| | Front-Matter/Back-Matter Nucleic Acids Research: VOLUME 36 ISSUE 19 2008 PMCID: PMC2577352 Nucleic Acids Res. 2008 November; 36(19): ii. Published online 2008 November. doi: 10.1093/nar/gkn907.PMCID: PMC2577332 Nucleic Acids Res. 2008 November; 36(19): iii. Published online 2008 November. doi: 10.1093/nar/gkn909.PMCID: PMC2577351 Gene Regulation, Chromatin and Epigenetics Long intronic GAA•TTC repeats induce epigenetic changes and reporter gene silencing in a molecular model of Friedreich ataxia E. Soragni, D. Herman, S. Y. R. Dent, J. M. Gottesfeld, R. D. Wells, and M. Napierala PMCID: PMC2577344 Sumoylation of LAP1 is involved in the HDAC4-mediated repression of COX-2 transcription Wen-Ling Wang, Yi-Chao Lee, Wen-Ming Yang, Wen-Chang Chang, and Ju-Ming Wang PMCID: PMC2577330 Human SWI/SNF directs sequence-specific chromatin changes on promoter polynucleosomes Hillel I. Sims, Cassandra B. Baughman, and Gavin R. Schnitzler PMCID: PMC2577362 Nonradioactive, ultrasensitive site-specific protein–protein photocrosslinking: interactions of α-helix 2 of TATA-binding protein with general transcription factor TFIIA and transcriptional repressor NC2 Younggyu Kim, Yon W. Ebright, Adam R. Goodman, Danny Reinberg, and Richard H. Ebright PMCID: PMC2577341 A novel DNA sequence periodicity decodes nucleosome positioning Kaifu Chen, Qingshu Meng, Lina Ma, Qingyou Liu, Petrus Tang, Chungshung Chiu, Songnian Hu, and Jun Yu PMCID: PMC2577358 Context dependent function of APPb enhancer identified using enhancer trap-containing BACs as transgenes in zebrafish Leighcraft A. Shakes, Tennison L. Malcolm, Kevin L. Allen, Supriyo De, Ken R. Harewood, and Pradeep K. Chatterjee PMCID: PMC2577333 Genome Integrity, Repair and Replication Identification of the Xenopus DNA2 protein as a major nuclease for the 5′→3′ strand-specific processing of DNA ends Shuren Liao, Thomas Toczylowski, and Hong Yan PMCID: PMC2577336 Impact of non-homologous end-joining deficiency on random and targeted DNA integration: implications for gene targeting Susumu Iiizumi, Aya Kurosawa, Sairei So, Yasuyuki Ishii, Yuichi Chikaraishi, Ayako Ishii, Hideki Koyama, and Noritaka Adachi PMCID: PMC2577324 Molecular Biology Nuclear export competence of pre-40S subunits in fission yeast requires the ribosomal protein Rps2 Audrey Perreault, Clément Bellemer, and Francois Bachand PMCID: PMC2577348 Overexpression of the LexA-regulated tisAB RNA in E. coli inhibits SOS functions; implications for regulation of the SOS response Ragnhild Weel-Sneve, Magnar Bjørås, and Knut Ivan Kristiansen PMCID: PMC2577331 Rapid regulation of telomere length is mediated by poly(ADP-ribose) polymerase-1 Sascha Beneke, Odile Cohausz, Maria Malanga, Petra Boukamp, Felix Althaus, and Alexander Bürkle PMCID: PMC2577345 RNA Stress-induced tRNA-derived RNAs: a novel class of small RNAs in the primitive eukaryote Giardia lamblia Yan Li, Jun Luo, Hui Zhou, Jian-You Liao, Li-Ming Ma, Yue-Qin Chen, and Liang-Hu Qu PMCID: PMC2577346 Amino acid sequence variations in Nicotiana CRR4 orthologs determine the species-specific efficiency of RNA editing in plastids Kenji Okuda, Yuya Habata, Yoshichika Kobayashi, and Toshiharu Shikanai PMCID: PMC2577327 Identification of the Rem-responsive element of mouse mammary tumor virus Matthias Müllner, Brian Salmons, Walter H. Günzburg, and Stanislav Indik PMCID: PMC2577329 MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic β-actin gene Tanay Ghosh, Kartik Soni, Vinod Scaria, Mahantappa Halimani, Chaitali Bhattacharjee, and Beena Pillai PMCID: PMC2577349 Structural Biology Central base pair flipping and discrimination by PspGI Roman H. Szczepanowski, Michael A. Carpenter, Honorata Czapinska, Mindaugas Zaremba, Gintautas Tamulaitis, Virginijus Siksnys, Ashok S. Bhagwat, and Matthias Bochtler PMCID: PMC2577326 Ribosomal protein L3 functions as a ‘rocker switch’ to aid in coordinating of large subunit-associated functions in eukaryotes and Archaea Arturas Meskauskas and Jonathan D. Dinman PMCID: PMC2577335 Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit Alexey N. Petrov, Arturas Meskauskas, Sara C. Roshwalb, and Jonathan D. Dinman PMCID: PMC2577338 Survey and Summary MECP2 genomic structure and function: insights from ENCODE Jasmine Singh, Alka Saxena, John Christodoulou, and David Ravine PMCID: PMC2577328 Genomics Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element Raquel S. Linheiro and Casey M. Bergman PMCID: PMC2577343 G-quadruplexes: the beginning and end of UTRs Julian Leon Huppert, Anthony Bugaut, Sunita Kumari, and Shankar Balasubramanian PMCID: PMC2577360 Evolutionary origins of human apoptosis and genome-stability gene networks Mauro A. A. Castro, Rodrigo J. S. Dalmolin, José C. F. Moreira, José C. M. Mombach, and Rita M. C. de Almeida PMCID: PMC2577361 Methods Online Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology Richard Cronn, Aaron Liston, Matthew Parks, David S. Gernandt, Rongkun Shen, and Todd Mockler PMCID: PMC2577356 Fluorescence detection of single nucleotide polymorphisms using a universal molecular beacon Yang-Wei Lin, Hsin-Tsung Ho, Chih-Ching Huang, and Huan-Tsung Chang PMCID: PMC2577337 Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli Juliane Neupert, Daniel Karcher, and Ralph Bock PMCID: PMC2577334 Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments Xiaochun Fan, Nathan Lamarre-Vincent, Qian Wang, and Kevin Struhl PMCID: PMC2577354 Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms Sharon J. Diskin, Mingyao Li, Cuiping Hou, Shuzhang Yang, Joseph Glessner, Hakon Hakonarson, Maja Bucan, John M. Maris, and Kai Wang PMCID: PMC2577347 Epitope tagging of endogenous genes in diverse human cell lines Jung-Sik Kim, Challice Bonifant, Fred Bunz, William S. Lane, and Todd Waldman PMCID: PMC2577350 Cell-free selection of RNA-binding proteins using in vitro compartmentalization Yu Chen, Jana Mandic, and Gabriele Varani PMCID: PMC2577342 Tentacle probe sandwich assay in porous polymer monolith improves
specificity, sensitivity and kinetics Brent C. Satterfield, Michael R. Caplan, and Jay A. A. West PMCID: PMC2577359 Computational Biology Predicting transcription factor specificity with all-atom models Sahand Jamal Rahi, Peter Virnau, Leonid A. Mirny, and Mehran Kardar PMCID: PMC2577325 Nucleic Acid Enzymes Regulation of the catalytic function of topoisomerase II alpha through association with RNA Seung-Won Park, Andrew M. Parrott, David T. Fritz, Yongkyu Park, Michael B. Mathews, and Chee-Gun Lee PMCID: PMC2577339 How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets Gintautas Tamulaitis, Mindaugas Zaremba, Roman H. Szczepanowski, Matthias Bochtler, and Virginijus Siksnys PMCID: PMC2577355 Hairpin structures formed by alpha satellite DNA of human centromeres are cleaved by human topoisomerase IIα Anette Thyssen Jonstrup, Tina Thomsen, Yong Wang, Birgitta R. Knudsen, Jørn Koch, and Anni H. Andersen PMCID: PMC2577340 Archaeal RNA ligase is a homodimeric protein that catalyzes intramolecular ligation of single-stranded RNA and DNA Christopher Torchia, Yuko Takagi, and C. Kiong Ho PMCID: PMC2577357 Biochemical analysis of human PIF1 helicase and functions of its N-terminal domain Yongqing Gu, Yuji Masuda, and Kenji Kamiya PMCID: PMC2577353 |
