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2013 Feature Articles

2012 Feature Articles

SYNTHETIC BIOLOGY AND CHEMISTRY

Computational identification of functional introns: high positional conservation of introns that harbor RNA genes.
Chorev M, Carmel L.
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Allelic exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells
Holwerda SJ, van de Werken HJ, Ribeiro de Almeida C, Bergen IM, de Bruijn MJ, Verstegen MJ, Simonis M, Splinter E, Wijchers PJ, Hendriks RW, de Laat W.
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COMPUTATIONAL BIOLOGY

Development and application of a DNA microarray-based yeast two-hybrid system
Suter B, Fontaine JF, Yildirimman R, Raskó T, Schaefer MH, Rasche A, Porras P, Vázquez-Álvarez BM, Russ J, Rau K, Foulle R, Zenkner M, Saar K, Herwig R, Andrade-Navarro MA, Wanker EE.
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TherMos: Estimating protein-DNA binding energies from in vivo binding profiles.
Sun W, Hu X, Lim MH, Ng CK, Choo SH, Castro DS, Drechsel D, Guillemot F, Kolatkar PR, Jauch R, Prabhakar S.
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Loss of heterozygosity preferentially occurs in early replicating regions in cancer genomes
Pedersen BS, De S.
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Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA
Iyer LM, Zhang D, Maxwell Burroughs A, Aravind L.
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GENE REGULATION, CHROMATIN AND EPIGENETICS

NIPP1 maintains EZH2 phosphorylation and promoter occupancy at proliferation-related target genes
Minnebo N, Görnemann J, O'Connell N, Van Dessel N, Derua R, Vermunt MW, Page R, Beullens M, Peti W, Van Eynde A, Bollen M.
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Integrative annotation of chromatin elements from ENCODE data
Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS.
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Imprinting at the PLAGL1 domain is contained within a 70-kb CTCF/cohesin-mediated non-allelic chromatin loop
Iglesias-Platas I, Court F, Camprubi C, Sparago A, Guillaumet-Adkins A, Martin-Trujillo A, Riccio A, Moore GE, Monk D.
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Acetylated Histone H3K9 is associated with meiotic recombination hotspots, and plays a role in recombination redundantly with other factors including the H3K4 methylase Set1 in fission yeast.
Yamada, Takatomi
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Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing
Li S, Breaker RR.
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Linker Histone H1.0 Interacts with an Extensive Network of Proteins Found in the Nucleolus
Kalashnikova AA, Winkler DD, McBryant SJ, Henderson RK, Herman JA, Deluca JG, Luger K, Prenni JE, Hansen JC.
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Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub
Gavrilov AA, Gushchanskaya ES, Strelkova O, Zhironkina O, Kireev II, Iarovaia OV, Razin SV.
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MBNL1 and PTB cooperate to repress splicing of Tpm1 exon 3
Gooding C, Edge C, Lorenz M, Coelho MB, Winters M, Kaminski CF, Cherny D, Eperon IC, Smith CW.
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Nrf2 activation is associated with Z-DNA formation in the human HO-1 promoter.
Maruyama A, Mimura J, Harada N, Itoh K.
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A bistable hysteretic switch in an activator-repressor regulated restriction-modification system.
Williams K, Savageau MA, Blumenthal RM.
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Progesterone receptor induces bcl-x expression through intragenic binding sites favoring RNA polymerase II elongation.
Bertucci PY, Nacht AS, Alló M, Rocha-Viegas L, Ballaré C, Soronellas D, Castellano G, Zaurin R, Kornblihtt AR, Beato M, Vicent GP, Pecci A.
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Expression of a large LINE-1-driven antisense RNA is linked to epigenetic silencing of the metastasis suppressor gene TFPI-2 in cancer.
Cruickshanks HA, Vafadar-Isfahani N, Dunican DS, Lee A, Sproul D, Lund JN, Meehan RR, Tufarelli C.
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KDM4B is a Master Regulator of the Estrogen Receptor Signalling Cascade.
Gaughan L, Stockley J, Coffey K, O'Neill D, Jones DL, Wade M, Wright J, Moore M, Tse S, Rogerson L, Robson CN.
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GENOME INTEGRITY, REPAIR AND REPLICATION

Bacteriophage SPP1 DNA replication strategies promote viral and disable host replication in vitro
Seco EM, Zinder JC, Manhart CM, Lo Piano A, McHenry CS, Ayora S.
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A non-catalytic role of DNA polymerase η in recruiting Rad18 and promoting PCNA monoubiquitination at stalled replication forks
Durando M, Tateishi S, Vaziri C.
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A new structural framework for integrating replication protein A into DNA processing machinery
Brosey CA, Yan C, Tsutakawa SE, Heller WT, Rambo RP, Tainer JA, Ivanov I, Chazin WJ.
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Single-molecule sorting reveals how ubiquitylation affects substrate recognition and activities of FBH1 helicase
Masuda-Ozawa T, Hoang T, Seo YS, Chen LF, Spies M.
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Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits α, ε, θ and β reveals a highly flexible arrangement of the proofreading domain
Ozawa K, Horan NP, Robinson A, Yagi H, Hill FR, Jergic S, Xu ZQ, Loscha KV, Li N, Tehei M, Oakley AJ, Otting G, Huber T, Dixon NE.
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MOLECULAR BIOLOGY

AT-rich sequence elements promote nascent transcript cleavage leading to RNA polymerase II termination
White E, Kamieniarz-Gdula K, Dye MJ, Proudfoot NJ.
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Quantitative Analysis of TALE-DNA Interactions Suggests Polarity Effects
Meckler JF, Bhakta MS, Kim MS, Ovadia R, Habrian CH, Zykovich A, Yu A, Lockwood SH, Morbitzer R, Elsäesser J, Lahaye T, Segal DJ, Baldwin EP.
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Investigation of DNA sequence recognition by a streptomycete MarR family transcriptional regulator through surface plasmon resonance and X-ray crystallography
Stevenson CE, Assaad A, Chandra G, Le TB, Greive SJ, Bibb MJ, Lawson DM.
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NUCLEIC ACID ENZYMES

RAG and HMGB1 create a large bend in the 23RSS in the V(D)J recombination synaptic complexes
Ciubotaru M, Trexler AJ, Spiridon LN, Surleac MD, Rhoades E, Petrescu AJ, Schatz DG.
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Monomeric PcrA helicase processively unwinds plasmid lengths of DNA in the presence of the initiator protein RepD
Chisty LT, Toseland CP, Fili N, Mashanov GI, Dillingham MS, Molloy JE, Webb MR.
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Structural insight into negative DNA supercoiling by DNA gyrase, a bacterial type 2A DNA topoisomerase
Papillon J, Ménétret JF, Batisse C, Hélye R, Schultz P, Potier N, Lamour V.
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RNA

Implication of the SMN complex in the biogenesis and steady state level of the Signal Recognition Particle
Piazzon N, Schlotter F, Lefebvre S, Dodré M, Méreau A, Soret J, Besse A, Barkats M, Bordonné R, Branlant C, Massenet S.
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De novo design of a synthetic riboswitch that regulates transcription termination
Wachsmuth M, Findeiß S, Weissheimer N, Stadler PF, Mörl M.
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Circularized synthetic oligodeoxynucleotides serve as promoterless RNA polymerase III templates for small RNA generation in human cells
Seidl CI, Lama L, Ryan K.
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Rbm20 regulates titin alternative splicing as a splicing repressor
Li S, Guo W, Dewey CN, Greaser ML.
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Single-molecule chemical denaturation of riboswitches
Dalgarno PA, Bordello J, Morris R, St-Pierre P, Dubé A, Samuel ID, Lafontaine DA, Penedo JC.
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Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation
Sun C, Querol-Audí J, Mortimer SA, Arias-Palomo E, Doudna JA, Nogales E, Cate JH.
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Hepatitis C virus 3’UTR regulates viral translation through direct interactions with the host translation machinery
Bai Y, Zhou K, Doudna JA.
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STRUCTURAL BIOLOGY

Conformational rearrangements of RIG-I receptor on formation of a multiprotein:dsRNA assembly
Beckham SA, Brouwer J, Roth A, Wang D, Sadler AJ, John M, Jahn-Hofmann K, Williams BR, Wilce JA, Wilce MC.
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Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers spectroscopy
Long X, Parks JW, Bagshaw CR, Stone MD.
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U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs
Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf CL.
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A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli
Sharma A, Kottur J, Narayanan N, Nair DT.
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Co-transcriptional formation of DNA:RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control.
Zheng KW, Xiao S, Liu JQ, Zhang JY, Hao YH, Tan Z.
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METHODS ONLINE

Differential strand separation at critical temperature: A minimally disruptive enrichment method for low-abundance unknown DNA mutations
Guha M, Castellanos-Rizaldos E, Liu P, Mamon H, Makrigiorgos GM.
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Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies
Ramasamy A, Trabzuni D, Gibbs JR, Dillman A, Hernandez DG, Arepalli S, Walker R, Smith C, Ilori GP, Shabalin AA, Li Y, Singleton AB, Cookson MR; for NABEC, Hardy J; for UKBEC, Ryten M, Weale ME.
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Harnessing mutagenic homologous recombination for targeted mutagenesis in vivo by TaGTEAM
Finney-Manchester SP, Maheshri N.
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DATABASE SPECIAL ISSUE

The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events
Colaert N, Maddelein D, Impens F, Van Damme P, Plasman K, Helsens K, Hulstaert N, Vandekerckhove J, Gevaert K, Martens L.
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The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy
Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, Boutte C, Burgaud G, de Vargas C, Decelle J, Del Campo J, Dolan JR, Dunthorn M, Edvardsen B, Holzmann M, Kooistra WH, Lara E, Le Bescot N, Logares R, Mahé F, Massana R, Montresor M, Morard R, Not
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MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data
Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, González-Beltrán A, Sansone SA, Griffin JL, Steinbeck C.
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Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells
Yang W, Soares J, Greninger P, Edelman EJ, Lightfoot H, Forbes S, Bindal N, Beare D, Smith JA, Thompson IR, Ramaswamy S, Futreal PA, Haber DA, Stratton MR, Benes C, McDermott U, Garnett MJ.
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GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences
Antonov I, Baranov P, Borodovsky M.
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Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system
Sunkin SM, Ng L, Lau C, Dolbeare T, Gilbert TL, Thompson CL, Hawrylycz M, Dang C.
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Dfam: a database of repetitive DNA based on profile hidden Markov models
Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD.
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Rfam 11.0: 10 years of RNA families
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A.
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO.
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STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ.
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PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins
Minguez P, Letunic I, Parca L, Bork P.
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The UCSC Genome Browser database: extensions and updates 2013
Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita
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New and continuing developments at PROSITE
Sigrist CJ, de Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret L, Xenarios I.
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ENCODE Data in the UCSC Genome Browser: year 5 update
Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ.
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Update on activities at the Universal Protein Resource (UniProt) in 2013
The UniProt Consortium.
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metaMicrobesOnline: phylogenomic analysis of microbial communities
Chivian D, Dehal PS, Keller K, Arkin AP.
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EcoGene 3.0
Zhou J, Rudd KE.
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WEB SERVER SPECIAL ISSUE

RNAstructure: web servers for RNA secondary structure prediction and analysis.
Bellaousov S, Reuter JS, Seetin MG, Mathews DH.
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NAFlex: a web server for the study of nucleic acid flexibility.
Hospital A, Faustino I, Collepardo-Guevara R, González C, Gelpí JL, Orozco M.
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Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications.
Margreitter C, Petrov D, Zagrovic B.
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BeEP Server: using evolutionary information for quality assessment of protein structure models
Palopoli N, Lanzarotti E, Parisi G.
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PELE Web Server: atomistic study of biomolecular systems at your fingertips
Madadkar-Sobhani A, Guallar V.
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