| | Other Issues: previous | next | latest | archiveFront-Matter/Back-Matter Nucleic Acids Research: VOLUME 36 ISSUE 20 2008 PMCID: PMC2582598 Nucleic Acids Res. 2008 November; 36(20): ii. Published online 2008 November. doi: 10.1093/nar/gkn949.PMCID: PMC2582623 Nucleic Acids Res. 2008 November; 36(20): iii. Published online 2008 November. doi: 10.1093/nar/gkn951.PMCID: PMC2582605 Gene regulation, Chromatin and Epigenetics Stra13/DEC1 and DEC2 inhibit sterol regulatory element binding protein-1c in a hypoxia-inducible factor-dependent mechanism Su Mi Choi, Hyun-Ju Cho, Heesang Cho, Kang Ho Kim, Jae Bum Kim, and Hyunsung Park PMCID: PMC2582599 The Cohesin loading factor NIPBL recruits histone deacetylases to mediate local chromatin modifications Philipp Jahnke, Weizhen Xu, Manuela Wülling, Melanie Albrecht, Heinz Gabriel, Gabriele Gillessen-Kaesbach, and Frank J. Kaiser PMCID: PMC2582609 Analysis of regulatory network topology reveals functionally distinct classes of microRNAs Xueping Yu, Jimmy Lin, Donald J. Zack, Joshua T. Mendell, and Jiang Qian PMCID: PMC2582613 CRX controls retinal expression of the X-linked juvenile retinoschisis (RS1) gene Thomas Langmann, Christine C. L. Lai, Karin Weigelt, Beatrice M. Tam, Regina Warneke-Wittstock, Orson L. Moritz, and Bernhard H. F. Weber PMCID: PMC2582616 NF-Y substitutes H2A-H2B on active cell-cycle promoters: recruitment of CoREST-KDM1 and fine-tuning of H3 methylations Raffaella Gatta and Roberto Mantovani PMCID: PMC2582630 Genome Integrity, Repair and Replication Rad9 plays an important role in DNA mismatch repair through physical interaction with MLH1 Wei He, Yun Zhao, Chunbo Zhang, Lili An, Zhishang Hu, Yuheng Liu, Lu Han, Lijun Bi, Zhensheng Xie, Peng Xue, Fuquan Yang, and Haiying Hang PMCID: PMC2582629 Rad51 gain-of-function mutants that exhibit high affinity DNA binding cause DNA damage sensitivity in the absence of Srs2 Punjab S. Malik and Lorraine S. Symington PMCID: PMC2582631 Molecular Biology Delivery of steric block morpholino oligomers by (R-X-R)4 peptides: structure–activity studies Rachida Abes, Hong M. Moulton, Philippe Clair, Sung-Tae Yang, Said Abes, Kamran Melikov, Paul Prevot, Derek S. Youngblood, Patrick L. Iversen, Leonid V. Chernomordik, and Bernard Lebleu PMCID: PMC2582615 Regional mutagenesis of the gene encoding the phage Mu late gene activator C identifies two separate regions important for DNA binding Yide Jiang and Martha M. Howe PMCID: PMC2582627 Improved cell-penetrating peptide–PNA conjugates for splicing redirection in HeLa cells and exon skipping in mdx mouse muscle Gabriela D. Ivanova, Andrey Arzumanov, Rachida Abes, Haifang Yin, Matthew J. A. Wood, Bernard Lebleu, and Michael J. Gait PMCID: PMC2582604 Transcription elongation past O6-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase Alexandra Dimitri, John A. Burns, Suse Broyde, and David A. Scicchitano PMCID: PMC2582612 Epstein–Barr virus latent membrane protein 1 trans-activates miR-155 transcription through the NF-κB pathway Graziana Gatto, Annalisa Rossi, Daniela Rossi, Sven Kroening, Stefano Bonatti, and Massimo Mallardo PMCID: PMC2582607 RNA Evolution of Arabidopsis MIR genes generates novel microRNA classes Franck Vazquez, Todd Blevins, Jérôme Ailhas, Thomas Boller, and Frederick Meins, Jr PMCID: PMC2582634 Fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy reveal the cytoplasmic origination of loaded nuclear RISC in vivo in human cells Thomas Ohrt, Jörg Mütze, Wolfgang Staroske, Lasse Weinmann, Julia Höck, Karin Crell, Gunter Meister, and Petra Schwille PMCID: PMC2582625 Translation affects YoeB and MazF messenger RNA interferase activities by different mechanisms Mikkel Christensen-Dalsgaard and Kenn Gerdes PMCID: PMC2582610 A role for the Dicer helicase domain in the processing of thermodynamically unstable hairpin RNAs Harris S. Soifer, Masayuki Sano, Kumi Sakurai, Pritsana Chomchan, Pål Sætrom, Mark A. Sherman, Michael A. Collingwood, Mark A. Behlke, and John J. Rossi PMCID: PMC2582626 Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNAMet Hrvoje Lusic, Estella M. Gustilo, Franck A.P. Vendeix, Rob Kaiser, Michael O. Delaney, William D. Graham, Virginia A. Moye, William A. Cantara, Paul F. Agris, and Alexander Deiters PMCID: PMC2582600 Novel mechanism of hexamer ring assembly in protein/RNA interactions revealed by single molecule imaging Feng Xiao, Hui Zhang, and Peixuan Guo PMCID: PMC2582624 Structural Biology The N-clasp of human DNA polymerase κ promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions Lei Jia, Nicholas E. Geacintov, and Suse Broyde PMCID: PMC2582633 Structural explanation for the role of Mn2+ in the activity of ϕ6 RNA-dependent RNA polymerase Minna M. Poranen, Paula S. Salgado, Minni R. L. Koivunen, Sam Wright, Dennis H. Bamford, David I. Stuart, and Jonathan M. Grimes PMCID: PMC2582606 Survey and Summary The assembly of a spliceosomal small nuclear ribonucleoprotein particle Snehal Bhikhu Patel and Michel Bellini PMCID: PMC2582628 Genomics Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs Jun-ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, Yoshiharu Sato, Masahide Seki, Takuma Irie, Nono Takeuchi, Takuya Ueda, Mitsuteru Nakao, Sumio Sugano, Takashi Gojobori, and Tadashi Imanishi PMCID: PMC2582632 Whole genome exon arrays identify differential expression of alternatively spliced, cancer-related genes in lung cancer Liqiang Xi, Andrew Feber, Vanita Gupta, Maoxin Wu, Andrew D. Bergemann, Rodney J. Landreneau, Virginia R. Litle, Arjun Pennathur, James D. Luketich, and Tony E. Godfrey PMCID: PMC2582617 Methods Online A sensitive array-based assay for identifying multiple TMPRSS2:ERG fusion gene variants Qing Lu, Esperanza Nunez, Chunrun Lin, Kimberly Christensen, Tracy Downs, Dennis A. Carson, Jessica Wang-Rodriguez, and Yu-Tsueng Liu PMCID: PMC2582611 Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance Alexandre V. Lebedev, Natasha Paul, Joyclyn Yee, Victor A. Timoshchuk, Jonathan Shum, Kei Miyagi, Jack Kellum, Richard I. Hogrefe, and Gerald Zon PMCID: PMC2582603 Multi-stringency wash of partially hybridized 60-mer probes reveals that the stringency along the probe decreases with distance from the microarray surface Lena Poulsen, Martin Jensen Søe, Detlef Snakenborg, Lisbeth Birk Møller, and Martin Dufva PMCID: PMC2582620 Enhanced gene trapping in mouse embryonic stem cells Frank Schnütgen, Jens Hansen, Silke De-Zolt, Carsten Horn, Marcus Lutz, Thomas Floss, Wolfgang Wurst, Patricia Ruiz Noppinger, and Harald von Melchner PMCID: PMC2582619 In vivo evaluation of PhiC31 recombinase activity using a self-excision cassette Eugenio Sangiorgi, Zhang Shuhua, and Mario R. Capecchi PMCID: PMC2582622 Analysis of factor interactions with RNA polymerase II elongation complexes using a new electrophoretic mobility shift assay Bo Cheng and David H. Price PMCID: PMC2582608 Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species KiYoung Lee, Han-Yu Chuang, Andreas Beyer, Min-Kyung Sung, Won-Ki Huh, Bonghee Lee, and Trey Ideker PMCID: PMC2582614 Gene expression module-based chemical function similarity search Yun Li, Pei Hao, Siyuan Zheng, Kang Tu, Haiwei Fan, Ruixin Zhu, Guohui Ding, Changzheng Dong, Chuan Wang, Xuan Li, H.-J. Thiesen, Y. Eugene Chen, Hualiang Jiang, Lei Liu, and Yixue Li PMCID: PMC2582597 Computational Biology Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments Stefan E. Seemann, Jan Gorodkin, and Rolf Backofen PMCID: PMC2582601 A competitive hybridization model predicts probe signal intensity on high density DNA microarrays Shuzhao Li, Alex Pozhitkov, and Marius Brouwer PMCID: PMC2582621 Nucleic Acid Enzymes Examining the ribonuclease H primer grip of HIV-1 reverse transcriptase by charge neutralization of RNA/DNA hybrids Chandravanu Dash, Brian J. Scarth, Christopher Badorrek, Matthias Götte, and Stuart F. J. Le Grice PMCID: PMC2582618 MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection Richard D. Morgan, Tanya K. Bhatia, Lindsay Lovasco, and Theodore B. Davis PMCID: PMC2582602 |
