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Volume 37, Issue 9, 1 May 2009
Gene Regulation, Chromatin and Epigenetics
Long 3′-UTRs target wild-type mRNAs for nonsense-mediated mRNA decay in Saccharomyces cerevisiae
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2771–2778, https://doi.org/10.1093/nar/gkp146
Distinctive sequence patterns in metazoan and yeast nucleosomes: Implications for linker histone binding to AT-rich and methylated DNA
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2818–2829, https://doi.org/10.1093/nar/gkp113
Heat shock factor-1 modulates p53 activity in the transcriptional response to DNA damage
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2962–2973, https://doi.org/10.1093/nar/gkp180
Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2984–2995, https://doi.org/10.1093/nar/gkp127
The transcriptional coactivator MAML1 regulates p300 autoacetylation and HAT activity
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2996–3006, https://doi.org/10.1093/nar/gkp163
Dazap2 modulates transcription driven by the Wnt effector TCF-4
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 3007–3020, https://doi.org/10.1093/nar/gkp179
Genome Integrity, Repair and Replication
Contributions of the individual hydrophobic clefts of the Escherichia coli β sliding clamp to clamp loading, DNA replication and clamp recycling
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2796–2809, https://doi.org/10.1093/nar/gkp128
The efficiency and fidelity of 8-oxo-guanine bypass by DNA polymerases δ and η
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2830–2840, https://doi.org/10.1093/nar/gkp103
Genomics
Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2926–2939, https://doi.org/10.1093/nar/gkp164
From damaged genome to cell surface: transcriptome changes during bacterial cell death triggered by loss of a restriction–modification gene complex
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 3021–3031, https://doi.org/10.1093/nar/gkp148
Molecular Biology
Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2779–2788, https://doi.org/10.1093/nar/gkp135
Protein hnRNP A1 and its derivative Up1 unfold quadruplex DNA in the human KRAS promoter: implications for transcription
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2841–2853, https://doi.org/10.1093/nar/gkp138
AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2940–2950, https://doi.org/10.1093/nar/gkp149
Creation of the two isoforms of rodent NKG2D was driven by a B1 retrotransposon insertion
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 3032–3043, https://doi.org/10.1093/nar/gkp174
The proapoptotic dp5 gene is a direct target of the MLK-JNK-c-Jun pathway in sympathetic neurons
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 3044–3060, https://doi.org/10.1093/nar/gkp175
Retracted: CK1δ modulates the transcriptional activity of ERα via AIB1 in an estrogen-dependent manner and regulates ERα–AIB1 interactions
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 3110–3123, https://doi.org/10.1093/nar/gkp136
Nucleic Acid Enzymes
Proofreading exonuclease activity of human DNA polymerase δ and its effects on lesion-bypass DNA synthesis
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2854–2866, https://doi.org/10.1093/nar/gkp155
Creation of a type IIS restriction endonuclease with a long recognition sequence
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 3061–3073, https://doi.org/10.1093/nar/gkp182
RNA
A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2867–2881, https://doi.org/10.1093/nar/gkp106
The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2894–2909, https://doi.org/10.1093/nar/gkp152
A role for hydrophobicity in a Diels–Alder reaction catalyzed by pyridyl-modified RNA
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 3074–3082, https://doi.org/10.1093/nar/gkp177
Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 3083–3093, https://doi.org/10.1093/nar/gkp189
Selection, characterization and application of new RNA HIV gp 120 aptamers for facile delivery of Dicer substrate siRNAs into HIV infected cells
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 3094–3109, https://doi.org/10.1093/nar/gkp185
Structural Biology
Direct demonstration and quantification of long-range DNA looping by the λ bacteriophage repressor
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2789–2795, https://doi.org/10.1093/nar/gkp134
The poly dA helix: a new structural motif for high performance DNA-based molecular switches
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2810–2817, https://doi.org/10.1093/nar/gkp133
Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2882–2893, https://doi.org/10.1093/nar/gkp137
Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2910–2925, https://doi.org/10.1093/nar/gkp158
The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2951–2961, https://doi.org/10.1093/nar/gkp166
The RRM domain in GW182 proteins contributes to miRNA-mediated gene silencing
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Pages 2974–2983, https://doi.org/10.1093/nar/gkp173
Methods Online
Identification and classification of ncRNA molecules using graph properties
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Page e66, https://doi.org/10.1093/nar/gkp206
Human Splicing Finder: an online bioinformatics tool to predict splicing signals
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Page e67, https://doi.org/10.1093/nar/gkp215
Comparative analysis of different laser systems to study cellular responses to DNA damage in mammalian cells
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Page e68, https://doi.org/10.1093/nar/gkp221
Mining small RNA sequencing data: a new approach to identify small nucleolar RNAs in Arabidopsis
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Page e69, https://doi.org/10.1093/nar/gkp225
Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Page e70, https://doi.org/10.1093/nar/gkp211
Composite RNA aptamers as functional mimics of proteins
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Page e71, https://doi.org/10.1093/nar/gkp243
Corrigendum
Database resources of the National Center for Biotechnology Information
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Page 3124, https://doi.org/10.1093/nar/gkp382
Front-Matter/Back-Matter
Nucleic Acids Research: VOLUME 37 ISSUE 9 2009
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Page i, https://doi.org/10.1093/nar/gkp459
Nucleic Acids Research
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Page ii, https://doi.org/10.1093/nar/gkp458
Subscriptions
Nucleic Acids Research, Volume 37, Issue 9, 1 May 2009, Page iii, https://doi.org/10.1093/nar/gkp472
