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2010 Featured Articles

Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation
Tanizawa H, Iwasaki O, Tanaka A, Capizzi JR, Wickramasinghe P, Lee M, Fu Z, Noma KI.
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Characterization of the relationship between integrase, excisionase and antirepressor activities associated with a superinfecting Shiga toxin encoding bacteriophage
Fogg PC, Rigden DJ, Saunders JR, McCarthy AJ, Allison HE.
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A distinct first replication cycle of DNA introduced in mammalian cells
Chandok GS, Kapoor KK, Brick RM, Sidorova JM, Krasilnikova MM.
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EpiChIP: Gene-by-gene quantification of epigenetic modification levels
Hebenstreit D, Gu M, Haider S, Turner DJ, Liò P, Teichmann SA.
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Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast
Belew AT, Advani VM, Dinman JD.
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Discovering Pathways by Orienting Edges in Protein Interaction Networks
Gitter A, Klein-Seetharaman J, Gupta A, Bar-Joseph Z.
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The group II intron ribonucleoprotein precursor is a large, loosely packed structure
Huang T, Shaikh TR, Gupta K, Contreras-Martin LM, Grassucci RA, Van Duyne GD, Frank J, Belfort M.
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Cyclin E is recruited to the nuclear matrix during differentiation, but is not recruited in cancer cells
Munkley J, Copeland NA, Moignard V, Knight JR, Greaves E, Ramsbottom SA, Pownall ME, Southgate J, Ainscough JF, Coverley D.
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Expression of distinct RNAs from 3' untranslated regions
Mercer TR, Wilhelm D, Dinger ME, Soldà G, Korbie DJ, Glazov EA, Truong V, Schwenke M, Simons C, Matthaei KI, Saint R, Koopman P, Mattick JS.
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α-MSH regulates intergenic splicing of MC1R and TUBB3 in human melanocytes
Dalziel M, Kolesnichenko M, das Neves RP, Iborra F, Goding C, Furger A.
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Arabidopsis thaliana telomeres exhibit euchromatic features
Vaquero-Sedas MI, Gámez-Arjona FM, Vega-Palas MA.
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hSSB1 rapidly binds at the sites of DNA double-strand breaks and is required for the efficient recruitment of the MRN complex
Richard DJ, Savage K, Bolderson E, Cubeddu L, So S, Ghita M, Chen DJ, White MF, Richard K, Prise KM, Schettino G, Khanna KK.
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YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes
Handa Y, Inaho N, Nameki N.
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Trans-cleaving hammerhead ribozymes with tertiary stabilizing motifs: in vitro and in vivo activity against a structured viroid RNA
Carbonell A, Flores R, Gago S.
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Genome-wide detection of a TFIID localization element from an initial human disease mutation
Yang MQ, Laflamme K, Gotea V, Joiner CH, Seidel NE, Wong C, Petrykowska HM, Lichtenberg J, Lee S, Welch L, Gallagher PG, Bodine DM, Elnitski L.
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A role for human Dicer in pre-RISC loading of siRNAs
Sakurai K, Amarzguioui M, Kim DH, Alluin J, Heale B, Song MS, Gatignol A, Behlke MA, Rossi JJ.
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The Bowen-Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Ψ1191 in yeast 18S rRNA
Meyer B, Wurm JP, Kötter P, Leisegang MS, Schilling V, Buchhaupt M, Held M, Bahr U, Karas M, Heckel A, Bohnsack MT, Wöhnert J, Entian KD.
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Assembly of a fragmented ribonucleotide reductase by protein interaction domains derived from a mobile genetic element
Crona M, Moffatt C, Friedrich NC, Hofer A, Sjöberg BM, Edgell DR.
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Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification
Kato M, Araiso Y, Noma A, Nagao A, Suzuki T, Ishitani R, Nureki O.
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Co-transcriptional RNA cleavage provides a failsafe termination mechanism for yeast RNA polymerase I
Braglia P, Kawauchi J, Proudfoot NJ.
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The expression of myogenic microRNAs indirectly requires protein arginine methyltransferase (Prmt)5 but directly requires Prmt4
Mallappa C, Hu YJ, Shamulailatpam P, Tae S, Sif S, Imbalzano AN.
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Systematically fragmented genes in a multipartite mitochondrial genome
Vlcek C, Marande W, Teijeiro S, Lukes J, Burger G.
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The evolution and expression of the snaR family of small non-coding RNAs
Parrott AM, Tsai M, Batchu P, Ryan K, Ozer HL, Tian B, Mathews MB.
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Structural basis for the dual RNA-recognition modes of human Tra2-β RRM
Tsuda K, Someya T, Kuwasako K, Takahashi M, He F, Unzai S, Inoue M, Harada T, Watanabe S, Terada T, Kobayashi N, Shirouzu M, Kigawa T, Tanaka A, Sugano S, Güntert P, Yokoyama S, Muto Y.
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The translational response of the human mdm2 gene in HEK293T cells exposed to rapamycin: a role for the 5'-UTRs
Genolet R, Rahim G, Gubler-Jaquier P, Curran J.
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DNA intercalation without flipping in the specific ThaI-DNA complex
Firczuk M, Wojciechowski M, Czapinska H, Bochtler M.
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The human Pat1b protein: a novel mRNA deadenylation factor identified by a new immunoprecipitation technique
Totaro A, Renzi F, La Fata G, Mattioli C, Raabe M, Urlaub H, Achsel T.
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The linker domain of basal transcription factor TFIIB controls distinct recruitment and transcription stimulation functions
Wiesler SC, Weinzierl RO.
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BRCC36A is epistatic to BRCA1 in DNA crosslink repair and homologous recombination in Arabidopsis thaliana
Astrid S. Block-Schmidt, Stefanie Dukowic-Schulze, Kristina Wanieck, Wim Reidt, and Holger Puchta
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M-ORBIS: Mapping of mOleculaR Binding sItes and Surfaces
Laurent-Philippe Albou, Olivier Poch, and Dino Moras
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Efficient use of accessibility in microRNA target prediction
Ray M. Marín and Jiří Vaníček
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Natural and engineered nicking endonucleases—from cleavage mechanism to engineering of strand-specificity
Siu-Hong Chan, Barry L. Stoddard, and Shuang-yong Xu
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Crucial contribution of the multiple copies of the initiator tRNA genes in the fidelity of tRNAfMet selection on the ribosomal P-site in Escherichia coli
Suman Kapoor, Gautam Das, and Umesh Varshney
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Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE
Morana Vitezic, Timo Lassmann, Alistair R. R. Forrest, Masanori Suzuki, Yasuhiro Tomaru, Jun Kawai, Piero Carninci, Harukazu Suzuki, Yoshihide Hayashizaki, and Carsten O. Daub
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Archaeal/Eukaryal RNase P: subunits, functions and RNA diversification
Nayef Jarrous and Venkat Gopalan
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A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding
Michael H. J. Rhodin and Jonathan D. Dinman
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A network of conserved co-occurring motifs for the regulation of alternative splicing
Mikita Suyama, Eoghan D. Harrington, Svetlana Vinokourova, Magnus von Knebel Doeberitz, Osamu Ohara, and Peer Bork
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TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain
Ting Li, Sheng Huang, Wen Zhi Jiang, David Wright, Martin H. Spalding, Donald P. Weeks, and Bing Yang
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Conformational plasticity of RNA for target recognition as revealed by the 2.15 Å crystal structure of a human IgG–aptamer complex
Yusuke Nomura, Shigeru Sugiyama, Taiichi Sakamoto, Shin Miyakawa, Hiroaki Adachi,
Kazufumi Takano, Satoshi Murakami,
Tsuyoshi Inoue, Yusuke Mori, Yoshikazu Nakamura, and Hiroyoshi Matsumura
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Genomic analysis of codon, sequence and structural conservation with selective biochemical-structure mapping reveals highly conserved and dynamic structures in rotavirus RNAs with potential cis-acting functions
Wilson Li, Emily Manktelow, Johann C. von Kirchbach, Julia R. Gog, Ulrich Desselberger, and Andrew M. Lever
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Characterization and prediction of protein nucleolar localization sequences
Michelle S. Scott, François-Michel Boisvert, Mark D. McDowall, Angus I. Lamond, and Geoffrey J. Barton
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Novel regulatory cascades controlling expression of nitrogen-fixation genes in Geobacter sulfurreducens
Toshiyuki Ueki and Derek R. Lovley
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A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella
Tiegang Xu, Fen Yao, Xiufen Zhou, Zixin Deng, and Delin You
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Cooperation between myogenic regulatory factors and SIX family transcription factors is important for myoblast differentiation
Yubing Liu, Alphonse Chu, Imane Chakroun, Uzma Islam, and Alexandre Blais
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Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer
Juliann Chmielecki, Martin Peifer, Peilin Jia, Nicholas D. Socci, Katherine Hutchinson, Agnes Viale, Zhongming Zhao, Roman K. Thomas, and William Pao
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Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA
Randall A. Hughes and Andrew D. Ellington
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Time-dependent increase in ribosome processivity
Jennifer M. Bonderoff and Richard E. Lloyd
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DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme
Mindaugas Zaremba, Amelia Owsicka, Gintautas Tamulaitis, Giedrius Sasnauskas, Luda S. Shlyakhtenko, Alexander Y. Lushnikov, Yuri L. Lyubchenko, Niels Laurens, Bram van den Broek, Gijs J. L. Wuite, and Virginijus Siksnys
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Maintenance of respiratory chain function in mouse hearts with severely impaired mtDNA transcription
Christoph Freyer, Chan Bae Park, Mats I. Ekstrand, Yonghong Shi, Julia Khvorostova, Rolf Wibom, Maria Falkenberg, Claes M. Gustafsson, and Nils-Göran Larsson
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Effect of pseudouridylation on the structure and activity of the catalytically essential P6.1 hairpin in human telomerase RNA
Nak-Kyoon Kim, Carla A. Theimer, James R. Mitchell, Kathleen Collins, and Juli Feigon
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RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
Pavel S. Novichkov, Dmitry A. Rodionov, Elena D. Stavrovskaya, Elena S. Novichkova, Alexey E. Kazakov, Mikhail S. Gelfand, Adam P. Arkin, Andrey A. Mironov, and Inna Dubchak
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ICM Web: the interactive chromatin modeling web server
Richard C. Stolz and Thomas C. Bishop
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PINT: Pathways INtegration Tool
Y.-T. Wang, Y.-H. Huang, Y.-C. Chen, C.-L. Hsu, and U.-C. Yang
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PARP1 ADP-ribosylates lysine residues of the core histone tails
Simon Messner, Matthias Altmeyer, Hongtao Zhao, Andrea Pozivil, Bernd Roschitzki, Peter Gehrig, Dorothea Rutishauser, Danzhi Huang, Amedeo Caflisch, and Michael O. Hottiger
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SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs
Norman E. Davey, Niall J. Haslam, Denis C. Shields, and Richard J. Edwards
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BioCatalogue: a universal catalogue of web services for the life sciences
Jiten Bhagat, Franck Tanoh, Eric Nzuobontane, Thomas Laurent, Jerzy Orlowski, Marco Roos, Katy Wolstencroft, Sergejs Aleksejevs, Robert Stevens, Steve Pettifer, Rodrigo Lopez, and Carole A. Goble
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Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
Ignacio Medina, José Carbonell, Luis Pulido, Sara C. Madeira, Stefan Goetz, Ana Conesa, Joaquín Tárraga, Alberto Pascual-Montano, Ruben Nogales-Cadenas, Javier Santoyo, Francisco García, Martina Marbà, David Montaner, and Joaquín Dopazo
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RosettaBackrub—a web server for flexible backbone protein structure modeling and design
Florian Lauck, Colin A. Smith, Gregory F. Friedland, Elisabeth L. Humphris, and Tanja Kortemme
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The EMBRACE web service collection
Steve Pettifer, Jon Ison, Matúš Kalaš, Dave Thorne, Philip McDermott, Inge Jonassen, Ali Liaquat, José M. Fernández, Jose M. Rodriguez, INB- Partners, David G. Pisano, Christophe Blanchet, Mahmut Uludag, Peter Rice, Edita Bartaseviciute, Kristoffer Rapacki, Maarten Hekkelman, Olivier Sand, Heinz Stockinger, Andrew B. Clegg, Erik Bongcam-Rudloff, Jean Salzemann, Vincent Breton, Teresa K. Attwood, Graham Cameron, and Gert Vriend
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GRAPE: GRaphical Abstracted Protein Explorer
Gregory Cipriano, Gary Wesenberg, Tom Grim, George N. Phillips, Jr., and Michael Gleicher
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HexServer: an FFT-based protein docking server powered by graphics processors
Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, and David W. Ritchie
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SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction
Raffi Hagopian, John R. Davidson, Ruchira S. Datta, Bushra Samad, Glen R. Jarvis, and Kimmen Sjölander
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Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs
Justin Ashworth, Gregory K. Taylor, James J. Havranek, S. Arshiya Quadri, Barry L. Stoddard, and David Baker
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Active and passive mechanisms of helicases
Maria Manosas, Xu Guang Xi, David Bensimon, and Vincent Croquette
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A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex
Gavin W. Collie, Shozeb M. Haider, Stephen Neidle, and Gary N. Parkinson
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Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma
Johannes H. Schulte, Tobias Marschall, Marcel Martin, Philipp Rosenstiel, Pieter Mestdagh, Stefanie Schlierf, Theresa Thor, Jo Vandesompele, Angelika Eggert, Stefan Schreiber, Sven Rahmann, and Alexander Schramm
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The non-coding RNA TERRA is a natural ligand and direct inhibitor of human telomerase
Sophie Redon, Patrick Reichenbach, and Joachim Lingner
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Multiple roles of the RNA polymerase β' SW2 region in transcription initiation, promoter escape, and RNA elongation
Danil Pupov, Nataliya Miropolskaya, Anastasiya Sevostyanova, Irina Bass, Irina Artsimovitch, and Andrey Kulbachinskiy
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The archaeal transamidosome for RNA-dependent glutamine biosynthesis
Theodoros Rampias, Kelly Sheppard, and Dieter Söll
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A unique family of Mrr-like modification-dependent restriction endonucleases
Yu Zheng, Devora Cohen-Karni, Derrick Xu, Hang Gyeong Chin, Geoffrey Wilson, Sriharsa Pradhan, and Richard J. Roberts
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Three prime exonuclease I (TREX1) is Fos/AP-1 regulated by genotoxic stress and protects against ultraviolet light and benzo(a)pyrene-induced DNA damage
Markus Christmann, Maja T. Tomicic, Dorthe Aasland, Nicole Berdelle, and Bernd Kaina
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Two distinct overstretched DNA states
Hongxia Fu, Hu Chen, John F. Marko, and Jie Yan
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Quantitative analysis of processive RNA degradation by the archaeal RNA exosome
Sophia Hartung, Theresa Niederberger, Marianne Hartung, Achim Tresch, and Karl-Peter Hopfner
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Dynamics on multiple timescales in the RNA-directed RNA polymerase from the cystovirus phi6
Zhen Ren, Hsin Wang, and Ranajeet Ghose
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Functional selection and systematic analysis of intronic splicing elements identifies active sequence motifs and associated splicing factors
Stephanie J. Culler, Kevin G. Hoff, Rodger B. Voelker, J. Andrew Berglund, and Christina D. Smolke
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Global and local depletion of ternary complex limits translational elongation
Gong Zhang, Ivan Fedyunin, Oskar Miekley, Angelo Valleriani, Alessandro Moura, and Zoya Ignatova
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Resolution and characterization of the structural polymorphism of a single quadruplex-forming sequence
Magdalena M. Dailey, M. Clarke Miller, Paula J. Bates, Andrew N. Lane, and John O. Trent
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Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics
Allison J. DePaul, Erik J. Thompson, Sarav S. Patel, Kristin Haldeman, and Eric J. Sorin
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Genetic instability triggered by G-quadruplex interacting Phen-DC compounds in Saccharomyces cerevisiae
Aurèle Piazza, Jean-Baptiste Boulé, Judith Lopes, Katie Mingo, Eric Largy, Marie-Paule Teulade-Fichou, and Alain Nicolas
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The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex
Xiang-Jun Lu, Wilma K. Olson, and Harmen J. Bussemaker
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Efficient inhibition of miR-155 function in vivo by peptide nucleic acids
Martin M. Fabani, Cei Abreu-Goodger, Donna Williams, Paul A. Lyons, Adrian G. Torres, Kenneth G. C. Smith, Anton J. Enright, Michael J. Gait, and Elena Vigorito
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Transposases are the most abundant, most ubiquitous genes in nature
Ramy K. Aziz, Mya Breitbart, and Robert A. Edwards
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Direct observation of the temperature-induced melting process of the Salmonella fourU RNA thermometer at base-pair resolution
Jörg Rinnenthal, Birgit Klinkert, Franz Narberhaus, and Harald Schwalbe
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Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing
Fabian Birzele, Jochen Schaub, Werner Rust, Christoph Clemens, Patrick Baum, Hitto Kaufmann, Andreas Weith, Torsten W. Schulz, and Tobias Hildebrandt
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Directed evolution of recombinase specificity by split gene reassembly
Charles A. Gersbach, Thomas Gaj, Russell M. Gordley, and Carlos F. Barbas, III
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Functional replacement of the endogenous tyrosyl-tRNA synthetase–tRNATyr pair by the archaeal tyrosine pair in Escherichia coli for genetic code expansion
Fumie Iraha, Kenji Oki, Takatsugu Kobayashi, Satoshi Ohno, Takashi Yokogawa, Kazuya Nishikawa, Shigeyuki Yokoyama, and Kensaku Sakamoto
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RNPC1 modulates the RNA-binding activity of, and cooperates with, HuR to regulate p21 mRNA stability
Seong Jun Cho, Jin Zhang, and Xinbin Chen
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The ribosome assembly factor Nep1 responsible for Bowen–Conradi syndrome is a pseudouridine-N1-specific methyltransferase
Jan Philip Wurm, Britta Meyer, Ute Bahr, Martin Held, Olga Frolow, Peter Kötter, Joachim W. Engels, Alexander Heckel, Michael Karas, Karl-Dieter Entian, and Jens Wöhnert
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Yeast arginine methyltransferase Hmt1p regulates transcription elongation and termination by methylating Npl3p
Chi-Ming Wong, Hei-Man Vincent Tang, Ka-Yiu Edwin Kong, Gee-Wan Oscar Wong, Hongfang Qiu, Dong-Yan Jin, and Alan G. Hinnebusch
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Riboswitch structure: an internal residue mimicking the purine ligand
Vanessa Delfosse, Patricia Bouchard, Eric Bonneau, Pierre Dagenais, Jean-François Lemay, Daniel A. Lafontaine, and Pascale Legault
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Mining regulatory 5'UTRs from cDNA deep sequencing datasets
Jonathan Livny and Matthew K. Waldor
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An intermolecular RNA triplex provides insight into structural determinants for the pseudoknot stimulator of –1 ribosomal frameshifting
Ming-Yuan Chou and Kung-Yao Chang
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Crystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-tRNA synthetase
Xianchi Dong, Minyun Zhou, Chen Zhong, Bei Yang, Ning Shen and Jianping Ding
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Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling
Christian Schudoma, Patrick May, Viktoria Nikiforova and Dirk Walther
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Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition
Akiyoshi Nakamura, Kelly Sheppard, Junji Yamane, Min Yao, Dieter Söll and Isao Tanaka
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