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  • Overexpression of RAD51 suppresses recombination defects: a possible mechanism to reverse genomic instability.
    We are defining these proteins here as 'recombination co-mediators'. Defects in either recombination mediators or co-mediators, incl...
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  • Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.
    We discover a set of 38 candidate cis-regulatory coding exons (RCEs) with predicted target genes. These elements demonstrate evoluti...
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  • A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms.
    We compared the nuclear and cytosolic transcriptomes of HepG2 and HeLa cells. HepG2 and HeLa cells vary significantly in the differe...
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  • The CCAAT-binding complex coordinates the oxidative stress response in eukaryotes.
    We demonstrate that AnCF senses the redox status of the cell via oxidative modification of thiol groups within the histone fold moti...
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  • Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential.
    We extend these findings to human cells. Using microarrays to measure mRNAs obtained from human fibroblasts deficient for various Re...
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  • Hierarchy of lesion processing governs the repair, double-strand break formation and mutability of three-lesion clustered DNA damage.
    We have designed synthetic oligonucleotides to give a variety of three-lesion clusters containing abasic sites and 8-oxo-7, 8-dihydr...
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  • Opposing regulatory roles of phosphorylation and acetylation in DNA mispair processing by thymine DNA glycosylase.
    We report that protein kinase C alpha (PKCalpha) interacts with TDG and phosphorylates amino-terminal serine residues adjacent to ly...
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  • DNA structure and the Werner protein modulate human DNA polymerase delta-dependent replication dynamics within the common fragile site FRA16D.
    We used an in vitro primer extension assay to examine the progression of DNA synthesis through various sequences within FRA16D by th...
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  • Discovery of short pseudogenes derived from messenger RNAs.
    We report that the human genome contains many previously unidentified short pseudogenes generated by retrotransposition of mRNAs. Ge...
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  • The most frequent short sequences in non-coding DNA.
    We present a simple method for the detection and analysis of such sequences in several genomes, including Arabidopsis thaliana, Caen...
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  • Essential roles of three enhancer sites in {sigma}54-dependent transcription by the nitric oxide sensing regulatory protein NorR.
    We show that all three sites are required for NorR-dependent catalysis of open complex formation by sigma(54)-RNAP holoenzyme (Esigm...
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  • Elevated dNTP levels suppress hyper-recombination in Saccharomyces cerevisiae S-phase checkpoint mutants.
    We previously observed a 6-, 10- and 30-fold higher rate of spontaneous sister chromatid exchange (SCE), heteroallelic recombination...
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  • Precise targeted integration by a chimaeric transposase zinc-finger fusion protein.
    We show that fusion of the zinc-finger DNA-binding domain of Zif268 to the C-terminus of ISY100 transposase leads to highly specific...
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  • A tale of two functions: enzymatic activity and translational repression by carboxyltransferase.
    We report that carboxyltransferase regulates its own translation by binding the mRNA encoding its subunits. This interaction is medi...
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  • Dr1 (NC2) is present at tRNA genes and represses their transcription in human cells.
    We demonstrate that endogenous Dr1 is present at pol III templates in human cells, as is its dimerization partner DRAP1 (also called...
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  • Lin28-mediated post-transcriptional regulation of Oct4 expression in human embryonic stem cells.
    We report that in human embryonic stem cells Lin28 facilitates the expression of the pivotal pluripotency factor Oct4 at the post-tr...
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  • The transcriptional transactivator Tat selectively regulates viral splicing.
    We present evidence for an unexpected function of Tat in viral splicing regulation. We used a series of HIV-1 reporter minigenes to...
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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.
    We obtained and characterized yeast strains in which the wild-type yeast rpS5 was replaced by its truncated variants, lacking 13, 24...
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  • Promoter and regulon analysis of nitrogen assimilation factor, {sigma}54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis.
    We identify 40 in vivo targets of sigma(54), the nitrogen assimilation sigma factor, and estimate that there are 70 sigma(54) promot...
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  • Translational activation of rpoS mRNA by the non-coding RNA DsrA and Hfq does not require ribosome binding.
    We show by ribosome profiling that Hfq partitions with the cytoplasmic fraction rather than with 30S subunits. Besides, by employing...
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  • Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs.
    We have generated nicking variants of BtsCI that specifically nick the bottom-strand or the top-strand of the target site. By treati...
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  • Mutational analysis of the 5'-OH oligonucleotide phosphate acceptor site of T4 polynucleotide kinase.
    We probed by mutagenesis the roles of individual amino acids that comprise the acceptor binding site. We thereby identified Glu57 as...
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  • Phosphate release contributes to the rate-limiting step for unwinding by an RNA helicase.
    We have established an RNA substrate for NS3 that can be unwound in a single sub-step. Our studies are consistent with a model in wh...
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  • Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.
    We investigate a region including the elbow-shaped kink-turn (Kt-38) in the Haloarcula marismortui archaeal ribosome, and equivalent...
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  • Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA.
    We have identified two previously uncharacterized genes in E. coli that are required for m(4)Cm formation. mraW (renamed rsmH) and y...
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  • Antagonistic factors control the unproductive splicing of SC35 terminal intron.
    We identified in the highly conserved last exon a number of exonic splicing enhancer elements responding specifically to SC35, and s...
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  • A new type of IRES within gag coding region recruits three initiation complexes on HIV-2 genomic RNA.
    We have modelled the secondary structure of HIV-1, HIV-2 and SIV(Mac) coding region. This approach brings to light conserved seconda...
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  • Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development.
    We examined auxin responsiveness of miR390 expression, which comprises a regulatory step for the biogenesis pathway of tasiRNA-ARF (...
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  • Atomistic basis for the on-off signaling mechanism in SAM-II riboswitch.
    We report the results of molecular dynamics simulation studies of the S-adenosylmethionine (SAM)-II riboswitch that is involved in r...
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  • Crystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-tRNA synthetase.
    We present the first crystal structure of an archaeal TrpRS, the structure of Pyrococcus horikoshii TrpRS (pTrpRS) in complex with t...
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  • MMBGX: a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays
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  • Tandem affinity purification of miRNA target mRNAs (TAP-Tar).
    We describe a biochemical approach, based on tandem affinity purification, in which mRNA/miRNA complexes are sequentially pulled dow...
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  • Selection of DNA aptamers using atomic force microscopy.
    We propose the Systematic Evolution of Ligands by an EXponential enrichment (SELEX) method using AFM to obtain aptamers that have a...
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  • A comprehensive analysis of filamentous phage display vectors for cytoplasmic proteins: an analysis with different fluorescent proteins.
    We have analyzed the ability of filamentous phage to display a stable form of green fluorescent protein and modified variants in nin...
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  • A calibrated diversity assay for nucleic acid libraries using DiStRO--a Diversity Standard of Random Oligonucleotides.
    We have determined diversities exceeding 10(12) different sequences in an annealing and melting assay using synthetic randomized oli...
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  • Analysis of differential DNA damage in the mitochondrial genome employing a semi-long run real-time PCR approach.
    We developed a rapid and quantitative method to evaluate the relative levels of damage in mitochondrial DNA by using the real time-P...
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  • Selection of bacteriophage {lambda} integrases with altered recombination specificity by in vitro compartmentalization.
    We describe provides a robust, completely in vitro platform for the development of novel integrase reagent tools for in vitro DNA ma...
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  • A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans.
    We describe an in vivo tagging system coupled to chromatin purification for genome-wide epigenetic profiling in Caenorhabditis elega...
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  • Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization.
    We set out to improve BLASTN accuracy by modifying the substitution matrix and gap penalties. We generated gene expression microarra...
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  • Nucleic Acids Research: VOLUME 38 ISSUE 4 2010.
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  • Nucleic acids research.
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  • Subscriptions.
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