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Hypothesis Do anticodons of misacylated tRNAs preferentially mismatch codons coding for the misloaded amino acid? Hervé Seligmann PMCID: PMC2887445 Research articles Multipoint-likelihood maximization mapping on 4 segregating populations to achieve an integrated framework map for QTL analysis in pot azalea (Rhododendron simsii hybrids) Ellen De Keyser, Qing Yan Shu, Erik Van Bockstaele, and Jan De Riek PMCID: PMC2837023 Non-consensus GLI binding sites in Hedgehog target gene regulation Martina Winklmayr, Carmen Schmid, Sandra Laner-Plamberger, Alexandra Kaser, Fritz Aberger, Thomas Eichberger, and Anna-Maria Frischauf PMCID: PMC2830928 The transforming acidic coiled coil (TACC1) protein modulates the transcriptional activity of the nuclear receptors TR and RAR Romain Guyot, Séverine Vincent, Julie Bertin, Jacques Samarut, and Patrick Ravel-Chapuis PMCID: PMC2822774 Halogenated imidazole derivatives block RNA polymerase II elongation along mitogen inducible genes Michal Mikula, Karolina Hanusek, Agnieszka Paziewska, Artur Dzwonek, Tymon Rubel, Karol Bomsztyk, and Jerzy Ostrowski PMCID: PMC2824761 Upstream Stimulating Factors 1 and 2 Enhance Transcription from the Placenta-Specific Promoter 1.1 of the Bovine Cyp19 Gene Rainer Fürbass, Wolfgang Tomek, and Jens Vanselow PMCID: PMC2822775 Expression profiling and cross-species RNA interference (RNAi) of desiccation-induced transcripts in the anhydrobiotic nematode Aphelenchus avenae Wesley Reardon, Sohini Chakrabortee, Tiago Campos Pereira, Trevor Tyson, Matthew C Banton, Katharine M Dolan, Bridget A Culleton, Michael J Wise, Ann M Burnell, and Alan Tunnacliffe PMCID: PMC2825203 Reference genes for normalising gene expression data in collagenase-induced rat intracerebral haemorrhage Naomi L Cook, Timothy J Kleinig, Corinna van den Heuvel, and Robert Vink PMCID: PMC2823748 Validation of reference genes for quantitative RT-PCR studies of gene expression in perennial ryegrass (Lolium perenne L.) Julia M Lee, John R Roche, Danny J Donaghy, Anthony Thrush, and Puthigae Sathish PMCID: PMC2827471 Regulation of UGT1A1 and HNF1 transcription factor gene expression by DNA methylation in colon cancer cells Anne-Sophie Bélanger, Jelena Tojcic, Mario Harvey, and Chantal Guillemette PMCID: PMC2835698 TAF6δ orchestrates an apoptotic transcriptome profile and interacts functionally with p53 Emmanuelle Wilhelm, Mara Kornete, Brice Targat, Jimmy Vigneault-Edwards, Mattia Frontini, Laszlo Tora, Arndt Benecke, and Brendan Bell PMCID: PMC2827470 Correlation between ribonucleoside-diphosphate reductase and three replication proteins in Escherichia coli M Antonia Sánchez-Romero, Felipe Molina, and Alfonso Jiménez-Sánchez PMCID: PMC2826317 Identification of endogenous control genes for normalisation of real-time quantitative PCR data in colorectal cancer Elrasheid AH Kheirelseid, Kah Hoong Chang, John Newell, Michael J Kerin, and Nicola Miller PMCID: PMC2825202 SLUG: a new target of lymphoid enhancer factor-1 in human osteoblasts Elisabetta Lambertini, Tiziana Franceschetti, Elena Torreggiani, Letizia Penolazzi, Antonio Pastore, Stefano Pelucchi, Roberto Gambari, and Roberta Piva PMCID: PMC2834684 Transcription factors Elk-1 and SRF are engaged in IL1-dependent regulation of ZC3H12A expression Aneta Kasza, Paulina Wyrzykowska, Irena Horwacik, Piotr Tymoszuk, Danuta Mizgalska, Karren Palmer, Hanna Rokita, Andrew D Sharrocks, and Jolanta Jura PMCID: PMC2829564 Validation of reference genes for gene expression analysis in chicory (Cichorium intybus) using quantitative real-time PCR Asad Maroufi, Erik Van Bockstaele, and Marc De Loose PMCID: PMC2830926 In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection François Bolduc, Christopher Hoareau, Patrick St-Pierre, and Jean-Pierre Perreault PMCID: PMC2830927 Hfq affects mRNA levels independently of degradation Jacques Le Derout, Irina V Boni, Philippe Régnier, and Eliane Hajnsdorf PMCID: PMC2834685 DNA-PKcs plays a dominant role in the regulation of H2AX phosphorylation in response to DNA damage and cell cycle progression Jing An, Yue-Cheng Huang, Qing-Zhi Xu, Li-Jun Zhou, Zeng-Fu Shang, Bo Huang, Yu Wang, Xiao-Dan Liu, De-Chang Wu, and Ping-Kun Zhou PMCID: PMC2844398 Characterization of the octamer, a cis-regulatory element that modulates excretory cell gene-expression in Caenorhabditis elegans Allan K Mah, Domena K Tu, Robert C Johnsen, Jeffrey S Chu, Nansheng Chen, and David L Baillie PMCID: PMC2841177 Identification of regulatory elements flanking human XIST reveals species differences Samuel C Chang and Carolyn J Brown PMCID: PMC2841178 Regulation of TFIIIB during F9 cell differentiation Dimitris Athineos, Lynne Marshall, and Robert J White PMCID: PMC2842266 Reference gene alternatives to Gapdh in rodent and human heart failure gene expression studies Trond Brattelid, Lisbeth H Winer, Finn Olav Levy, Knut Liestøl, Ole M Sejersted, and Kristin B Andersson PMCID: PMC2907514 The four hexamerin genes in the honey bee: structure, molecular evolution and function deduced from expression patterns in queens, workers and drones Juliana R Martins, Francis MF Nunes, Alexandre S Cristino, Zilá LP Simões, and Márcia MG Bitondi PMCID: PMC2861669 Transcriptomic analysis of the venom gland of the red-headed krait (Bungarus flaviceps) using expressed sequence tags Ang Swee Siang, Robin Doley, Freek J Vonk, and R Manjunatha Kini PMCID: PMC2861064 Phylogeny and expression of carbonic anhydrase-related proteins Ashok Aspatwar, Martti EE Tolvanen, and Seppo Parkkila PMCID: PMC2873310 Elasmobranch qPCR reference genes: a case study of hypoxia preconditioned epaulette sharks Kalle T Rytkönen, Gillian MC Renshaw, Kevin J Ashton, Grant Williams-Pritchard, Erica H Leder, and Mikko Nikinmaa PMCID: PMC2864272 Socio-environmental and endocrine influences on developmental and caste-regulatory gene expression in the eusocial termite Reticulitermes flavipes Matthew R Tarver, Xuguo Zhou, and Michael E Scharf PMCID: PMC2873311 Characterization of microRNA expression in bovine adipose tissues: a potential regulatory mechanism of subcutaneous adipose tissue development Weiwu Jin, Michael V Dodson, Stephen S Moore, John A Basarab, and Le Luo Guan PMCID: PMC2874793 Deficiency of the dual ubiquitin/SUMO ligase Topors results in genetic instability and an increased rate of malignancy in mice Henderson Marshall, Mantu Bhaumik, Hana Aviv, Dirk Moore, Ming Yao, Jayeeta Dutta, Hussein Rahim, Murugesan Gounder, Shridar Ganesan, Ahamed Saleem, and Eric Rubin PMCID: PMC2873312 Genetic variations regulate alternative splicing in the 5' untranslated regions of the mouse glioma-associated oncogene 1, Gli1 Ramesh Palaniswamy, Stephan Teglund, Matthias Lauth, Peter G Zaphiropoulos, and Takashi Shimokawa PMCID: PMC2880320 The human RPS4 paralogue on Yq11.223 encodes a structurally conserved ribosomal protein and is preferentially expressed during spermatogenesis Alexandra M Lopes, Ricardo N Miguel, Carole A Sargent, Peter J Ellis, António Amorim, and Nabeel A Affara PMCID: PMC2884166 Sequence features involved in the mechanism of 3' splice junction wobbling Kuo-Wang Tsai, Wen-Ching Chan, Chun-Nan Hsu, and Wen-chang Lin PMCID: PMC2875228 Analysis of illegitimate genomic integration mediated by zinc-finger nucleases: implications for specificity of targeted gene correction Petter A Olsen, Monika Gelazauskaite, Markus Randøl, and Stefan Krauss PMCID: PMC2875229 Evaluation of potential reference genes for real time RT-PCR studies in Atlantic halibut (Hippoglossus Hippoglossus L.); during development, in tissues of healthy and NNV-injected fish, and in anterior kidney leucocytes Aina-Cathrine Øvergård, Audun Helge Nerland, and Sonal Patel PMCID: PMC2882370 Identification of a novel transforming growth factor-β (TGF-β6) gene in fish: regulation in skeletal muscle by nutritional state Bruria Funkenstein, Elena Olekh, and Sonia B Jakowlew PMCID: PMC2881917 The leukemia associated ETO nuclear repressor gene is regulated by the GATA-1 transcription factor in erythroid/megakaryocytic cells Ram Ajore, Rakesh Singh Dhanda, Urban Gullberg, and Inge Olsson PMCID: PMC2882371 Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples Rohini Mehta, Aybike Birerdinc, Noreen Hossain, Arian Afendy, Vikas Chandhoke, Zobair Younossi, and Ancha Baranova PMCID: PMC2886049 Transcriptional control by two leucine-responsive regulatory proteins in Halobacterium salinarum R1 Rita Schwaiger, Christoph Schwarz, Katarina Furtwängler, Valery Tarasov, Andy Wende, and Dieter Oesterhelt PMCID: PMC2894021 Bioinformatic analysis of the human DHRS4 gene cluster and a proposed mechanism for its transcriptional regulation Zhong-Jing Su, Qiao-Xia Zhang, Ge-Fei Liu, Xu-Hong Song, Qi Li, Rui-Jian Wang, Hai-Bin Chen, Xiao-Yuan Xu, Xu-Xia Sui, and Dong-Yang Huang PMCID: PMC2892492 Identification and expression analysis of splice variants of mouse enabled homologue during development and in adult tissues Sylvie Veniere, Davy Waterschoot, Joël Vandekerckhove, Anja Lambrechts, and Christophe Ampe PMCID: PMC2898656 Research Articles Alternative trans-splicing of Caenorhabditis elegans sma-9/schnurri generates a short transcript that provides tissue-specific function in BMP signaling Jianghua Yin, Ling Yu, and Cathy Savage-Dunn PMCID: PMC2904332 High-affinity consensus binding of target RNAs by the STAR/GSG proteins GLD-1, STAR-2 and Quaking Andrew B Carmel, Joann Wu, Katrina A Lehmann-Blount, and James R Williamson PMCID: PMC2905418 Sodium butyrate enhances the cytotoxic effect of cisplatin by abrogating the cisplatin imposed cell cycle arrest Miglena Koprinarova, Petya Markovska, Ivan Iliev, Boyka Anachkova, and George Russev PMCID: PMC2906439 Characterization of the human Activin-A receptor type II-like kinase 1 (ACVRL1) promoter and its regulation by Sp1 Eva M Garrido-Martin, Francisco J Blanco, Africa Fernandez-L, Carmen Langa, Calvin P Vary, Ursula E Lee, Scott L Friedman, Luisa M Botella, and Carmelo Bernabeu PMCID: PMC2906440 The YEATS family member GAS41 interacts with the general transcription factor TFIIF Sabrina Heisel, Nunja C Habel, Nicole Schuetz, Alessia Ruggieri, and Eckart Meese PMCID: PMC2908078 Single-stranded heteroduplex intermediates in λ Red homologous recombination Marcello Maresca, Axel Erler, Jun Fu, Anne Friedrich, Youming Zhang, and A Francis Stewart PMCID: PMC2918612 Identification of testis-relevant genes using in silico analysis from testis ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon) Thidathip Wongsurawat, Rungnapa Leelatanawit, Natechanok Thamniemdee, Umaporn Uawisetwathana, Nitsara Karoonuthaisiri, Piamsak Menasveta, and Sirawut Klinbunga PMCID: PMC2928233 Experimental comparison of relative RT-qPCR quantification approaches for gene expression studies in poplar Nicole Regier and Beat Frey PMCID: PMC2930637 Homologous illegitimate random integration of foreign DNA into the X chromosome of a transgenic mouse line Bowen Yan, Defa Li, and Kemian Gou PMCID: PMC2928235 Effect of experimental treatment on GAPDH mRNA expression as a housekeeping gene in human diploid fibroblasts Azalina Zainuddin, Kien Hui Chua, Norhazira Abdul Rahim, and Suzana Makpol PMCID: PMC2930638 Determination of reference genes for circadian studies in different tissues and mouse strains Rok Kosir, Jure Acimovic, Marko Golicnik, Martina Perse, Gregor Majdic, Martina Fink, and Damjana Rozman PMCID: PMC2928770 Methodology Articles Validation of endogenous controls for gene expression studies in peripheral lymphocytes from war veterans with and without PTSD Jelena Brkljačić, Nikola Tanić, Danijela Vojnović Milutinović, Ivana Elaković, Sanja Manitašević Jovanović, Tatjana Perišić, Jadranka Dundjerski, and Gordana Matić PMCID: PMC2858027 Quantitative polymerase chain reaction analysis by deconvolution of internal standard Yasuko Hirakawa, Rheem D Medh, and Stan Metzenberg PMCID: PMC2877679 Transcripts expressed using a bicistronic vector pIREShyg2 are sensitized to nonsense-mediated mRNA decay Yayoi Shikama, Huiyuan Hu, Makiko Ohno, Isao Matsuoka, Tsutomu Shichishima, and Junko Kimura PMCID: PMC2896932 New miRNA labeling method for bead-based quantification Alberto Biscontin, Silvia Casara, Stefano Cagnin, Lucia Tombolan, Angelo Rosolen, Gerolamo Lanfranchi, and Cristiano De Pittà PMCID: PMC2900262 κMicroarray analysis of relative gene expression stability for selection of internal reference genes in the rhesus macaque brain Nigel C Noriega, Steven G Kohama, and Henryk F Urbanski PMCID: PMC2914640 Characterisation of the sarcomeric myosin heavy chain multigene family in the laboratory guinea pig Daniel P Tonge, Simon W Jones, Ronald G Bardsley, and Tim Parr PMCID: PMC2911452 A method for selecting cis-acting regulatory sequences that respond to small molecule effectors Ülar Allas and Tanel Tenson PMCID: PMC2928234 Other Issues: Journal List
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