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Volume 40 Issue 10 May 2012

To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

Survey and Summary

    • Yuliang Wu and
    • Robert M. Brosh, Jr

    DNA helicase and helicase–nuclease enzymes with a conserved iron–sulfur cluster

    Nucl. Acids Res. (2012) 40(10): 4247-4260 first published online January 28, 2012 doi:10.1093/nar/gks039
    OPEN ACCESS

Computational Biology

    • Stefan Washietl,
    • Ivo L. Hofacker,
    • Peter F. Stadler,
    • and Manolis Kellis

    RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

    Nucl. Acids Res. (2012) 40(10): 4261-4272 first published online January 28, 2012 doi:10.1093/nar/gks009
    OPEN ACCESS
    • Martin H. Schaefer,
    • Erich E. Wanker,
    • and Miguel A. Andrade-Navarro

    Evolution and function of CAG/polyglutamine repeats in protein–protein interaction networks

    Nucl. Acids Res. (2012) 40(10): 4273-4287 first published online January 28, 2012 doi:10.1093/nar/gks011
    OPEN ACCESS
    • Davis J. McCarthy,
    • Yunshun Chen,
    • and Gordon K. Smyth

    Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

    Nucl. Acids Res. (2012) 40(10): 4288-4297 first published online January 28, 2012 doi:10.1093/nar/gks042
    OPEN ACCESS
    • Yue Li,
    • Zhuo Zhang,
    • Feng Liu,
    • Wanwipa Vongsangnak,
    • Qing Jing,
    • and Bairong Shen

    Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

    Nucl. Acids Res. (2012) 40(10): 4298-4305 first published online January 28, 2012 doi:10.1093/nar/gks043
    OPEN ACCESS

Gene Regulation, Chromatin and Epigenetics

    • Zghidi-Abouzid Ouafa,
    • Sylvie Reverchon,
    • Thomas Lautier,
    • Georgi Muskhelishvili,
    • and William Nasser

    The nucleoid-associated proteins H-NS and FIS modulate the DNA supercoiling response of the pel genes, the major virulence factors in the plant pathogen bacterium Dickeya dadantii

    Nucl. Acids Res. (2012) 40(10): 4306-4319 first published online January 24, 2012 doi:10.1093/nar/gks014
    OPEN ACCESS
    • Qing Wei,
    • Phu Nguyen Le Minh,
    • Andreas Dötsch,
    • Falk Hildebrand,
    • Warunya Panmanee,
    • Ameer Elfarash,
    • Sebastian Schulz,
    • Stéphane Plaisance,
    • Daniel Charlier,
    • Daniel Hassett,
    • Susanne Häussler,
    • and Pierre Cornelis

    Global regulation of gene expression by OxyR in an important human opportunistic pathogen

    Nucl. Acids Res. (2012) 40(10): 4320-4333 first published online January 24, 2012 doi:10.1093/nar/gks017
    OPEN ACCESS
    • Eriko G. Clements,
    • Helai P. Mohammad,
    • Benjamin R. Leadem,
    • Hariharan Easwaran,
    • Yi Cai,
    • Leander Van Neste,
    • and Stephen B. Baylin

    DNMT1 modulates gene expression without its catalytic activity partially through its interactions with histone-modifying enzymes

    Nucl. Acids Res. (2012) 40(10): 4334-4346 first published online January 25, 2012 doi:10.1093/nar/gks031
    OPEN ACCESS
    • Kristoffer S. Winther and
    • Kenn Gerdes

    Regulation of Enteric vapBC Transcription: Induction by VapC Toxin Dimer-Breaking

    Nucl. Acids Res. (2012) 40(10): 4347-4357 first published online January 27, 2012 doi:10.1093/nar/gks029
    OPEN ACCESS
    • Shweta Karambelkar,
    • Ganduri Swapna,
    • and Valakunja Nagaraja

    Silencing of toxic gene expression by Fis

    Nucl. Acids Res. (2012) 40(10): 4358-4367 first published online January 28, 2012 doi:10.1093/nar/gks037
    OPEN ACCESS
    • M. Carmen Ortells,
    • Beatriz Morancho,
    • Katherine Drews-Elger,
    • Benoit Viollet,
    • Keith R. Laderoute,
    • Cristina López-Rodríguez,
    • and Jose Aramburu

    Transcriptional regulation of gene expression during osmotic stress responses by the mammalian target of rapamycin

    Nucl. Acids Res. (2012) 40(10): 4368-4384 first published online January 28, 2012 doi:10.1093/nar/gks038
    OPEN ACCESS
    • Arumugam Srinivasan and
    • Rakesh K. Mishra

    Chromatin domain boundary element search tool for Drosophila

    Nucl. Acids Res. (2012) 40(10): 4385-4395 first published online January 28, 2012 doi:10.1093/nar/gks045
    OPEN ACCESS
    • T. Josse,
    • H. Mokrani-Benhelli,
    • R. Benferhat,
    • E. Shestakova,
    • Z. Mansuroglu,
    • H. Kakanakou,
    • A. Billecocq,
    • M. Bouloy,
    • and Eliette Bonnefoy

    Association of the interferon-β gene with pericentromeric heterochromatin is dynamically regulated during virus infection through a YY1-dependent mechanism

    Nucl. Acids Res. (2012) 40(10): 4396-4411 first published online January 28, 2012 doi:10.1093/nar/gks050
    OPEN ACCESS
    • Mekonnen Lemma Dechassa,
    • Swetansu K. Hota,
    • Payel Sen,
    • Nilanjana Chatterjee,
    • Punit Prasad,
    • and Blaine Bartholomew

    Disparity in the DNA translocase domains of SWI/SNF and ISW2

    Nucl. Acids Res. (2012) 40(10): 4412-4421 first published online January 31, 2012 doi:10.1093/nar/gks007
    OPEN ACCESS
    • Meng Xie,
    • Guodong Ren,
    • Pedro Costa-Nunes,
    • Olga Pontes,
    • and Bin Yu

    A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation

    Nucl. Acids Res. (2012) 40(10): 4422-4431 first published online February 1, 2012 doi:10.1093/nar/gks034
    OPEN ACCESS
    • Aaron R. Haeusler,
    • Kathy A. Goodson,
    • Todd D. Lillian,
    • Xiaoyu Wang,
    • Sachin Goyal,
    • Noel C. Perkins,
    • and Jason D. Kahn

    FRET studies of a landscape of Lac repressor-mediated DNA loops

    Nucl. Acids Res. (2012) 40(10): 4432-4445 first published online February 4, 2012 doi:10.1093/nar/gks019
    OPEN ACCESS
    • Elisabeth John,
    • Anke Wienecke-Baldacchino,
    • Maria Liivrand,
    • Merja Heinäniemi,
    • Carsten Carlberg,
    • and Lasse Sinkkonen

    Dataset integration identifies transcriptional regulation of microRNA genes by PPARγ in differentiating mouse 3T3-L1 adipocytes

    Nucl. Acids Res. (2012) 40(10): 4446-4460 first published online February 7, 2012 doi:10.1093/nar/gks025
    OPEN ACCESS
    • Bing-Mei Zhu,
    • Keunsoo Kang,
    • Ji Hoon Yu,
    • Weiping Chen,
    • Harold E. Smith,
    • Daeyoup Lee,
    • Hong-Wei Sun,
    • Lai Wei,
    • and Lothar Hennighausen

    Genome-wide analyses reveal the extent of opportunistic STAT5 binding that does not yield transcriptional activation of neighboring genes

    Nucl. Acids Res. (2012) 40(10): 4461-4472 first published online February 8, 2012 doi:10.1093/nar/gks056
    OPEN ACCESS

Genome Integrity, Repair and Replication

    • Sabine S. Lange,
    • John P. Wittschieben,
    • and Richard D. Wood

    DNA polymerase zeta is required for proliferation of normal mammalian cells

    Nucl. Acids Res. (2012) 40(10): 4473-4482 first published online February 7, 2012 doi:10.1093/nar/gks054
    OPEN ACCESS
    • Charles Vadnais,
    • Sayeh Davoudi,
    • Mojdeh Afshin,
    • Ryoko Harada,
    • Rachel Dudley,
    • Pier-Luc Clermont,
    • Elliot Drobetsky,
    • and Alain Nepveu

    CUX1 transcription factor is required for optimal ATM/ATR-mediated responses to DNA damage

    Nucl. Acids Res. (2012) 40(10): 4483-4495 first published online February 8, 2012 doi:10.1093/nar/gks041
    OPEN ACCESS
    • Shuren Liao,
    • Catherine Guay,
    • Thomas Toczylowski,
    • and Hong Yan

    Analysis of MRE11's function in the 5′→3′ processing of DNA double-strand breaks

    Nucl. Acids Res. (2012) 40(10): 4496-4506 first published online February 8, 2012 doi:10.1093/nar/gks044
    OPEN ACCESS
    • Nikesh Patel,
    • John M. Atack,
    • L. David Finger,
    • Jack C. Exell,
    • Peter Thompson,
    • Susan Tsutakawa,
    • John A. Tainer,
    • David M. Williams,
    • and Jane A. Grasby

    Flap endonucleases pass 5′-flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5′-ends

    Nucl. Acids Res. (2012) 40(10): 4507-4519 first published online February 8, 2012 doi:10.1093/nar/gks051
    OPEN ACCESS

Molecular Biology

    • David Cárdenas,
    • Jesús Revuelta-Cervantes,
    • Antonio Jiménez-Díaz,
    • Hendricka Camargo,
    • Miguel Remacha,
    • and Juan P. G. Ballesta

    P1 and P2 protein heterodimer binding to the P0 protein of Saccharomyces cerevisiae is relatively non-specific and a source of ribosomal heterogeneity

    Nucl. Acids Res. (2012) 40(10): 4520-4529 first published online January 24, 2012 doi:10.1093/nar/gks036
    OPEN ACCESS
    • Bin Liu,
    • Bo Hu,
    • Zhemin Zhou,
    • Dan Guo,
    • Xi Guo,
    • Peng Ding,
    • Lu Feng,
    • and Lei Wang

    A novel non-homologous recombination-mediated mechanism for Escherichia coli unilateral flagellar phase variation

    Nucl. Acids Res. (2012) 40(10): 4530-4538 first published online January 28, 2012 doi:10.1093/nar/gks040
    OPEN ACCESS
    • Jonathan Chang,
    • Beate Schwer,
    • and Stewart Shuman

    Structure–function analysis and genetic interactions of the yeast branchpoint binding protein Msl5

    Nucl. Acids Res. (2012) 40(10): 4539-4552 first published online January 28, 2012 doi:10.1093/nar/gks049
    OPEN ACCESS
    • Koichi Sato,
    • Kazue Toda,
    • Masamichi Ishiai,
    • Minoru Takata,
    • and Hitoshi Kurumizaka

    DNA robustly stimulates FANCD2 monoubiquitylation in the complex with FANCI

    Nucl. Acids Res. (2012) 40(10): 4553-4561 first published online January 28, 2012 doi:10.1093/nar/gks053
    OPEN ACCESS
    • Divyang Jani,
    • Sheila Lutz,
    • Ed Hurt,
    • Ronald A. Laskey,
    • Murray Stewart,
    • and Vihandha O. Wickramasinghe

    Functional and structural characterization of the mammalian TREX-2 complex that links transcription with nuclear messenger RNA export

    Nucl. Acids Res. (2012) 40(10): 4562-4573 first published online February 4, 2012 doi:10.1093/nar/gks059
    OPEN ACCESS
    • Kaori Shimoji,
    • Jelena Jakovljevic,
    • Kanako Tsuchihashi,
    • Yuka Umeki,
    • Kun Wan,
    • Suzuka Kawasaki,
    • Jason Talkish,
    • John L. Woolford, Jr,
    • and Keiko Mizuta

    Ebp2 and Brx1 function cooperatively in 60S ribosomal subunit assembly in Saccharomyces cerevisiae

    Nucl. Acids Res. (2012) 40(10): 4574-4588 first published online February 8, 2012 doi:10.1093/nar/gks057
    OPEN ACCESS

Nucleic Acid Enzymes

    • Bijoy K. Mohanty,
    • Valerie F. Maples,
    • and Sidney R. Kushner

    Polyadenylation helps regulate functional tRNA levels in Escherichia coli

    Nucl. Acids Res. (2012) 40(10): 4589-4603 first published online January 28, 2012 doi:10.1093/nar/gks006
    OPEN ACCESS
    • Heather Ordonez,
    • Mihaela Unciuleac,
    • and Stewart Shuman

    Mycobacterium smegmatis RqlH defines a novel clade of bacterial RecQ-like DNA helicases with ATP-dependent 3′–5′ translocase and duplex unwinding activities

    Nucl. Acids Res. (2012) 40(10): 4604-4614 first published online January 28, 2012 doi:10.1093/nar/gks046
    OPEN ACCESS

RNA

    • Ying Zhu,
    • Yang Lu,
    • Qi Zhang,
    • Jing-Jing Liu,
    • Tuan-Jie Li,
    • Jian-Rong Yang,
    • Chunxian Zeng,
    • and Shi-Mei Zhuang

    MicroRNA-26a/b and their host genes cooperate to inhibit the G1/S transition by activating the pRb protein

    Nucl. Acids Res. (2012) 40(10): 4615-4625 first published online December 30, 2011 doi:10.1093/nar/gkr1278
    OPEN ACCESS
    • Mallory A. Havens,
    • Ashley A. Reich,
    • Dominik M. Duelli,
    • and Michelle L. Hastings

    Biogenesis of mammalian microRNAs by a non-canonical processing pathway

    Nucl. Acids Res. (2012) 40(10): 4626-4640 first published online January 23, 2012 doi:10.1093/nar/gks026
    OPEN ACCESS
    • Hsin-Chuan Chen,
    • Lih-Ren Kong,
    • Ting-Yu Yeh,
    • Chi-Ping Cheng,
    • Yau-Heiu Hsu,
    • and Na-Sheng Lin

    The conserved 5′ apical hairpin stem loops of bamboo mosaic virus and its satellite RNA contribute to replication competence

    Nucl. Acids Res. (2012) 40(10): 4641-4652 first published online January 25, 2012 doi:10.1093/nar/gks030
    OPEN ACCESS
    • Brian Dall Schyth,
    • Jesper Bertram Bramsen,
    • Malgorzata Maria Pakula,
    • Sekar Larashati,
    • Jørgen Kjems,
    • Jesper Wengel,
    • and Niels Lorenzen

    In vivo screening of modified siRNAs for non-specific antiviral effect in a small fish model: number and localization in the strands are important

    Nucl. Acids Res. (2012) 40(10): 4653-4665 first published online January 28, 2012 doi:10.1093/nar/gks033
    OPEN ACCESS
    • Wen-Yi Chen,
    • Deepali Singh,
    • Lien B. Lai,
    • Michael A. Stiffler,
    • Hue D. Lai,
    • Mark P. Foster,
    • and Venkat Gopalan

    Fidelity of tRNA 5′-maturation: a possible basis for the functional dependence of archaeal and eukaryal RNase P on multiple protein cofactors

    Nucl. Acids Res. (2012) 40(10): 4666-4680 first published online January 31, 2012 doi:10.1093/nar/gks013
    OPEN ACCESS
    • Song Cao and
    • Shi-Jie Chen

    Predicting kissing interactions in microRNA–target complex and assessment of microRNA activity

    Nucl. Acids Res. (2012) 40(10): 4681-4690 first published online February 3, 2012 doi:10.1093/nar/gks052
    OPEN ACCESS

Structural Biology

    • Dengguo Wei,
    • Gary N. Parkinson,
    • Anthony P. Reszka,
    • and Stephen Neidle

    Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation

    Nucl. Acids Res. (2012) 40(10): 4691-4700 first published online January 28, 2012 doi:10.1093/nar/gks023
    OPEN ACCESS

Synthetic Biology and Chemistry

    • Scott F. Hickey,
    • Malathy Sridhar,
    • Alexander J. Westermann,
    • Qian Qin,
    • Pooja Vijayendra,
    • Geoffrey Liou,
    • and Ming C. Hammond

    Transgene regulation in plants by alternative splicing of a suicide exon

    Nucl. Acids Res. (2012) 40(10): 4701-4710 first published online February 6, 2012 doi:10.1093/nar/gks032
    OPEN ACCESS
    • Julien Derr,
    • Michael L. Manapat,
    • Sudha Rajamani,
    • Kevin Leu,
    • Ramon Xulvi-Brunet,
    • Isaac Joseph,
    • Martin A. Nowak,
    • and Irene A. Chen

    Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences

    Nucl. Acids Res. (2012) 40(10): 4711-4722 first published online February 7, 2012 doi:10.1093/nar/gks065
    OPEN ACCESS

Corrigenda

    • Anastassia Voronova,
    • Ashraf Al Madhoun,
    • Anna Fischer,
    • Michael Shelton,
    • Christina Karamboulas,
    • and Ilona Sylvia Skerjanc

    Gli2 and MEF2C activate each other’s expression and function synergistically during cardiomyogenesis in vitro

    Nucl. Acids Res. (2012) 40(10): 4723-4724 doi:10.1093/nar/gks415
    OPEN ACCESS
    • Sarah Hunter,
    • Philip Jones,
    • Alex Mitchell,
    • Rolf Apweiler,
    • Teresa K. Attwood,
    • Alex Bateman,
    • Thomas Bernard,
    • David Binns,
    • Peer Bork,
    • Sarah Burge,
    • Edouard de Castro,
    • Penny Coggill,
    • Matthew Corbett,
    • Ujjwal Das,
    • Louise Daugherty,
    • Lauranne Duquenne,
    • Robert D. Finn,
    • Matthew Fraser,
    • Julian Gough,
    • Daniel Haft,
    • Nicolas Hulo,
    • Daniel Kahn,
    • Elizabeth Kelly,
    • Ivica Letunic,
    • David Lonsdale,
    • Rodrigo Lopez,
    • Martin Madera,
    • John Maslen,
    • Craig McAnulla,
    • Jennifer McDowall,
    • Conor McMenamin,
    • Huaiyu Mi,
    • Prudence Mutowo-Muellenet,
    • Nicola Mulder,
    • Darren Natale,
    • Christine Orengo,
    • Sebastien Pesseat,
    • Marco Punta,
    • Antony F. Quinn,
    • Catherine Rivoire,
    • Amaia Sangrador-Vegas,
    • Jeremy D. Selengut,
    • Christian J. A. Sigrist,
    • Maxim Scheremetjew,
    • John Tate,
    • Manjulapramila Thimmajanarthanan,
    • Paul D. Thomas,
    • Cathy H. Wu,
    • Corin Yeats,
    • Siew-Yit Yong,
    • Jonathan Lees,
    • Corin Yeats,
    • James Perkins,
    • Ian Sillitoe,
    • Robert Rentzsch,
    • Benoit H. Dessailly,
    • and Christine Orengo

    InterPro in 2011: new developments in the family and domain prediction databaseGene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis

    Nucl. Acids Res. (2012) 40(10): 4725 doi:10.1093/nar/gks456
    OPEN ACCESS
    • Rafael Núñez-Ramírez,
    • Sebastian Klinge,
    • Ludovic Sauguet,
    • Roberto Melero,
    • María A. Recuero-Checa,
    • Mairi Kilkenny,
    • Rajika L. Perera,
    • Begoña García-Alvarez,
    • Richard J. Hall,
    • Eva Nogales,
    • Luca Pellegrini,
    • and Oscar Llorca

    Flexible tethering of primase and DNA Pol α in the eukaryotic primosome

    Nucl. Acids Res. (2012) 40(10): 4726 doi:10.1093/nar/gks431
    OPEN ACCESS

Methods Online

    • Yuval Benjamini and
    • Terence P. Speed

    Summarizing and correcting the GC content bias in high-throughput sequencing

    Nucl. Acids Res. (2012) 40(10): e72 first published online February 9, 2012 doi:10.1093/nar/gks001
    OPEN ACCESS
    • Kun-Nan Tsai and
    • Daryi Wang

    Identification of activated cryptic 5′ splice sites using structure profiles and odds measure

    Nucl. Acids Res. (2012) 40(10): e73 first published online February 9, 2012 doi:10.1093/nar/gks061
    OPEN ACCESS
    • Elizabeth G. Wilbanks,
    • David J. Larsen,
    • Russell Y. Neches,
    • Andrew I. Yao,
    • Chia-Ying Wu,
    • Rachel A. S. Kjolby,
    • and Marc T. Facciotti

    A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq

    Nucl. Acids Res. (2012) 40(10): e74 first published online February 9, 2012 doi:10.1093/nar/gks063
    OPEN ACCESS
    • Joop Gäken,
    • Azim M. Mohamedali,
    • Jie Jiang,
    • Farooq Malik,
    • Doris Stangl,
    • Alexander E. Smith,
    • Constantinos Chronis,
    • Austin G. Kulasekararaj,
    • N. Shaun B. Thomas,
    • Farzin Farzaneh,
    • Mahvash Tavassoli,
    • and Ghulam J. Mufti

    A functional assay for microRNA target identification and validation

    Nucl. Acids Res. (2012) 40(10): e75 first published online February 9, 2012 doi:10.1093/nar/gks145
    OPEN ACCESS
    • Jan-Peter van Pijkeren and
    • Robert A. Britton

    High efficiency recombineering in lactic acid bacteria

    Nucl. Acids Res. (2012) 40(10): e76 first published online February 10, 2012 doi:10.1093/nar/gks147
    OPEN ACCESS
    • Michael Fernández and
    • Diego Miranda-Saavedra

    Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines

    Nucl. Acids Res. (2012) 40(10): e77 first published online February 10, 2012 doi:10.1093/nar/gks149
    OPEN ACCESS
    • Marie-Luise Winz,
    • Ayan Samanta,
    • Dirk Benzinger,
    • and Andres Jäschke

    Site-specific terminal and internal labeling of RNA by poly(A) polymerase tailing and copper-catalyzed or copper-free strain-promoted click chemistry

    Nucl. Acids Res. (2012) 40(10): e78 first published online February 16, 2012 doi:10.1093/nar/gks062
    OPEN ACCESS
    • Aniruddha Chatterjee,
    • Peter A. Stockwell,
    • Euan J. Rodger,
    • and Ian M. Morison

    Comparison of alignment software for genome-wide bisulphite sequence data

    Nucl. Acids Res. (2012) 40(10): e79 first published online February 16, 2012 doi:10.1093/nar/gks150
    OPEN ACCESS

Front-Matter/Back-Matter

To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

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This Issue

May 2012 40 (10)
Nucleic Acids Research
  1. Survey and Summary
  2. Computational Biology
  3. Gene Regulation, Chromatin and Epigenetics
  4. Genome Integrity, Repair and Replication
  5. Molecular Biology
  6. Nucleic Acid Enzymes
  7. RNA
  8. Structural Biology
  9. Synthetic Biology and Chemistry
  10. Corrigenda
  11. Methods Online
  12. Front-Matter/Back-Matter

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