| | Gene regulation, Chromatin and Epigenetics An intronic microRNA silences genes that are functionally antagonistic to its host gene Sailen Barik PMCID: PMC2532712 The orphan receptor ERRα interferes with steroid signaling Catherine Teyssier, Stéphanie Bianco, Olivia Lanvin, and Jean-Marc Vanacker PMCID: PMC2532727 Genome Integrity, Repair and Replication The Bloom's syndrome helicase (BLM) interacts physically and functionally with p12, the smallest subunit of human DNA polymerase δ Nives Selak, Csanád Z. Bachrati, Igor Shevelev, Tobias Dietschy, Barbara van Loon, Anette Jacob, Ulrich Hübscher, Joerg D. Hoheisel, Ian D. Hickson, and Igor Stagljar PMCID: PMC2532730 Dissecting the role of p53 phosphorylation in homologous recombination provides new clues for gain-of-function mutants Anja Restle, Martin Färber, Cindy Baumann, Michael Böhringer, Karl Heinz Scheidtmann, Carsten Müller-Tidow, and Lisa Wiesmüller PMCID: PMC2532731 Molecular Biology Molecular interactions of ASPP1 and ASPP2 with the p53 protein family and the apoptotic promoters PUMA and Bax Seema Patel, Roger George, Flavia Autore, Franca Fraternali, John E. Ladbury, and Penka V. Nikolova PMCID: PMC2532732 A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis Jana Prikryl, Kenneth P. Watkins, Giulia Friso, Klaas J. van Wijk, and Alice Barkan PMCID: PMC2532728 Positive roles of SAS2 in DNA replication and transcriptional silencing in yeast Yanfei Zou and Xin Bi PMCID: PMC2532737 Formation of an RNA polymerase II preinitiation complex on an RNA promoter derived from the hepatitis delta virus RNA genome Abrahem Abrahem and Martin Pelchat PMCID: PMC2532721 The RecU Holliday junction resolvase acts at early stages of homologous recombination Cristina Cañas, Begoña Carrasco, Silvia Ayora, and Juan C. Alonso PMCID: PMC2532717 A functional genome-wide RNAi screen identifies TAF1 as a regulator for apoptosis in response to genotoxic stress Junko Kimura, Su Tien Nguyen, Hanshao Liu, Naoe Taira, Yoshio Miki, and Kiyotsugu Yoshida PMCID: PMC2532742 Stringent promoter recognition and autoregulation by the group 3 σ-factor SigF in the cyanobacterium Synechocystis sp. strain PCC 6803 Munehiko Asayama and Sousuke Imamura PMCID: PMC2532724 Intragenic suppressors of temperature-sensitive rne mutations lead to the dissociation of RNase E activity on mRNA and tRNA substrates in Escherichia coli Tariq Perwez, Danyal Hami, Valerie F. Maples, Zhao Min, Bi-Cheng Wang, and Sidney R. Kushner PMCID: PMC2532720 N-Myc downstream-regulated gene 2 is involved in p53-mediated apoptosis Na Liu, Lifeng Wang, Xia Li, Qi Yang, Xinping Liu, Jing Zhang, Jian Zhang, Yousheng Wu, Shaoping Ji, Yingqi Zhang, Angang Yang, Hua Han, and Libo Yao PMCID: PMC2532733 RNA Frequency and fate of microRNA editing in human brain Yukio Kawahara, Molly Megraw, Edward Kreider, Hisashi Iizasa, Louis Valente, Artemis G. Hatzigeorgiou, and Kazuko Nishikura PMCID: PMC2532740 Tetrahymena thermophila and Candida albicans Group I intron-derived ribozymes can catalyze the trans-excision-splicing reaction P. Patrick Dotson, II, Ashley K. Johnson, and Stephen M. Testa PMCID: PMC2532722 The sequence selectivity of KSRP explains its flexibility in the recognition of the RNA targets María Flor García-Mayoral, Irene Díaz-Moreno, David Hollingworth, and Andres Ramos PMCID: PMC2532734 miR-16 family induces cell cycle arrest by regulating multiple cell cycle genes Qin Liu, Hanjiang Fu, Fang Sun, Haoming Zhang, Yi Tie, Jie Zhu, Ruiyun Xing, Zhixian Sun, and Xiaofei Zheng PMCID: PMC2532718 Structural Biology The structure of SgrAI bound to DNA; recognition of an 8 base pair target Pete W. Dunten, Elizabeth J. Little, Mark T. Gregory, Veena M. Manohar, Michael Dalton, David Hough, Jurate Bitinaite, and Nancy C. Horton PMCID: PMC2532715 Survey and Summary The triple helix: 50 years later, the outcome Maria Duca, Pierre Vekhoff, Kahina Oussedik, Ludovic Halby, and Paola B. Arimondo PMCID: PMC2532714 Genomics A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library Chaysavanh Manichanh, Charles E. Chapple, Lionel Frangeul, Karine Gloux, Roderic Guigo, and Joel Dore PMCID: PMC2532719 Methods Online Specific ligation to double-stranded RNA for analysis of cellular RNA::RNA interactions Omid R. Faridani, Gerald M. McInerney, Katarina Gradin, and Liam Good PMCID: PMC2532711 Detection of Adriamycin–DNA adducts by accelerator mass spectrometry at clinically relevant Adriamycin concentrations Kate E. Coldwell, Suzanne M. Cutts, Ted J. Ognibene, Paul T. Henderson, and Don R. Phillips PMCID: PMC2532723 Intronically encoded siRNAs improve dynamic range of mammalian gene regulation systems and toggle switch David Greber, Marie Daoud El-Baba, and Martin Fussenegger PMCID: PMC2532736 Phenotypic engineering by reprogramming gene transcription using novel artificial transcription factors in Escherichia coli Ju Young Lee, Bong Hyun Sung, Byung Jo Yu, Jun Hyoung Lee, Sang Hee Lee, Mi Sun Kim, Michael D. Koob, and Sun Chang Kim PMCID: PMC2532725 Transduction of artificial transcriptional regulatory proteins into human cells Chae-Ok Yun, Hyun-Chul Shin, Tae-Dong Kim, Wan-Hee Yoon, Yoon-A Kang, Heung-Sun Kwon, Seong Keun Kim, and Jin-Soo Kim PMCID: PMC2532713 End-joining long nucleic acid polymers M. van den Hout, S. Hage, C. Dekker, and N. H. Dekker PMCID: PMC2532729 Substantial biases in ultra-short read data sets from high-throughput DNA sequencing Juliane C. Dohm, Claudio Lottaz, Tatiana Borodina, and Heinz Himmelbauer PMCID: PMC2532726 Computational Biology Genome-wide identification of in vivo protein–DNA binding sites from ChIP-Seq data Raja Jothi, Suresh Cuddapah, Artem Barski, Kairong Cui, and Keji Zhao PMCID: PMC2532738 The cis-regulatory map of Shewanella genomes Jiajian Liu, Xing Xu, and Gary D. Stormo PMCID: PMC2532739 Nucleic Acid Enzymes A comparative analysis of two conserved motifs in bacterial poly(A) polymerase and CCA-adding enzyme Andrea Just, Falk Butter, Michelle Trenkmann, Tony Heitkam, Mario Mörl, and Heike Betat PMCID: PMC2532741 Hyperthermophilic Aquifex aeolicus initiates primer synthesis on a limited set of trinucleotides comprised of cytosines and guanines Marilynn A. Larson, Rafael Bressani, Khalid Sayood, Jacob E. Corn, James M. Berger, Mark A. Griep, and Steven H. Hinrichs PMCID: PMC2532735 Interactions between branched DNAs and peptide inhibitors of DNA repair Kevin V. Kepple, Namita Patel, Peter Salamon, and Anca M. Segall PMCID: PMC2532710 DNA base flipping by both members of the PspGI restriction–modification system Michael A. Carpenter and Ashok S. Bhagwat PMCID: PMC2532716 Corrigendum Short-hairpin RNAs synthesized by T7 phage polymerase do not induce interferon Takuma Gondai, Kazuya Yamaguchi, Naoko Miyano-Kurosaki, Yuichirou Habu, and Hiroshi Takaku PMCID: PMC2532709 Corrects: Takuma Gondai, et al. Short-hairpin RNAs synthesized by T7 phage polymerase do not induce interferon. Nucleic Acids Res. 2008 September; 36(16): 5426. |
