Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications.

abstract：:OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the al...

journal_title：Nucleic acids research

authors： Altenhoff AM,Schneider A,Gonnet GH,Dessimoz C

更新日期：2011-01-01 00:00:00

abstract：:Alternative splicing (AS) is a post-transcriptional process considered to be responsible for the huge diversity of proteins in higher eukaryotes. AS events are regulated by different splicing factors (SFs) that bind to sequence elements on the RNA. SFmap is a web server for predicting putative SF binding sites in geno...

journal_title：Nucleic acids research

authors： Paz I,Akerman M,Dror I,Kosti I,Mandel-Gutfreund Y

更新日期：2010-07-01 00:00:00

abstract：:The catalytic strategies of small self-cleaving ribozymes often involve interactions between nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply protonated, gaseous RNA has an intrinsic preference for the formation of ionic hydrogen bonds between adenine protonated at N3 and the phosphodies...

journal_title：Nucleic acids research

authors： Fuchs E,Falschlunger C,Micura R,Breuker K

更新日期：2019-08-22 00:00:00

abstract：:Human minisatellite probes cross-hybridize to mouse DNA and detect multiple variable loci. The resulting DNA "fingerprints" vary substantially between inbred strains but relatively little within an inbred strain. By studying the segregation of variable DNA fragments in BXD recombinant inbred strains of mice, at least ...

journal_title：Nucleic acids research

authors： Jeffreys AJ,Wilson V,Kelly R,Taylor BA,Bulfield G

更新日期：1987-04-10 00:00:00

abstract：:WorfDB (Worm ORFeome DataBase; http://worfdb.dfci.harvard.edu) was created to integrate and disseminate the data from the cloning of complete set of approximately 19 000 predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans (also referred to as the 'worm ORFeome'). WorfDB serves as a central ...

journal_title：Nucleic acids research

authors： Vaglio P,Lamesch P,Reboul J,Rual JF,Martinez M,Hill D,Vidal M

更新日期：2003-01-01 00:00:00

abstract：:Zar1 was one of the earliest mammalian maternal-effect genes to be identified. Embryos derived from Zar1-null female mice are blocked before zygotic genome activation; however, the underlying mechanism remains unclear. By knocking out Zar1 and its homolog Zar2 in mice, we revealed a novel function of these genes in oo...

journal_title：Nucleic acids research

authors： Rong Y,Ji SY,Zhu YZ,Wu YW,Shen L,Fan HY

更新日期：2019-12-02 00:00:00

abstract：:Chromatin boundaries regulate gene expression by modulating enhancer-promoter interactions and insulating transcriptional influences from organized chromatin. However, mechanistic distinctions between these two aspects of boundary function are not well understood. Here we show that SF1, a chromatin boundary located in...

journal_title：Nucleic acids research

authors： Majumder P,Roy S,Belozerov VE,Bosu D,Puppali M,Cai HN

更新日期：2009-07-01 00:00:00

abstract：:Eukaryotic cells possess several distinct mismatch repair pathways. A mismatch can be introduced in retroviral double-stranded DNA by a pre-existing mutation within the primer binding site (PBS) of the viral RNA genome. In order to evaluate mismatch repair of retroviral double-stranded DNA, Moloney leukemia virus (MLV...

journal_title：Nucleic acids research

authors： Tang LY,Zhang J

更新日期：2000-06-15 00:00:00

abstract：:This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology) in common alignment formats and a wide range of evolutionary ...

journal_title：Nucleic acids research

authors： Trifinopoulos J,Nguyen LT,von Haeseler A,Minh BQ

更新日期：2016-07-08 00:00:00

abstract：:The human Microprocessor complex cleaves primary microRNA (miRNA) transcripts (pri-miRNAs) to initiate miRNA synthesis. Microprocessor consists of DROSHA (an RNase III enzyme), and DGCR8. DROSHA contains two RNase III domains, RIIIDa and RIIIDb, which simultaneously cleave the 3p- and 5p-strands of pri-miRNAs, respect...

journal_title：Nucleic acids research

authors： Nguyen TL,Nguyen TD,Bao S,Li S,Nguyen TA

更新日期：2020-03-18 00:00:00

abstract：:Herein, we describe a case study into the population dynamics of in vitro selection, using RNA-cleaving DNAzymes as a model system. We sought to understand how the composition of the population can change over time in response to different levels of selection pressure, and how well these changes are correlated with se...

journal_title：Nucleic acids research

authors： Schlosser K,Lam JC,Li Y

更新日期：2009-06-01 00:00:00

abstract：:The entire intervening sequence of Tetrahymena thermophila ribosomal DNA has been determined. It is 413 nucleotides long and has the same splice junctions as those in T. pigmentosa. There is 93% homology between the intervening sequences in the two species, and 100% homology between their adjacent 26S RNA coding regio...

journal_title：Nucleic acids research

authors： Kan NC,Gall JG

更新日期：1982-05-11 00:00:00

abstract：:One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expressio...

journal_title：Nucleic acids research

authors： Chuchana P,Marchand D,Nugoli M,Rodriguez C,Molinari N,Garcia-Sanz JA

更新日期：2007-01-01 00:00:00

abstract：:Short repetitive DNA sequences are believed to be one of the primordial genetic elements that served as a source of complex large DNA found in the genome of modern organisms. However, the mechanism of its expansion (increase in repeat number) during the course of evolution is unclear. We demonstrate that the DNA polym...

journal_title：Nucleic acids research

authors： Ogata N,Morino H

更新日期：2000-10-15 00:00:00

abstract：:The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative...

journal_title：Nucleic acids research

authors： Davis JJ,Wattam AR,Aziz RK,Brettin T,Butler R,Butler RM,Chlenski P,Conrad N,Dickerman A,Dietrich EM,Gabbard JL,Gerdes S,Guard A,Kenyon RW,Machi D,Mao C,Murphy-Olson D,Nguyen M,Nordberg EK,Olsen GJ,Olson RD,Overb

更新日期：2020-01-08 00:00:00

abstract：:HIV-1 Tat protein reprograms cellular gene expression of infected as well as uninfected cells apart from its primary function of transactivating HIV-1 long terminal repeat (LTR) promoter by binding to a nascent RNA stem-loop structure known as the transactivator response region (TAR). Tat also induces chromatin remode...

journal_title：Nucleic acids research

authors： Dandekar DH,Ganesh KN,Mitra D

更新日期：2004-02-23 00:00:00

abstract：:Crotonaldehyde is a representative alpha,beta-unsaturated aldehyde endowed of mutagenic and carcinogenic properties related to its propensity to react with DNA. Cyclic crotonaldehyde-derived deoxyguanosine (CrA-PdG) adducts can undergo ring opening in duplex DNA to yield a highly reactive aldehydic moiety. Here, we de...

journal_title：Nucleic acids research

authors： Dexheimer TS,Kozekova A,Rizzo CJ,Stone MP,Pommier Y

更新日期：2008-07-01 00:00:00

abstract：:Despite two decades of study, the full scope of RNAi in mammalian cells has remained obscure. Here we combine: (i) Knockout of argonaute (AGO) variants; (ii) RNA sequencing analysis of gene expression changes and (iii) Enhanced Crosslinking Immunoprecipitation Sequencing (eCLIP-seq) using anti-AGO2 antibody to identif...

journal_title：Nucleic acids research

authors： Chu Y,Kilikevicius A,Liu J,Johnson KC,Yokota S,Corey DR

更新日期：2020-07-27 00:00:00

abstract：:To facilitate transcript mapping and to investigate alterations in genomic structure and gene expression in a defined genomic target, we developed a novel microarray-based method to detect transcriptional activity of the human chromosome 4q22-24 region. Loss of heterozygosity of human 4q22-24 is frequently observed in...

journal_title：Nucleic acids research

authors： Li LH,Li JC,Lin YF,Lin CY,Chen CY,Tsai SF

更新日期：2004-02-11 00:00:00

abstract：:p53 is thought to function in the maintenance of genomic stability by modulating transcription and interacting with cellular proteins to influence the cell cycle, DNA repair and apoptosis. p53 mutations occur in >50% of human cancers, and cells which lack wild type p53 accumulate karyotypic abnormalities such as ampli...

journal_title：Nucleic acids research

authors： Buchhop S,Gibson MK,Wang XW,Wagner P,Stürzbecher HW,Harris CC

更新日期：1997-10-01 00:00:00

abstract：:Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons. Enhancers, as well as their associated target genes, and transcription factors (TFs) that bind to them, are highly associated with human disease and biological processes. Alt...

journal_title：Nucleic acids research

authors： Bai X,Shi S,Ai B,Jiang Y,Liu Y,Han X,Xu M,Pan Q,Wang F,Wang Q,Zhang J,Li X,Feng C,Li Y,Wang Y,Song Y,Feng K,Li C

更新日期：2020-01-08 00:00:00

abstract：:Homologous recombination provides a means for the in vivo construction of recombinant DNA molecules that may be problematic to assemble in vitro. We have investigated the efficiency of recombination within the Caenorhabditis elegans germ line as a function of the length of homology between recombining molecules. Our f...

journal_title：Nucleic acids research

authors： Kemp BJ,Hatzold J,Sternick LA,Cornman-Homonoff J,Whitaker JM,Tieu PJ,Lambie EJ

更新日期：2007-01-01 00:00:00

abstract：:Despite the extensive use of Saccharomyces cerevisiae as a platform for synthetic biology, strain engineering remains slow and laborious. Here, we employ CRISPR/Cas9 technology to build a cloning-free toolkit that addresses commonly encountered obstacles in metabolic engineering, including chromosomal integration locu...

journal_title：Nucleic acids research

authors： Reider Apel A,d'Espaux L,Wehrs M,Sachs D,Li RA,Tong GJ,Garber M,Nnadi O,Zhuang W,Hillson NJ,Keasling JD,Mukhopadhyay A

更新日期：2017-01-09 00:00:00

abstract：:A non-enzymic protein factor that increases the in vitro rate of synthesis by HeLa DNA polymerase alpha 15- to 30-fold with denatured DNA as template has been partially purified from the cytoplasmic fraction of HeLa cells. The stimulatory effect is highly specific for HeLa DNA polymerase alpha and for DNA templates th...

journal_title：Nucleic acids research

authors： Novak B,Baril EF

更新日期：1978-01-01 00:00:00

abstract：:MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature approximately 22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally val...

journal_title：Nucleic acids research

authors： Gerlach D,Kriventseva EV,Rahman N,Vejnar CE,Zdobnov EM

更新日期：2009-01-01 00:00:00

abstract：:Nuclear extracts prepared from growth hormone-secreting (GC) and prolactin-secreting (235-1) rat anterior pituitary cell lines were compared for their ability to bind to the DNA sequences conferring tissue-specificity to the expression of the rat growth hormone (rGH) gene promoter. Cell-specific differences in the int...

journal_title：Nucleic acids research

authors： Schaufele F,West BL,Reudelhuber T

更新日期：1990-09-11 00:00:00

abstract：:The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has...

journal_title：Nucleic acids research

authors： Islam B,Sgobba M,Laughton C,Orozco M,Sponer J,Neidle S,Haider S

更新日期：2013-02-01 00:00:00

abstract：:The laboratory mouse is the premier animal model for studying human biology because all life stages can be accessed experimentally, a completely sequenced reference genome is publicly available and there exists a myriad of genomic tools for comparative and experimental research. In the current era of genome scale, dat...

journal_title：Nucleic acids research

authors： Bult CJ,Eppig JT,Blake JA,Kadin JA,Richardson JE,Mouse Genome Database Group.

更新日期：2013-01-01 00:00:00

abstract：:We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged ...

journal_title：Nucleic acids research

authors： Havrila M,Stadlbauer P,Kührová P,Banáš P,Mergny JL,Otyepka M,Šponer J

更新日期：2018-09-28 00:00:00

abstract：:Yeast uses nucleotide excision repair (NER) and photolyase (photoreactivation) to repair cyclobutane pyrimidine dimers (CPDs) generated by ultraviolet light. In active genes, NER preferentially repairs the transcribed strand (TS). In contrast, we recently showed that photolyase preferentially repairs the non-transcrib...

journal_title：Nucleic acids research

authors： Livingstone-Zatchej M,Meier A,Suter B,Thoma F

更新日期：1997-10-01 00:00:00