Volume 38, Issue 4, 1 March 2010

Survey and Summary

Overexpression of RAD51 suppresses recombination defects: a possible mechanism to reverse genomic instability

David Schild and Claudia Wiese

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1061–1070, https://doi.org/10.1093/nar/gkp1063

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Computational Biology

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons

Xianjun Dong and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1071–1085, https://doi.org/10.1093/nar/gkp1124

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A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms

Liang Chen

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1086–1097, https://doi.org/10.1093/nar/gkp1136

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Gene Regulation, Chromatin and Epigenetics

The CCAAT-binding complex coordinates the oxidative stress response in eukaryotes

Marcel Thön and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1098–1113, https://doi.org/10.1093/nar/gkp1091

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Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential

Jay E. Johnson and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1114–1122, https://doi.org/10.1093/nar/gkp1103

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Genome Integrity, Repair and Replication

Hierarchy of lesion processing governs the repair, double-strand break formation and mutability of three-lesion clustered DNA damage

Laura J. Eccles and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1123–1134, https://doi.org/10.1093/nar/gkp1070

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Opposing regulatory roles of phosphorylation and acetylation in DNA mispair processing by thymine DNA glycosylase

Ryan D. Mohan and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1135–1148, https://doi.org/10.1093/nar/gkp1097

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DNA structure and the Werner protein modulate human DNA polymerase delta-dependent replication dynamics within the common fragile site FRA16D

Sandeep N. Shah and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1149–1162, https://doi.org/10.1093/nar/gkp1131

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Genomics

Discovery of short pseudogenes derived from messenger RNAs

Goro Terai and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1163–1171, https://doi.org/10.1093/nar/gkp1098

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The most frequent short sequences in non-coding DNA

Juan A. Subirana and Xavier Messeguer

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1172–1181, https://doi.org/10.1093/nar/gkp1094

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Molecular Biology

Essential roles of three enhancer sites in σ⁵⁴-dependent transcription by the nitric oxide sensing regulatory protein NorR

Nicholas P. Tucker and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1182–1194, https://doi.org/10.1093/nar/gkp1065

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Elevated dNTP levels suppress hyper-recombination in Saccharomyces cerevisiae S-phase checkpoint mutants

Michael Fasullo and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1195–1203, https://doi.org/10.1093/nar/gkp1064

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Precise targeted integration by a chimaeric transposase zinc-finger fusion protein

Xiaofeng Feng and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1204–1216, https://doi.org/10.1093/nar/gkp1068

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A tale of two functions: enzymatic activity and translational repression by carboxyltransferase

Glen Meades and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1217–1227, https://doi.org/10.1093/nar/gkp1079

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Dr1 (NC2) is present at tRNA genes and represses their transcription in human cells

Theodoros Kantidakis and Robert J. White

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1228–1239, https://doi.org/10.1093/nar/gkp1102

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Lin28-mediated post-transcriptional regulation of Oct4 expression in human embryonic stem cells

Caihong Qiu and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1240–1248, https://doi.org/10.1093/nar/gkp1071

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The transcriptional transactivator Tat selectively regulates viral splicing

Joseph A. Jablonski and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1249–1260, https://doi.org/10.1093/nar/gkp1105

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Yeast strains with N-terminally truncated ribosomal protein S5: implications for the evolution, structure and function of the Rps5/Rps7 proteins

Thomas Lumsden and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1261–1272, https://doi.org/10.1093/nar/gkp1113

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Promoter and regulon analysis of nitrogen assimilation factor, σ⁵⁴, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis

Kai Zhao and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1273–1283, https://doi.org/10.1093/nar/gkp1123

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Translational activation of rpoS mRNA by the non-coding RNA DsrA and Hfq does not require ribosome binding

Branislav Večerek and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1284–1293, https://doi.org/10.1093/nar/gkp1125

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Nucleic Acid Enzymes

Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs

Priscilla Hiu-Mei Too and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1294–1303, https://doi.org/10.1093/nar/gkp1092

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Mutational analysis of the 5′-OH oligonucleotide phosphate acceptor site of T4 polynucleotide kinase

Li Kai Wang and Stewart Shuman

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1304–1311, https://doi.org/10.1093/nar/gkp1096

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Phosphate release contributes to the rate-limiting step for unwinding by an RNA helicase

Qixin Wang and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1312–1324, https://doi.org/10.1093/nar/gkp1118

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RNA

Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM

Kamila Réblová and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1325–1340, https://doi.org/10.1093/nar/gkp1057

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Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA

Satoshi Kimura and Tsutomu Suzuki

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1341–1352, https://doi.org/10.1093/nar/gkp1073

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Antagonistic factors control the unproductive splicing of SC35 terminal intron

Natacha Dreumont and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1353–1366, https://doi.org/10.1093/nar/gkp1086

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A new type of IRES within gag coding region recruits three initiation complexes on HIV-2 genomic RNA

Laure Weill and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1367–1381, https://doi.org/10.1093/nar/gkp1109

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Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development

Eun Kyung Yoon and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1382–1391, https://doi.org/10.1093/nar/gkp1128

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Atomistic basis for the on–off signaling mechanism in SAM-II riboswitch

Jennifer Munro Kelley and Donald Hamelberg

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1392–1400, https://doi.org/10.1093/nar/gkp1106

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Structural Biology

Crystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-tRNA synthetase

Xianchi Dong and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Pages 1401–1412, https://doi.org/10.1093/nar/gkp1053

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Corrigendum

MMBGX: a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays

Ernest Turro and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Page 1413, https://doi.org/10.1093/nar/gkq071

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Methods Online

Tandem affinity purification of miRNA target mRNAs (TAP-Tar)

Nora Nonne and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Page e20, https://doi.org/10.1093/nar/gkp1100

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Selection of DNA aptamers using atomic force microscopy

Yusuke Miyachi and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Page e21, https://doi.org/10.1093/nar/gkp1101

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A comprehensive analysis of filamentous phage display vectors for cytoplasmic proteins: an analysis with different fluorescent proteins

Nileena Velappan and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Page e22, https://doi.org/10.1093/nar/gkp809

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A calibrated diversity assay for nucleic acid libraries using DiStRO—a Diversity Standard of Random Oligonucleotides

Tatjana Schütze and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Page e23, https://doi.org/10.1093/nar/gkp1108

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Analysis of differential DNA damage in the mitochondrial genome employing a semi-long run real-time PCR approach

Oliver Rothfuss and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Page e24, https://doi.org/10.1093/nar/gkp1082

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Selection of bacteriophage λ integrases with altered recombination specificity by in vitro compartmentalization

Yvonne Tay and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Page e25, https://doi.org/10.1093/nar/gkp1089

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A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans

Siew Loon Ooi and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Page e26, https://doi.org/10.1093/nar/gkp1090

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Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization

Aron C. Eklund and others

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Page e27, https://doi.org/10.1093/nar/gkp1116

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Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 38 ISSUE 4 2010

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Page i, https://doi.org/10.1093/nar/gkq157

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Nucleic Acids Research

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Page ii, https://doi.org/10.1093/nar/gkq156

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Subscriptions

Nucleic Acids Research, Volume 38, Issue 4, 1 March 2010, Page iii, https://doi.org/10.1093/nar/gkq158

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