCID: PMC2504308 Efficient transfer of base changes from a vector to the rice genome by homologous recombination: involvement of heteroduplex formation and mismatch correction Yasuyo Johzuka-Hisatomi, Rie Terada, and Shigeru Iida PMCID: PMC2504299 The conserved N-terminal basic residues and zinc-finger motifs of HIV-1 nucleocapsid restrict the viral cDNA synthesis during virus formation and maturation Ludovic Didierlaurent, Laurent Houzet, Zakia Morichaud, Jean-Luc Darlix, and Marylène Mougel PMCID: PMC2504319 RNA The RNA-binding protein TbDRBD3 regulates the stability of a specific subset of mRNAs in trypanosomes Antonio M. Estévez PMCID: PMC2504296 MicroRNA regulation and the variability of human cortical gene expression Rui Zhang and Bing Su PMCID: PMC2504318 RNA secondary structure of the feline immunodeficiency virus 5′UTR and Gag coding region Laurie James and Bruno Sargueil PMCID: PMC2504303 Human DDX3 functions in translation and interacts with the translation initiation factor eIF3 Chung-Sheng Lee, Anusha P. Dias, Mark Jedrychowski, Arvind H. Patel, Jeanne L. Hsu, and Robin Reed PMCID: PMC2504307 Features of 80S mammalian ribosome and its subunits Tatyana V. Budkevich, Anna V. El'skaya, and Knud H. Nierhaus PMCID: PMC2504317 In vitro selection of small RNA-cleaving deoxyribozymes that cleave pyrimidine–pyrimidine junctions Kenny Schlosser, Jimmy Gu, Jeffrey C. F. Lam, and Yingfu Li PMCID: PMC2504313 Structural Biology Intramolecularly folded G-quadruplex and i-motif structures in the proximal promoter of the vascular endothelial growth factor gene Kexiao Guo, Vijay Gokhale, Laurence H. Hurley, and Daekyu Sun PMCID: PMC2504309 The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition Takashi Nagata, Sakura Suzuki, Ryuta Endo, Mikako Shirouzu, Takaho Terada, Makoto Inoue, Takanori Kigawa, Naohiro Kobayashi, Peter Güntert, Akiko Tanaka, Yoshihide Hayashizaki, Yutaka Muto, and Shigeyuki Yokoyama PMCID: PMC2504292 Structural analysis of the genetic switch that regulates the expression of restriction-modification genes John E. McGeehan, Simon D. Streeter, Sarah -J. Thresh, Neil Ball, Raimond B. G. Ravelli, and G. Geoff Kneale PMCID: PMC2504287 Dissecting direct and indirect readout of cAMP receptor protein DNA binding using an inosine and 2,6-diaminopurine in vitro selection system Søren Lindemose, Peter Eigil Nielsen, and Niels Erik Møllegaard PMCID: PMC2504297 Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector l-glutamine: implications of effector binding in molecular association and DNA binding Thirumananseri Kumarevel, Noboru Nakano, Karthe Ponnuraj, Subash C. B. Gopinath, Keiko Sakamoto, Akeo Shinkai, Penmetcha K. R. Kumar, and Shigeyuki Yokoyama PMCID: PMC2504300 Survey and Summary Survey of group I and group II introns in 29 sequenced genomes of the Bacillus cereus group: insights into their spread and evolution Nicolas J. Tourasse and Anne-Brit Kolstø PMCID: PMC2504315 Genomics Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing Elizabeth D. Wederell, Mikhail Bilenky, Rebecca Cullum, Nina Thiessen, Melis Dagpinar, Allen Delaney, Richard Varhol, YongJun Zhao, Thomas Zeng, Bridget Bernier, Matthew Ingham, Martin Hirst, Gordon Robertson, Marco A. Marra, Steven Jones, and Pamela A. Hoodless PMCID: PMC2504304 Spatial configuration of the chicken α-globin gene domain: immature and active chromatin hubs Alexey A. Gavrilov and Sergey V. Razin PMCID: PMC2504291 Methods Online Rapid and efficient construction of markerless deletions in the Escherichia coli genome Byung Jo Yu, Kui Hyeon Kang, Jun Hyoung Lee, Bong Hyun Sung, Mi Sun Kim, and Sun Chang Kim PMCID: PMC2504295 Real-time detection of Fe·EDTA/H2O2-induced DNA cleavage by linear dichroism Wei Wang, Gil Jun Lee, Kyeung Joo Jang, Tae Sub Cho, and Seog K. Kim PMCID: PMC2504293 Efficient delivery of RNA Interference to peripheral neurons in vivo using herpes simplex virus Anna-Maria Anesti, Pieter J. Peeters, Ines Royaux, and Robert S. Coffin PMCID: PMC2504301 Highly sensitive and specific microRNA expression profiling using BeadArray technology Jing Chen, Jean Lozach, Eliza Wickham Garcia, Bret Barnes, Shujun Luo, Ivan Mikoulitch, Lixin Zhou, Gary Schroth, and Jian-Bing Fan PMCID: PMC2504321 A protein–DNA docking benchmark Marc van Dijk and Alexandre M. J. J. Bonvin PMCID: PMC2504314 Multiple segmental and selective isotope labeling of large RNA for NMR structural studies Frank H. T. Nelissen, Adriaan J. van Gammeren, Marco Tessari, Frederic C. Girard, Hans A. Heus, and Sybren S. Wijmenga PMCID: PMC2504312 Light activation of transcription: photocaging of nucleotides for control over RNA polymerization André Vidal Pinheiro, Pedro Baptista, and João Carlos Lima PMCID: PMC2504310 A new method for robust quantitative and qualitative analysis of real-time PCR Eric B. Shain and John M. Clemens PMCID: PMC2504305 Computational Biology Revealing unique properties of the ribosome using a network based analysis Hilda David-Eden and Yael Mandel-Gutfreund PMCID: PMC2504294 Hit selection with false discovery rate control in genome-scale RNAi screens Xiaohua Douglas Zhang, Pei Fen Kuan, Marc Ferrer, Xiaohua Shu, Yingxue C. Liu, Adam T. Gates, Priya Kunapuli, Erica M. Stec, Min Xu, Shane D. Marine, Daniel J. Holder, Berta Strulovici, Joseph F. Heyse, and Amy S. Espeseth PMCID: PMC2504311 Nucleic Acid Enzymes An intrastrand three-DNA-base interaction is a key specificity determinant of F transfer initiation and of F TraI relaxase DNA recognition and cleavage Katherine Hekman, Kip Guja, Chris Larkin, and Joel F. Schildbach PMCID: PMC2504302 Dissection of reverse gyrase activities: insight into the evolution of a thermostable molecular machine Anna Valenti, Giuseppe Perugino, Anna D’Amaro, Andrea Cacace, Alessandra Napoli, Mosè Rossi, and Maria Ciaramella PMCID: PMC2504306 Partial reconstitution of DNA large loop repair with purified proteins from Saccharomyces cerevisiae Debbie Sommer, Carrie M. Stith, Peter M. J. Burgers, and Robert S. Lahue PMCID: PMC2504288 Inhibition of Mg2+ binding and DNA religation by bacterial topoisomerase I via introduction of an additional positive charge into the active site region Elena P. Sorokin, Bokun Cheng, Siddarth Rathi, Sandra J. Aedo, Maria V. Abrenica, and Yuk-Ching Tse-Dinh PMCID: PMC2504298 |
