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Volume 40(9);  May 2012
Front-Matter/Back-Matter
Nucleic Acids Research: VOLUME 40 ISSUE 9 2012
Nucleic Acids Res. 2012 May; 40(9): i. Published online 2012 May 10. doi: 10.1093/nar/gks113
PMCID:
PMC3351184
Full Text PDF–444K
Nucleic Acids Research - Editorial Board
Nucleic Acids Res. 2012 May; 40(9): ii. Published online 2012 May 10. doi: 10.1093/nar/gks091
PMCID:
PMC3351144
Full Text PDF–58K
Subscriptions
Nucleic Acids Res. 2012 May; 40(9): iii. Published online 2012 May 10. doi: 10.1093/nar/gks135
PMCID:
PMC3351175
Full Text PDF–49K
Gene Regulation, Chromatin and Epigenetics
Ectopic over-expression of tristetraprolin in human cancer cells promotes biogenesis of let-7 by down-regulation of Lin28
Chae Won Kim, Mai-Tram Vo, Hong Kyeung Kim, Hyun Hee Lee, Nal Ae Yoon, Byung Ju Lee, Young Joo Min, Won Duk Joo, Hee Jeong Cha, Jeong Woo Park, Wha Ja Cho
Nucleic Acids Res. 2012 May; 40(9): 3856–3869. Published online 2011 December 31. doi: 10.1093/nar/gkr1302
PMCID:
PMC3351177
Abstract Full Text PDF–1.5M Supplementary Material
Distal chromatin structure influences local nucleosome positions and gene expression
An Jansen, Elisa van der Zande, Wim Meert, Gerald R. Fink, Kevin J. Verstrepen
Nucleic Acids Res. 2012 May; 40(9): 3870–3885. Published online 2012 January 11. doi: 10.1093/nar/gkr1311
PMCID:
PMC3351160
Abstract Full Text PDF–8.1M Supplementary Material
Genome Integrity, Repair and Replication
Involvement of residues of the ϕ29 terminal protein intermediate and priming domains in the formation of a stable and functional heterodimer with the replicative DNA polymerase
Alicia del Prado, Laurentino Villar, Miguel de Vega, Margarita Salas
Nucleic Acids Res. 2012 May; 40(9): 3886–3897. Published online 2011 December 30. doi: 10.1093/nar/gkr1283
PMCID:
PMC3351185
Abstract Full Text PDF–6.9M Supplementary Material
Structural mechanism of the phosphorylation-dependent dimerization of the MDC1 forkhead-associated domain
Jinping Liu, Shukun Luo, Hongchang Zhao, Ji Liao, Jing Li, Chunying Yang, Bo Xu, David F. Stern, Xingzhi Xu, Keqiong Ye
Nucleic Acids Res. 2012 May; 40(9): 3898–3912. Published online 2012 January 10. doi: 10.1093/nar/gkr1296
PMCID:
PMC3351156
Abstract Full Text PDF–11M Supplementary Material
The molecular basis of ATM-dependent dimerization of the Mdc1 DNA damage checkpoint mediator
Stephanie Jungmichel, Julie A. Clapperton, Janette Lloyd, Flurina J. Hari, Christoph Spycher, Lucijana Pavic, Jiejin Li, Lesley F. Haire, Mario Bonalli, Dorthe H. Larsen, Claudia Lukas, Jiri Lukas, Derek MacMillan, Michael L. Nielsen, Manuel Stucki, Stephen J. Smerdon
Nucleic Acids Res. 2012 May; 40(9): 3913–3928. Published online 2012 January 10. doi: 10.1093/nar/gkr1300
PMCID:
PMC3351161
Abstract Full Text PDF–16M Supplementary Material
Stoichiometry of MutS and MutL at unrepaired mismatches in vivo suggests a mechanism of repair
Marina Elez, Miroslav Radman, Ivan Matic
Nucleic Acids Res. 2012 May; 40(9): 3929–3938. Published online 2012 January 11. doi: 10.1093/nar/gkr1298
PMCID:
PMC3351158
Abstract Full Text PDF–1.5M Supplementary Material
Conformational and thermodynamic properties modulate the nucleotide excision repair of 2-aminofluorene and 2-acetylaminofluorene dG adducts in the NarI sequence
Vipin Jain, Benjamin Hilton, Satyakam Patnaik, Yue Zou, M. Paul Chiarelli, Bongsup P. Cho
Nucleic Acids Res. 2012 May; 40(9): 3939–3951. Published online 2012 January 11. doi: 10.1093/nar/gkr1307
PMCID:
PMC3351159
Abstract Full Text PDF–3.0M Supplementary Material
Complex activities of the human Bloom's syndrome helicase are encoded in a core region comprising the RecA and Zn-binding domains
Máté Gyimesi, Gábor M. Harami, Kata Sarlós, Eszter Hazai, Zsolt Bikádi, Mihály Kovács
Nucleic Acids Res. 2012 May; 40(9): 3952–3963. Published online 2012 January 16. doi: 10.1093/nar/gks008
PMCID:
PMC3351180
Abstract Full Text PDF–2.9M Supplementary Material
Effects of Friedreich's ataxia GAA repeats on DNA replication in mammalian cells
Gurangad S. Chandok, Mayank P. Patel, Sergei M. Mirkin, Maria M. Krasilnikova
Nucleic Acids Res. 2012 May; 40(9): 3964–3974. Published online 2012 January 19. doi: 10.1093/nar/gks021
PMCID:
PMC3351192
Abstract Full Text PDF–6.3M Supplementary Material
ATM regulates proteasome-dependent subnuclear localization of TRF1, which is important for telomere maintenance
Megan McKerlie, Sichun Lin, Xu-Dong Zhu
Nucleic Acids Res. 2012 May; 40(9): 3975–3989. Published online 2012 January 20. doi: 10.1093/nar/gks035
PMCID:
PMC3351164
Abstract Full Text PDF–18M
Molecular Biology
C6 pyridinium ceramide influences alternative pre-mRNA splicing by inhibiting protein phosphatase-1
Chiranthani Sumanasekera, Olga Kelemen, Monique Beullens, Brandon E. Aubol, Joseph A. Adams, Manjula Sunkara, Andrew Morris, Mathieu Bollen, Athena Andreadis, Stefan Stamm
Nucleic Acids Res. 2012 May; 40(9): 4025–4039. Published online 2011 December 31. doi: 10.1093/nar/gkr1289
PMCID:
PMC3351148
Abstract Full Text PDF–11M Supplementary Material
C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation
Bas F. J. Wanschers, Radek Szklarczyk, Aleksandra Pajak, Mariël A. M. van den Brand, Jolein Gloerich, Richard J. T. Rodenburg, Robert N. Lightowlers, Leo G. Nijtmans, Martijn A. Huynen
Nucleic Acids Res. 2012 May; 40(9): 4040–4051. Published online 2012 January 11. doi: 10.1093/nar/gkr1271
PMCID:
PMC3351149
Abstract Full Text PDF–7.5M Supplementary Material
A novel phage-encoded transcription antiterminator acts by suppressing bacterial RNA polymerase pausing
Zhanna Berdygulova, Daria Esyunina, Nataliya Miropolskaya, Damir Mukhamedyarov, Konstantin Kuznedelov, Bryce E. Nickels, Konstantin Severinov, Andrey Kulbachinskiy, Leonid Minakhin
Nucleic Acids Res. 2012 May; 40(9): 4052–4063. Published online 2012 January 11. doi: 10.1093/nar/gkr1285
PMCID:
PMC3351154
Abstract Full Text PDF–8.0M Supplementary Material
RNA
Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity
Satoshi Kimura, Yoshiho Ikeuchi, Kei Kitahara, Yuriko Sakaguchi, Takeo Suzuki, Tsutomu Suzuki
Nucleic Acids Res. 2012 May; 40(9): 4071–4085. Published online 2011 December 31. doi: 10.1093/nar/gkr1287
PMCID:
PMC3351187
Abstract Full Text PDF–8.0M Supplementary Material
BC1-FMRP interaction is modulated by 2′-O-methylation: RNA-binding activity of the tudor domain and translational regulation at synapses
Caroline Lacoux, Daniele Di Marino, Pietro Pilo Boyl, Francesca Zalfa, Bing Yan, Maria Teresa Ciotti, Mattia Falconi, Henning Urlaub, Tilmann Achsel, Annie Mougin, Michèle Caizergues-Ferrer, Claudia Bagni
Nucleic Acids Res. 2012 May; 40(9): 4086–4096. Published online 2012 January 11. doi: 10.1093/nar/gkr1254
PMCID:
PMC3351191
Abstract Full Text PDF–6.4M Supplementary Material
C7orf30 is necessary for biogenesis of the large subunit of the mitochondrial ribosome
Joanna Rorbach, Payam A. Gammage, Michal Minczuk
Nucleic Acids Res. 2012 May; 40(9): 4097–4109. Published online 2012 January 11. doi: 10.1093/nar/gkr1282
PMCID:
PMC3351152
Abstract Full Text PDF–3.9M Supplementary Material
The RNA helicase RHAU (DHX36) unwinds a G4-quadruplex in human telomerase RNA and promotes the formation of the P1 helix template boundary
E. P. Booy, M. Meier, N. Okun, S. K. Novakowski, S. Xiong, J. Stetefeld, S. A. McKenna
Nucleic Acids Res. 2012 May; 40(9): 4110–4124. Published online 2012 January 11. doi: 10.1093/nar/gkr1306
PMCID:
PMC3351167
Abstract Full Text PDF–5.4M Supplementary Material
mRNA knockdown by single strand RNA is improved by chemical modifications
Henry J. Haringsma, Jenny J. Li, Ferdie Soriano, Denise M. Kenski, W. Michael Flanagan, Aarron T. Willingham
Nucleic Acids Res. 2012 May; 40(9): 4125–4136. Published online 2012 January 16. doi: 10.1093/nar/gkr1301
PMCID:
PMC3351186
Abstract Full Text PDF–3.2M Supplementary Material
The porphyrin TmPyP4 unfolds the extremely stable G-quadruplex in MT3-MMP mRNA and alleviates its repressive effect to enhance translation in eukaryotic cells
Mark J. Morris, Katherine L. Wingate, Jagannath Silwal, Thomas C. Leeper, Soumitra Basu
Nucleic Acids Res. 2012 May; 40(9): 4137–4145. Published online 2012 January 20. doi: 10.1093/nar/gkr1308
PMCID:
PMC3351169
Abstract Full Text PDF–3.4M Supplementary Material
Structural Biology
Crystal structure of human polynucleotide phosphorylase: insights into its domain function in RNA binding and degradation
Chia Liang Lin, Yi-Ting Wang, Wei-Zen Yang, Yu-Yuan Hsiao, Hanna S. Yuan
Nucleic Acids Res. 2012 May; 40(9): 4146–4157. Published online 2011 December 30. doi: 10.1093/nar/gkr1281
PMCID:
PMC3351181
Abstract Full Text PDF–17M
Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex
J. E. McGeehan, N. J. Ball, S. D. Streeter, S.-J. Thresh, G. G. Kneale
Nucleic Acids Res. 2012 May; 40(9): 4158–4167. Published online 2011 December 29. doi: 10.1093/nar/gkr1250
PMCID:
PMC3351150
Abstract Full Text PDF–8.3M Supplementary Material
Visualization of a DNA-PK/PARP1 complex
Laura Spagnolo, Jody Barbeau, Nicola J. Curtin, Edward P. Morris, Laurence H. Pearl
Nucleic Acids Res. 2012 May; 40(9): 4168–4177. Published online 2012 January 5. doi: 10.1093/nar/gkr1231
PMCID:
PMC3351162
Abstract Full Text PDF–4.7M Supplementary Material
Structural insights into the redox-switch mechanism of the MarR/DUF24-type regulator HypR
Gottfried J. Palm, Bui Khanh Chi, Paul Waack, Katrin Gronau, Dörte Becher, Dirk Albrecht, Winfried Hinrichs, Randy J. Read, Haike Antelmann
Nucleic Acids Res. 2012 May; 40(9): 4178–4192. Published online 2012 January 11. doi: 10.1093/nar/gkr1316
PMCID:
PMC3351151
Abstract Full Text PDF–7.9M Supplementary Material
The structural basis for the oligomerization of the N-terminal domain of SATB1
Zheng Wang, Xue Yang, Xinlei Chu, Jinxiu Zhang, Hao Zhou, Yuequan Shen, Jiafu Long
Nucleic Acids Res. 2012 May; 40(9): 4193–4202. Published online 2012 January 11. doi: 10.1093/nar/gkr1284
PMCID:
PMC3351170
Abstract Full Text PDF–5.8M Supplementary Material
G-quadruplex structure and stability illuminated by 2-aminopurine phasor plots
Robert Buscaglia, David M. Jameson, Jonathan B. Chaires
Nucleic Acids Res. 2012 May; 40(9): 4203–4215. Published online 2012 January 12. doi: 10.1093/nar/gkr1286
PMCID:
PMC3351194
Abstract Full Text PDF–3.3M Supplementary Material
Structural and biochemical characterization of HP0315 from Helicobacter pylori as a VapD protein with an endoribonuclease activity
Ae-Ran Kwon, Ji-Hun Kim, Sung Jean Park, Ki-Young Lee, Yu-Hong Min, Hookang Im, Ingyun Lee, Kyu-Yeon Lee, Bong-Jin Lee
Nucleic Acids Res. 2012 May; 40(9): 4216–4228. Published online 2012 January 11. doi: 10.1093/nar/gkr1305
PMCID:
PMC3351183
Abstract Full Text PDF–4.9M Supplementary Material
Kinetics and mechanism of G-quadruplex formation and conformational switch in a G-quadruplex of PS2.M induced by Pb2+
Wei Liu, Hong Zhu, Bin Zheng, Sheng Cheng, Yan Fu, Wei Li, Tai-Chu Lau, Haojun Liang
Nucleic Acids Res. 2012 May; 40(9): 4229–4236. Published online 2012 January 11. doi: 10.1093/nar/gkr1310
PMCID:
PMC3351173
Abstract Full Text PDF–3.5M
The plasticity of WDR5 peptide-binding cleft enables the binding of the SET1 family of histone methyltransferases
Pamela Zhang, Hwabin Lee, Joseph S. Brunzelle, Jean-Francois Couture
Nucleic Acids Res. 2012 May; 40(9): 4237–4246. Published online 2012 January 20. doi: 10.1093/nar/gkr1235
PMCID:
PMC3351189
Abstract Full Text PDF–6.5M Supplementary Material
Survey and Summary
Comprehensive literature review and statistical considerations for GWAS meta-analysis
Ferdouse Begum, Debashis Ghosh, George C. Tseng, Eleanor Feingold
Nucleic Acids Res. 2012 May; 40(9): 3777–3784. Published online 2012 January 19. doi: 10.1093/nar/gkr1255
PMCID:
PMC3351172
Abstract Full Text PDF–1.7M Supplementary Material
Comprehensive literature review and statistical considerations for microarray meta-analysis
George C. Tseng, Debashis Ghosh, Eleanor Feingold
Nucleic Acids Res. 2012 May; 40(9): 3785–3799. Published online 2012 January 19. doi: 10.1093/nar/gkr1265
PMCID:
PMC3351145
Abstract Full Text PDF–3.7M Supplementary Material
Genomics
Genome-wide occupancy links Hoxa2 to Wnt–β-catenin signaling in mouse embryonic development
Ian J. Donaldson, Shilu Amin, James J. Hensman, Eva Kutejova, Magnus Rattray, Neil Lawrence, Andrew Hayes, Christopher M. Ward, Nicoletta Bobola
Nucleic Acids Res. 2012 May; 40(9): 3990–4001. Published online 2012 January 2. doi: 10.1093/nar/gkr1240
PMCID:
PMC3351182
Abstract Full Text PDF–8.5M Supplementary Material
Young intragenic miRNAs are less coexpressed with host genes than old ones: implications of miRNA–host gene coevolution
Chunjiang He, Zejuan Li, Ping Chen, Hao Huang, Laurence D. Hurst, Jianjun Chen
Nucleic Acids Res. 2012 May; 40(9): 4002–4012. Published online 2012 January 11. doi: 10.1093/nar/gkr1312
PMCID:
PMC3351155
Abstract Full Text PDF–1.2M Supplementary Material
Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis
Marek Zywicki, Kamilla Bakowska-Zywicka, Norbert Polacek
Nucleic Acids Res. 2012 May; 40(9): 4013–4024. Published online 2012 January 20. doi: 10.1093/nar/gks020
PMCID:
PMC3351166
Abstract Full Text PDF–4.6M Supplementary Material
Methods Online
Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage
Michał J. Okoniewski, Anna Leśniewska, Alicja Szabelska, Joanna Zyprych-Walczak, Martin Ryan, Marco Wachtel, Tadeusz Morzy, Beat Schäfer, Ralph Schlapbach
Nucleic Acids Res. 2012 May; 40(9): e63. Published online 2011 December 29. doi: 10.1093/nar/gkr1249
PMCID:
PMC3351146
Abstract Full Text PDF–11M
Direct and specific chemical control of eukaryotic translation with a synthetic RNA–protein interaction
Stephen J. Goldfless, Brian J. Belmont, Alexandra M. de Paz, Jessica F. Liu, Jacquin C. Niles
Nucleic Acids Res. 2012 May; 40(9): e64. Published online 2012 January 24. doi: 10.1093/nar/gks028
PMCID:
PMC3351163
Abstract Full Text PDF–583K Supplementary Material
Amplified microRNA detection by templated chemistry
Emily M. Harcourt, Eric T. Kool
Nucleic Acids Res. 2012 May; 40(9): e65. Published online 2012 January 25. doi: 10.1093/nar/gkr1313
PMCID:
PMC3351153
Abstract Full Text PDF–2.1M Supplementary Material
Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses
V. G. Fonseca, B. Nichols, D. Lallias, C. Quince, G. R. Carvalho, D. M. Power, S. Creer
Nucleic Acids Res. 2012 May; 40(9): e66. Published online 2012 January 25. doi: 10.1093/nar/gks002
PMCID:
PMC3351157
Abstract Full Text PDF–805K Supplementary Material
R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data
Vinay K. Mittal, John F. McDonald
Nucleic Acids Res. 2012 May; 40(9): e67. Published online 2012 January 28. doi: 10.1093/nar/gks047
PMCID:
PMC3351179
Abstract Full Text PDF–2.7M Supplementary Material
An on-bead tailing/ligation approach for sequencing resin-bound RNA libraries
Anna Wiesmayr, Pierre Fournier, Andres Jäschke
Nucleic Acids Res. 2012 May; 40(9): e68. Published online 2012 January 31. doi: 10.1093/nar/gks004
PMCID:
PMC3351178
Abstract Full Text PDF–2.2M
cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate
Günter Klambauer, Karin Schwarzbauer, Andreas Mayr, Djork-Arné Clevert, Andreas Mitterecker, Ulrich Bodenhofer, Sepp Hochreiter
Nucleic Acids Res. 2012 May; 40(9): e69. Published online 2012 January 2. doi: 10.1093/nar/gks003
PMCID:
PMC3351174
Abstract Full Text PDF–2.1M Supplementary Material
Picking ChIP-seq peak detectors for analyzing chromatin modification experiments
Mariann Micsinai, Fabio Parisi, Francesco Strino, Patrik Asp, Brian D. Dynlacht, Yuval Kluger
Nucleic Acids Res. 2012 May; 40(9): e70. Published online 2012 February 14. doi: 10.1093/nar/gks048
PMCID:
PMC3351193
Abstract Full Text PDF–7.4M Supplementary Material
A transposase strategy for creating libraries of circularly permuted proteins
Manan M. Mehta, Shirley Liu, Jonathan J. Silberg
Nucleic Acids Res. 2012 May; 40(9): e71. Published online 2012 February 7. doi: 10.1093/nar/gks060
PMCID:
PMC3351165
Abstract Full Text PDF–2.2M Supplementary Material
Computational Biology
Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals
Aradhita Baral, Pankaj Kumar, Rashi Halder, Prithvi Mani, Vinod Kumar Yadav, Ankita Singh, Swapan K. Das, Shantanu Chowdhury
Nucleic Acids Res. 2012 May; 40(9): 3800–3811. Published online 2012 January 11. doi: 10.1093/nar/gkr1258
PMCID:
PMC3351168
Abstract Full Text PDF–7.2M Supplementary Material
End-to-end attraction of duplex DNA
Christopher Maffeo, Binquan Luan, Aleksei Aksimentiev
Nucleic Acids Res. 2012 May; 40(9): 3812–3821. Published online 2012 January 11. doi: 10.1093/nar/gkr1220
PMCID:
PMC3351176
Abstract Full Text PDF–3.2M Supplementary Material
New methods for finding common insertion sites and co-occurring common insertion sites in transposon- and virus-based genetic screens
Tracy L. Bergemann, Timothy K. Starr, Haoyu Yu, Michael Steinbach, Jesse Erdmann, Yun Chen, Robert T. Cormier, David A. Largaespada, Kevin A. T. Silverstein
Nucleic Acids Res. 2012 May; 40(9): 3822–3833. Published online 2012 January 11. doi: 10.1093/nar/gkr1295
PMCID:
PMC3351147
Abstract Full Text PDF–1.3M Supplementary Material
A computational pipeline to discover highly phylogenetically informative genes in sequenced genomes: application to Saccharomyces cerevisiae natural strains
Matteo Ramazzotti, Luisa Berná, Irene Stefanini, Duccio Cavalieri
Nucleic Acids Res. 2012 May; 40(9): 3834–3848. Published online 2012 January 20. doi: 10.1093/nar/gks005
PMCID:
PMC3351171
Abstract Full Text PDF–3.8M Supplementary Material
On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements
Daniela M. Witten, William Stafford Noble
Nucleic Acids Res. 2012 May; 40(9): 3849–3855. Published online 2012 January 20. doi: 10.1093/nar/gks012
PMCID:
PMC3351188
Abstract Full Text PDF–167K Supplementary Material
Nucleic Acid Enzymes
The rotation-coupled sliding of EcoRV
Jasmina Dikić, Carolin Menges, Samuel Clarke, Michael Kokkinidis, Alfred Pingoud, Wolfgang Wende, Pierre Desbiolles
Nucleic Acids Res. 2012 May; 40(9): 4064–4070. Published online 2012 January 11. doi: 10.1093/nar/gkr1309
PMCID:
PMC3351190
Abstract Full Text PDF–2.3M Supplementary Material
Articles from Nucleic Acids Research are provided here courtesy of
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