Nucleic Acids Research

Survey and Summary

Get checked abstract Arnold Stein, Taichi E. Takasuka, and Clayton K. Collings

Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: 709-719; doi:10.1093/nar/gkp1043 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology

Get checked abstract David A. Lee, Robert Rentzsch, and Christine Orengo

GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains
Nucleic Acids Research Advance Access published on November 18, 2009
Nucl. Acids Res. 2010 38: 720-737; doi:10.1093/nar/gkp1049 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gene Regulation, Chromatin and Epigenetics

Get checked abstract Larry N. Singh and Sridhar Hannenhalli

Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families
Nucleic Acids Research Advance Access published on November 19, 2009
Nucl. Acids Res. 2010 38: 738-749; doi:10.1093/nar/gkp989 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Oscar Aparicio, Elena Carnero, Xabier Abad, Nerea Razquin, Elizabeth Guruceaga, Victor Segura, and Puri Fortes

Adenovirus VA RNA-derived miRNAs target cellular genes involved in cell growth, gene expression and DNA repair
Nucleic Acids Research Advance Access published on November 19, 2009
Nucl. Acids Res. 2010 38: 750-763; doi:10.1093/nar/gkp1028 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yi-Jiun Chen, Bertrand Chin-Ming Tan, Ya-Yun Cheng, Jin-Shin Chen, and Sheng-Chung Lee

Differential regulation of CHOP translation by phosphorylated eIF4E under stress conditions
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: 764-777; doi:10.1093/nar/gkp1034 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Wenge Li, Nehal Thakor, Eugenia Y. Xu, Ying Huang, Chi Chen, Rong Yu, Martin Holcik, and Ah-Ng Kong

An internal ribosomal entry site mediates redox-sensitive translation of Nrf2
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: 778-788; doi:10.1093/nar/gkp1048 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Chase T. Archer and Thomas Kodadek

The hydrophobic patch of ubiquitin is required to protect transactivator–promoter complexes from destabilization by the proteasomal ATPases
Nucleic Acids Research Advance Access published on November 25, 2009
Nucl. Acids Res. 2010 38: 789-796; doi:10.1093/nar/gkp1066 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Hamid Reza Rezvani, Walid Mahfouf, Nsrein Ali, Cecile Chemin, Cecile Ged, Arianna L. Kim, Hubert de Verneuil, Alain Taïeb, David R. Bickers, and Frédéric Mazurier

Hypoxia-inducible factor-1 regulates the expression of nucleotide excision repair proteins in keratinocytes
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: 797-809; doi:10.1093/nar/gkp1072 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Toshiyuki Ueki and Derek R. Lovley

Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species
Nucleic Acids Research Advance Access published on November 25, 2009
Nucl. Acids Res. 2010 38: 810-821; doi:10.1093/nar/gkp1085 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Moo-Rim Kang, Sang-Wang Lee, Elisa Um, Hyun Tae Kang, Eun Seong Hwang, Eun-Joo Kim, and Soo-Jong Um

Reciprocal roles of SIRT1 and SKIP in the regulation of RAR activity: implication in the retinoic acid-induced neuronal differentiation of P19 cells
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: 822-831; doi:10.1093/nar/gkp1056 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genome Integrity, Repair and Replication

Get checked abstract Tohru Yamamori, Jeremy DeRicco, Asma Naqvi, Timothy A. Hoffman, Ilwola Mattagajasingh, Kenji Kasuno, Saet-Byel Jung, Cuk-Seong Kim, and Kaikobad Irani

SIRT1 deacetylates APE1 and regulates cellular base excision repair
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: 832-845; doi:10.1093/nar/gkp1039 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Stuart J. Haring, Troy D. Humphreys, and Marc S. Wold

A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression
Nucleic Acids Research Advance Access published on November 26, 2009
Nucl. Acids Res. 2010 38: 846-858; doi:10.1093/nar/gkp1062 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Atsushi Katafuchi, Akira Sassa, Naoko Niimi, Petr Grúz, Hirofumi Fujimoto, Chikahide Masutani, Fumio Hanaoka, Toshihiro Ohta, and Takehiko Nohmi

Critical amino acids in human DNA polymerases and involved in erroneous incorporation of oxidized nucleotides
Nucleic Acids Research Advance Access published on November 25, 2009
Nucl. Acids Res. 2010 38: 859-867; doi:10.1093/nar/gkp1095 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract Marco Albrecht, Cynthia M. Sharma, Richard Reinhardt, Jörg Vogel, and Thomas Rudel

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome
Nucleic Acids Research Advance Access published on November 18, 2009
Nucl. Acids Res. 2010 38: 868-877; doi:10.1093/nar/gkp1032 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract M. Banerjee, M. Datta, P. Majumder, D. Mukhopadhyay, and N. P. Bhattacharyya

Transcription regulation of caspase-1 by R393 of HIPPI and its molecular partner HIP-1
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: 878-892; doi:10.1093/nar/gkp1011 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sridharan Rajagopalan, Robert S. Sade, Fiona M. Townsley, and Alan R. Fersht

Mechanistic differences in the transcriptional activation of p53 by 14-3-3 isoforms
Nucleic Acids Research Advance Access published on November 20, 2009
Nucl. Acids Res. 2010 38: 893-906; doi:10.1093/nar/gkp1041 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jesper Sejrup Nielsen, Lisbeth Kristensen Lei, Tine Ebersbach, Anders Steno Olsen, Janne Kudsk Klitgaard, Poul Valentin-Hansen, and Birgitte Haahr Kallipolitis

Defining a role for Hfq in Gram-positive bacteria: evidence for Hfq-dependent antisense regulation in Listeria monocytogenes
Nucleic Acids Research Advance Access published on November 26, 2009
Nucl. Acids Res. 2010 38: 907-919; doi:10.1093/nar/gkp1081 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Jason A. Stewart, Judith L. Campbell, and Robert A. Bambara

Dna2 is a structure-specific nuclease, with affinity for 5'-flap intermediates
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: 920-930; doi:10.1093/nar/gkp1055 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jana Rudolf, Christophe Rouillon, Ulrich Schwarz-Linek, and Malcolm F. White

The helicase XPD unwinds bubble structures and is not stalled by DNA lesions removed by the nucleotide excision repair pathway
Nucleic Acids Research Advance Access published on November 20, 2009
Nucl. Acids Res. 2010 38: 931-941; doi:10.1093/nar/gkp1058 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Chie Tomikawa, Takashi Yokogawa, Tamotsu Kanai, and Hiroyuki Hori

N⁷-Methylguanine at position 46 (m⁷G46) in tRNA from Thermus thermophilus is required for cell viability at high temperatures through a tRNA modification network
Nucleic Acids Research Advance Access published on November 24, 2009
Nucl. Acids Res. 2010 38: 942-957; doi:10.1093/nar/gkp1059 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jennifer Laprise, Sumiko Yoneji, and Jeffrey F. Gardner

Homology-dependent interactions determine the order of strand exchange by IntDOT recombinase
Nucleic Acids Research Advance Access published on December 1, 2009
Nucl. Acids Res. 2010 38: 958-969; doi:10.1093/nar/gkp927 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Christian Schudoma, Patrick May, Viktoria Nikiforova, and Dirk Walther

Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling
Nucleic Acids Research Advance Access published on November 18, 2009
Nucl. Acids Res. 2010 38: 970-980; doi:10.1093/nar/gkp1010 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Changying Zeng, Wenquan Wang, Yun Zheng, Xin Chen, Weiping Bo, Shun Song, Weixiong Zhang, and Ming Peng

Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants
Nucleic Acids Research Advance Access published on November 26, 2009
Nucl. Acids Res. 2010 38: 981-995; doi:10.1093/nar/gkp1035 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Helen Elina and Gregory G. Brown

Extensive mis-splicing of a bi-partite plant mitochondrial group II intron
Nucleic Acids Research Advance Access published on November 17, 2009
Nucl. Acids Res. 2010 38: 996-1008; doi:10.1093/nar/gkp994 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Zhenjiang Zhang, Jixun Dai, Elizabeth Veliath, Roger A. Jones, and Danzhou Yang

Structure of a two-G-tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K⁺ solution: insights into the interconversion of human telomeric G-quadruplex structures
Nucleic Acids Research Advance Access published on November 27, 2009
Nucl. Acids Res. 2010 38: 1009-1021; doi:10.1093/nar/gkp1029 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Qianfan Yang, Junfeng Xiang, Shu Yang, Qian Li, Qiuju Zhou, Aijiao Guan, Xiufeng Zhang, Hong Zhang, Yalin Tang, and Guangzhi Xu

Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: II. The binding characterization with specific intramolecular G-quadruplex and the recognizing mechanism
Nucleic Acids Research Advance Access published on November 19, 2009
Nucl. Acids Res. 2010 38: 1022-1033; doi:10.1093/nar/gkp1045 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Brahim Heddi, Christophe Oguey, Christophe Lavelle, Nicolas Foloppe, and Brigitte Hartmann

Intrinsic flexibility of B-DNA: the experimental TRX scale
Nucleic Acids Research Advance Access published on November 17, 2009
Nucl. Acids Res. 2010 38: 1034-1047; doi:10.1093/nar/gkp962 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Synthetic Biology and Chemistry

Get checked abstract Alexander S. Wahba, Abbasali Esmaeili, Masad J. Damha, and Robert H. E. Hudson

A single-label phenylpyrrolocytidine provides a molecular beacon-like response reporting HIV-1 RT RNase H activity
Nucleic Acids Research Advance Access published on November 20, 2009
Nucl. Acids Res. 2010 38: 1048-1056; doi:10.1093/nar/gkp1022 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Obituary

Jeffrey F. Gardner and Olke C. Uhlenbeck

Obituary
Nucleic Acids Research Advance Access published on January 8, 2010
Nucl. Acids Res. 2010 38: 1057-1058; doi:10.1093/nar/gkp1156 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Corrigendum

Anne-Kathrin Schultz, Ming Zhang, Ingo Bulla, Thomas Leitner, Bette Korber, Burkhard Morgenstern, and Mario Stanke

jpHMM: improving the reliability of recombination prediction in HIV-1
Nucl. Acids Res. 2010 38: 1059; doi:10.1093/nar/gkq015 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Kimberly R. Blahnik, Lei Dou, Henriette O’Geen, Timothy McPhillips, Xiaoqin Xu, Alina R. Cao, Sushma Iyengar, Charles M. Nicolet, Bertram Ludäscher, Ian Korf, and Peggy J. Farnham

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: e13; doi:10.1093/nar/gkp1012 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract D. Träutlein, M. Deibler, A. Leitenstorfer, and E. Ferrando-May

Specific local induction of DNA strand breaks by infrared multi-photon absorption
Nucleic Acids Research Advance Access published on November 11, 2009
Nucl. Acids Res. 2010 38: e14; doi:10.1093/nar/gkp932 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Nikolay E. Shirokikh, Elena Z. Alkalaeva, Konstantin S. Vassilenko, Zhanna A. Afonina, Olga M. Alekhina, Lev L. Kisselev, and Alexander S. Spirin

Quantitative analysis of ribosome–mRNA complexes at different translation stages
Nucleic Acids Research Advance Access published on November 12, 2009
Nucl. Acids Res. 2010 38: e15; doi:10.1093/nar/gkp1025 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract John Y. Wu, Michael D. Stone, and Xiaowei Zhuang

A single-molecule assay for telomerase structure-function analysis
Nucleic Acids Research Advance Access published on November 17, 2009
Nucl. Acids Res. 2010 38: e16; doi:10.1093/nar/gkp1033 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Nuno L. Barbosa-Morais, Mark J. Dunning, Shamith A. Samarajiwa, Jeremy F. J. Darot, Matthew E. Ritchie, Andy G. Lynch, and Simon Tavaré

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data
Nucleic Acids Research Advance Access published on November 18, 2009
Nucl. Acids Res. 2010 38: e17; doi:10.1093/nar/gkp942 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Joséphine Abi-Ghanem, Brahim Heddi, Nicolas Foloppe, and Brigitte Hartmann

DNA structures from phosphate chemical shifts
Nucleic Acids Research Advance Access published on November 26, 2009
Nucl. Acids Res. 2010 38: e18; doi:10.1093/nar/gkp1061 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Annette Lasham, Mike Herbert, Natacha Coppieters ‘t Wallant, Rachna Patel, Sheryl Feng, Marika Eszes, Helen Cao, and Glen Reid

A rapid and sensitive method to detect siRNA-mediated mRNA cleavage in vivo using 5' RACE and a molecular beacon probe
Nucleic Acids Research Advance Access published on November 26, 2009
Nucl. Acids Res. 2010 38: e19; doi:10.1093/nar/gkp1076 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 38 ISSUE 3 2010
Nucl. Acids Res. 2010 38: i; doi:10.1093/nar/gkq104 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2010 38: ii; doi:10.1093/nar/gkq103 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2010 38: iii; doi:10.1093/nar/gkq105 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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