Skip Navigation

Featured Articles

Featured Articles highlight the best papers published in NAR. These articles are chosen by the Executive Editors on the recommendation of Editorial Board Members and Referees. They represent the top 5% of papers in terms of originality, significance and scientific excellence. The articles are accompanied by a brief synopsis explaining the findings of the paper and where they fit in the broader context of nucleic acids research.

Recently Added Featured Articles

The UCSC genome browser database: update 2010
and
ENCODE whole-genome data in the UCSC Genome Browser
UCSC Genome Browser is a widely used tool for viewing, searching, analyzing, and downloading specific regions of the reference genome sequence together with aligned annotations. The browser database includes data generated by large-scale measurements of RNA expression by microarray and RNA-seq; human polymorphisms and their associated phenotypes; gene regulation through ChIP-chip or ChIP-sequencing of transcription factor binding sites, epigenetic chromatin modifications and hypersensitive sites; protein–protein interactions; and in situ images showing expression patterns. It also includes the reference collections of human protein-coding genes, miRNAs, noncoding RNA genes, signaling pathways and regulatory pathways.

The UCSC Genome Browser also serves as the primary data repository and platform for data mining and visualization of experimental results generated by investigators in the Encyclopedia of DNA Elements (ENCODE) project. ENCODE is an international project to analyze the human genome with the goal of producing a comprehensive catalog of functional elements expressed in 7 designated common cell types and 51 additional human cell lines and tissues. Read more here and here

The Pfam protein families database
This latest update on the Pfam protein families database describes the move to version 3 of the HMMER software. This move greatly increases the range of uses for Pfam because searches are now 100-fold faster than in previous versions. Previously daunting tasks, such as annotating metagenomic datasets, can now become routine. The database includes almost 3,000 new families giving a total of 11,912 protein families and a large fraction of the pre-existing families have been improved. Read on

Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling
Base-paired segments in RNA molecules fold into regular helical structures, while unpaired segments (loops) are seemingly unstructured. However, loops adopt a wide range of structural motifs, impart structural flexibility, and can therefore be seen as the actual source of not only the structural, but also the functional diversity of RNA molecules influencing the binding of small molecules, proteins, or other nucleic acids. Hence, loops are important carriers of RNA function. This article reports results from a systematic survey of experimentally determined RNA loop structures and establishes the basis for the application of homology modeling to RNA loops. By exploring sequence-structure relationships, the level of sequence divergence was identified above which two RNA loops are less likely to adopt similar structures. Thus, a critical guiding threshold for homology-based modeling efforts was identified. The article introduces a web database application for RNA loop homology modeling. Read on

An overview of the PubChem BioAssay resource
PubChem is designed to serve as an archive for the large volume of screening data generated by the NIH Molecular Libraries Program, as well as for bioactivity information contributed by the broader scientific community. The PubChem BioAssay information system provides a comprehensive platform to select and summarize the bioactivities of tested substances. This work describes the public resource including BioAssay data model and facilities to support research in the fields of chemical biology, medicinal chemistry, and drug discovery. Read on

WormBase: a comprehensive resource for nematode research
WormBase is a comprehensive resource for researchers studying basic problems in biology using the model organism C. elegans. The resource now includes information on related nematodes of both medical and agricultural importance. Read on

Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition
Aminoacyl-tRNA is the essential substrate for protein synthesis mostly made by direct acylation of the tRNA with the correct amino acid. However, many organisms and organelles form the amide aminoacyl-tRNAs, Gln-tRNAGln and Asn-tRNAAsn, by amidation of misacylated Glu-tRNAGln or Asp-tRNAAsn to the correct aminoacyl-tRNA catalyzed by a tRNA-dependent amidotransferase. This biosynthetic route of aminoacyl-tRNA synthesis is believed to precede evolutionarily the direct acylation by aminoacyl-tRNA synthetases. Structural and biochemical studies with the heterotrimeric Staphylococcus aureus GatCAB amidotransferase reveal two protein domains that interact with tRNA to ensure correct amide aminoacyl-tRNA formation.
(i) The tail domain of the amidotransferase specifically recognizes D-loop and the variable loop of the tRNA. (ii) A 310 turn structural motif in the catalytic domain provides specific recognition of the tRNA’s U1-A72 base allowing for discrimination of tRNAGln and tRNAAsn from tRNAGlu and tRNAAsp. Read on

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer
COSMIC is the largest system curating and detailing somatic mutations in cancer, using information gathered from the scientific literature, the WTSI Cancer Genome Project and other large scale cancer sequencing projects. It currently holds information on over 90,000 mutations and recent upgrades to encompass full-genome sequencing results will further expand the database. Its user-friendly format makes COSMIC a valuable resource for scientists working in the field of cancer genetics. Read on

Gene Expression Atlas at the European Bioinformatics Institute
Gene Expression Atlas is a new database at EBI that allows user to query gene expression by genes names or properties, such as Gene Ontology terms, or by tissue types, cell types, disease states or other conditions where the genes are expressed. It is an added value database with regularly growing content that is a part of ArrayExpress infrastructure and adds value to the archived data by curation, re-annotation and statistical computations to enable gene or biological condition based queries. Read on

The comprehensive microbial resource
The Comprehensive Microbial Resource (CMR, http://cmr.jcvi.org) provides a web-based central resource for the display, search, and analysis of the sequence and annotation for complete and publicly available bacterial and archaeal genomes. The data and tools provided by the CMR aid comparative genomic analysis. Read on

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes
The RegPrecise database aims at assisting genome-scale annotation of regulatory features and reconstruction of transcriptional regulatory networks in a variety of diverse microorganisms. It lists comparative-genomic predictions of transcription factor regulons in prokaryotes, including transcription factors, their cognate DNA motifs, and regulated genes linked to the candidate transcription factor binding sites. Read on

Xenbase: gene expression and improved integration
This paper describes updates to Xenbase, a model organism database for the frog species Xenopus tropicalis and X. laevis. Both species have unique experimental advantages and combining data from the two enhances their usefulness. Many of the genes and fundamental mechanism governing early embryonic development were first discovered in the Xenopus system. Xenopus females generate thousands of embryos in response to a simple hormone injection and the large robust embryos are simple to microinject with mRNA or anti-sense reagents. As the embryos develop a full set of differentiated organs within days of fertilization, very rapid high-throughput screens of gene function can be performed. Read on

PDBe: Protein Data Bank in Europe
The EMBL-EBI’s Protein Data Bank in Europe (PDBe) is the European resource for the collection, organization and dissemination of data about biological macromolecular structures, one of the four partners in the worldwide Protein Data Bank (wwPDB). PDBe uses a relational database that presents the data derived from the Protein Data Bank (PDB) in a consistent way and allows users to retrieve meaningful data using complex and sophisticated searches that range from simple textual queries to more complex 3D-structure-based queries. In collaboration with the scientific community, PDBe is developing improved tools and resources for structure deposition and analysis of macromolecules. Read on

The RNA polymerase activity of SARS-coronavirus nsp12 is primer dependent
Positive-stranded RNA viruses (i.e. viruses with a genome of mRNA polarity) include many important pathogens of plants and animals. Their replication depends on a viral RNA-synthesizing complex that directs the amplification and expression of the genome. The central subunit in this process is an RNA polymerase that copies the viral genome sequence. Thus far, technical complications prevented the purification of an active form of the RNA polymerase of SARS-coronavirus, the virus that caused the 2003 outbreak of Severe Acute Respiratory Syndrome in humans. Such an enzyme preparation and its biochemical characterization are crucial for the development of antiviral strategies, including specific inhibitors of coronavirus RNA synthesis. This article reports the purification of a stable form of the SARS-coronavirus polymerase from a bacterial expression system, and its subsequent characterization. The protein possesses robust in vitro RNA polymerase activity and thus provides a solid starting point for further fundamental and applied studies of this important viral enzyme. Read on

Ensembl genomes: Extending ensembl across the taxonomic space
Ensembl is a powerful system for genome display and analysis, originally developed for the vertebrate species. As the cost of generating genome-scale data falls with the development of new technology, such information is increasingly available for a wider range of speices. Ensembl Genomes is a new service developed to complement Ensembl by providing access to genome scale data from non-vertebrate species. The use of a common interface facilitates comparative and inter-species analysis from across the taxonomy. Read on

The Mouse Genome Database: enhancements and updates
The Mouse Genome Database (MGD) is the community model organism database for the laboratory mouse. The mission of MGD is to facilitate the use of the mouse as a model system for understanding human biology and disease. This manuscript describes recent enhancements to MGD including new features to support data mining and the comprehensive representation of gene trap and gene targeting data for the mouse. Read on

Sequence context outside the target region influences the effectiveness of miR-223 target sites in the RhoB 3'UTR
The studies presented in this manuscript describe sequence features in the 3' UTR of the RhoB mRNA that serve as enhancers for microRNA function. The results are significant in that they demonstrate that certain AU rich motifs serve as enhancers for miRNA function, and that these are position dependent with respect to the miRNA binding site. This work represents the first detailed study of the role of specific sequence motifs in miRNA function in human cells. Read on

TransmiR: a transcription factor–microRNA regulation database
MicroRNAs (miRNAs), which regulate target genes, are, in turn, regulated by various transcription factors (TFs). Increasing evidence indicates that aberrant regulation of miRNAs by TFs can cause phenotypic variations and diseases. This work presents a TF-miRNA regulation database (TransmiR, http://cmbi.bjmu.edu.cn/transmir), which contains 82 TFs and 100 miRNAs with 243 experimentally supported regulatory pairs between TFs and miRNAs. Read on

Ion-induced folding of a kink turn that departs from the conventional sequence
Kink turns (k-turns) are important structural motifs that create a sharp axial bend in RNA. k-turns seem to be involved in almost every aspect of RNA function, including the translation and modification of RNA, spliceosome assembly and the control of gene expression. Most conform to a consensus in which a three-nucleotide bulge is followed by consecutive G•A and A•G basepairs, and when these G•A pairs are modified in vitro this generally leads to a failure to adopt the k-turn conformation. Kt-23 in the 30S ribosomal subunit of T. thermophilus is a rare exception in which the bulge-distal A•G pair is replaced by a non-Watson-Crick A•U pair. In this work it is shown that Kt-23 is intrinsically stable despite lacking the key A•G pair; its formation requires neither tertiary interactions nor protein binding. This requires some revision of our ideas about the sequence requirements for stable k-turn formation. Read on

Crystal structure of the EndoG/EndoGI complex: mechanism of EndoG inhibition
This paper reports on the crystal structure of a complex of the EndoG nuclease from drosophila and its inhibitor, EndoGI. Eukaryotic Endonuclease G is a non-specific "beta-beta-alpha-Metal" nuclease taking part in caspase-independent apoptotic DNA-fragmentation after translocation from the mitochondria into the nucleus of a cell. Drosophila is the only known eukaryote that expresses an inhibitory protein which controls the potentially cytotoxic activity of Endonuclease G inside the nucleus. In prokaryotes. at least two nuclease/inhibitor complexes of related enzymes are known, the cyanobacterial NucA/NuiA-complex and the complexes of colicins E7 and E9 with their immunity proteins Im7 and Im9, respectively. The structure of the EndoG/EndoGI complex is the first example of a eukaryotic bba-Me-finger enzyme/inhibitor complex and, in addition, contains the first crystallographic analysis of a eukaryotic Endonuclease G. Read on