Design and in vivo characterization of self-inactivating human and non-human lentiviral expression vectors engineered for streptogramin-adjustable transgene expression.

abstract：:Transposable elements are found throughout the genomes of all organisms. Repressive marks such as DNA methylation and histone H3 lysine 9 (H3K9) methylation silence these elements and maintain genome integrity. However, how silencing mechanisms are themselves regulated to avoid the silencing of genes remains unclear. ...

journal_title：Nucleic acids research

authors： Li S,Liu L,Li S,Gao L,Zhao Y,Kim YJ,Chen X

更新日期：2016-01-29 00:00:00

abstract：:By successively assembling genetic parts such as BioBrick according to grammatical models, complex genetic constructs composed of dozens of functional blocks can be built. However, usually every category of genetic parts includes a few or many parts. With increasing quantity of genetic parts, the process of assembling...

journal_title：Nucleic acids research

authors： Fang G,Zhang S,Dong Y

更新日期：2017-12-15 00:00:00

abstract：:Pseudomonas aeruginosa is an opportunistic pathogen with a relatively large genome, and has been shown to routinely lose genomic fragments during environmental selection. However, the underlying molecular mechanisms that promote chromosomal deletion are still poorly understood. In a recent study, we showed that by del...

journal_title：Nucleic acids research

authors： Shen M,Zhang H,Shen W,Zou Z,Lu S,Li G,He X,Agnello M,Shi W,Hu F,Le S

更新日期：2018-05-18 00:00:00

abstract：:Two DNA polymerases have been purified from the 105,000 x g supernatant of ungerminated wheat. The purification stages included: high speed centrifugation, salt fractionation, DEAE-cellulose chromatography, Sephadex G-150 filtration and phosphocellulose chromatography. Several properties of the two enzyme (called A an...

journal_title：Nucleic acids research

authors： Castroviejo M,Tarragó-Litvak L,Litvak S

更新日期：1975-11-01 00:00:00

abstract：:Cpf1 nucleases were recently reported to be highly specific and programmable nucleases with efficiencies comparable to those of SpCas9. AsCpf1 and LbCpf1 require a single crRNA and recognize a 5'-TTTN-3' protospacer adjacent motif (PAM) at the 5' end of the protospacer for genome editing. For widespread application in...

journal_title：Nucleic acids research

authors： Tu M,Lin L,Cheng Y,He X,Sun H,Xie H,Fu J,Liu C,Li J,Chen D,Xi H,Xue D,Liu Q,Zhao J,Gao C,Song Z,Qu J,Gu F

更新日期：2017-11-02 00:00:00

abstract：:Yaf9 is an integral part of the NuA4 acetyltransferase and the SWR1 chromatin remodeling complexes. Here, we show that Yaf9 associates with acetylated histone H3 with high preference for H3K27ac. The crystal structure of the Yaf9 YEATS domain bound to the H3K27ac peptide reveals that the sequence C-terminal to K27ac s...

journal_title：Nucleic acids research

authors： Klein BJ,Ahmad S,Vann KR,Andrews FH,Mayo ZA,Bourriquen G,Bridgers JB,Zhang J,Strahl BD,Côté J,Kutateladze TG

更新日期：2018-01-09 00:00:00

abstract：:Argonaute (AGO) proteins have a well-established role in post-transcriptional regulation of gene expression as key component of the RNA silencing pathways. Recent evidence involves AGO proteins in mammalian nuclear processes such as transcription and splicing, though the mechanistic aspects of AGO nuclear functions re...

journal_title：Nucleic acids research

authors： Carissimi C,Laudadio I,Cipolletta E,Gioiosa S,Mihailovich M,Bonaldi T,Macino G,Fulci V

更新日期：2015-02-18 00:00:00

abstract：:The family Picornaviridae contains important pathogens including, for example, hepatitis A virus and foot-and-mouth disease virus. The genome of these viruses is a single messenger-active (+)-RNA of 7200-8500 nt. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, a...

journal_title：Nucleic acids research

authors： Witwer C,Rauscher S,Hofacker IL,Stadler PF

更新日期：2001-12-15 00:00:00

abstract：:DNA primases recognize single-stranded DNA (ssDNA) sequences to synthesize RNA primers during lagging-strand replication. Arabidopsis thaliana encodes an ortholog of the DNA primase-helicase from bacteriophage T7, dubbed AtTwinkle, that localizes in chloroplasts and mitochondria. Herein, we report that AtTwinkle synth...

journal_title：Nucleic acids research

authors： Peralta-Castro A,Baruch-Torres N,Brieba LG

更新日期：2017-10-13 00:00:00

abstract：:Contrary to the expectation, the Merrifield polystyrene resin, 2% cross-linked by divinylbenzene, is as efficient as the polyacrylmorpholide resin for the synthesis of polydeoxyribonucleotides using a phosphotriester method. On the Merrifield resin, the tetradecamer, dTpCpGpTpCpApApCpTpGpGpCpTpT, and the hexadecamer, ...

journal_title：Nucleic acids research

authors： Miyoshi K,Arentzen R,Huang T,Itakura K

更新日期：1980-11-25 00:00:00

abstract：:Current literature describes several methods for the design of efficient siRNAs with 19 perfectly matched base pairs and 2 nt overhangs. Using four independent databases totaling 3336 experimentally verified siRNAs, we compared how well several of these methods predict siRNA cleavage efficiency. According to receiver ...

journal_title：Nucleic acids research

authors： Matveeva O,Nechipurenko Y,Rossi L,Moore B,Saetrom P,Ogurtsov AY,Atkins JF,Shabalina SA

更新日期：2007-01-01 00:00:00

abstract：:Nucleosomes released from oviduct nuclei during brief micrococcal nuclease digestions are enriched in transcribed sequences (bloom K.S. and Anderson, J.N. (1978) Cell, 15, 141-150). Such nucleosomes released into this 1Sf supernatant fraction are enriched in proteins HMG14, 17 and a third lower molecular weight protei...

journal_title：Nucleic acids research

authors： Goodwin GH,Wright CA,Johns EW

更新日期：1981-06-25 00:00:00

abstract：:An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the map...

journal_title：Nucleic acids research

authors： Yamagata K,Yamanishi A,Kokubu C,Takeda J,Sese J

更新日期：2016-05-05 00:00:00

abstract：:Here we report that the poor binding of methylphosphonate oligodeoxynucleosides (MP-ODNs) to their nucleic acid targets can be improved by additional inversion of the anomeric configuration (from beta to alpha) in the sugar moieties to give a new class of analogs, MP alpha-oligonucleosides. MP alpha-dT12and MP 5' alph...

journal_title：Nucleic acids research

authors： Debart F,Meyer A,Vasseur JJ,Rayner B

更新日期：1998-10-15 00:00:00

abstract：:The DNA-binding specificity and affinity of the dimeric human transcription factor (TF) STAT1, were assessed by total internal reflectance fluorescence protein-binding microarrays (TIRF-PBM) to evaluate the effects of protein phosphorylation, higher-order polymerization and small-molecule inhibition. Active, phosphory...

journal_title：Nucleic acids research

authors： Bonham AJ,Wenta N,Osslund LM,Prussin AJ 2nd,Vinkemeier U,Reich NO

更新日期：2013-01-01 00:00:00

abstract：:The template requirements for efficient adenovirus DNA replication were studied in vitro in a reconstituted system with cloned DNA fragments, containing the Ad2 origin region, as templates. Replication is enhanced by nuclear factor I, a cellular protein that binds specifically to the Ad2 origin. This stimulation is sh...

journal_title：Nucleic acids research

authors： de Vries E,van Driel W,Tromp M,van Boom J,van der Vliet PC

更新日期：1985-07-11 00:00:00

abstract：:The COXPRESdb (http://coxpresdb.jp) provides gene coexpression relationships for animal species. Here, we report the updates of the database, mainly focusing on the following two points. For the first point, we added RNAseq-based gene coexpression data for three species (human, mouse and fly), and largely increased th...

journal_title：Nucleic acids research

authors： Okamura Y,Aoki Y,Obayashi T,Tadaka S,Ito S,Narise T,Kinoshita K

更新日期：2015-01-01 00:00:00

abstract：:Our web server, PIZSA (http://cospi.iiserpune.ac.in/pizsa), assesses the likelihood of protein-protein interactions by assigning a Z Score computed from interface residue contacts. Our score takes into account the optimal number of atoms that mediate the interaction between pairs of residues and whether these contacts...

journal_title：Nucleic acids research

authors： Roy AA,Dhawanjewar AS,Sharma P,Singh G,Madhusudhan MS

更新日期：2019-07-02 00:00:00

abstract：:Granulocyte macrophage-colony stimulating factor (GM-CSF) is produced by T cells, but not B cells, in response to immune signals. GM-CSF gene activation in response to T-cell stimulation requires remodelling of chromatin associated with the gene promoter, and these changes do not occur in B cells. While the CpG methyl...

journal_title：Nucleic acids research

authors： Brettingham-Moore KH,Sprod OR,Chen X,Oakford P,Shannon MF,Holloway AF

更新日期：2008-05-01 00:00:00

abstract：:Three-dimensional protein structures provide invaluable information for understanding and regulating biological functions of proteins. The GalaxyWEB server predicts protein structure from sequence by template-based modeling and refines loop or terminus regions by ab initio modeling. This web server is based on the met...

journal_title：Nucleic acids research

authors： Ko J,Park H,Heo L,Seok C

更新日期：2012-07-01 00:00:00

abstract：:Increasing numbers of proteins, nucleic acids and other molecular entities have been explored as therapeutic targets, hundreds of which are targets of approved and clinical trial drugs. Knowledge of these targets and corresponding drugs, particularly those in clinical uses and trials, is highly useful for facilitating...

journal_title：Nucleic acids research

authors： Zhu F,Han B,Kumar P,Liu X,Ma X,Wei X,Huang L,Guo Y,Han L,Zheng C,Chen Y

更新日期：2010-01-01 00:00:00

abstract：:A single base change in 16S rRNA (C726 to G) has previously been shown to have a dramatic effect on protein synthesis in E. coli (1). This paper more specifically details the effects of the mutation on mRNA binding and translation-termination. The in vitro technique of toeprinting (2) was used to demonstrate that 30S ...

journal_title：Nucleic acids research

authors： Prescott CD,Göringer HU

更新日期：1990-09-25 00:00:00

abstract：:Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5'-untranslated region of mRNA transcripts, thereby modifying the stability of the target transcr...

journal_title：Nucleic acids research

authors： Eggenhofer F,Tafer H,Stadler PF,Hofacker IL

更新日期：2011-07-01 00:00:00

abstract：:RNA levels in a cell are regulated by the relative rates of RNA synthesis and decay. We recently developed a new approach for measuring both RNA synthesis and decay in a single experimental setting by biosynthetic labeling of newly transcribed RNA. Here, we show that this provides measurements of RNA half-lives from m...

journal_title：Nucleic acids research

authors： Friedel CC,Dölken L,Ruzsics Z,Koszinowski UH,Zimmer R

更新日期：2009-09-01 00:00:00

abstract：:A linear DNA plasmid, designated pLLE1, has been isolated from a mitochondrial fraction of a strain of Lentinus edodes. pLLE1(11.0 kbp) was sensitive to the 3'----5'-acting exonuclease III and resistant to the 5'----3'-acting lambda exonuclease. It showed no homology with mitochondrial and nuclear genomic DNAs of plas...

journal_title：Nucleic acids research

authors： Katayose Y,Kajiwara S,Shishido K

更新日期：1990-03-25 00:00:00

abstract：:The relationship between the similarity of expression patterns for a pair of genes and interaction of the proteins they encode is demonstrated both for the simple genome of the bacteriophage T7 and the considerably more complex genome of the yeast Saccharomyces cerevisiae. Statistical analysis of large-scale gene expr...

journal_title：Nucleic acids research

authors： Grigoriev A

更新日期：2001-09-01 00:00:00

abstract：:The regulation of the Sso II restriction-modification system from Shigella sonnei was studied in vivo and in vitro . In lacZ fusion experiments, Sso II methyltransferase (M. Sso II) was found to repress its own synthesis but stimulate expression of the cognate restriction endonuclease (ENase). The N-terminal 72 amino ...

journal_title：Nucleic acids research

authors： Karyagina A,Shilov I,Tashlitskii V,Khodoun M,Vasil'ev S,Lau PC,Nikolskaya I

更新日期：1997-06-01 00:00:00

abstract：:Previous studies have established a critical role of both TFIIB and RNA polymerase II (RNAPII) in start site selection in the yeast Saccharomyces cerevisiae. However, it remains unclear how the TFIIB-RNAPII interaction impacts on this process since such an interaction can potentially influence both preinitiation compl...

journal_title：Nucleic acids research

authors： Zhang DY,Carson DJ,Ma J

更新日期：2002-07-15 00:00:00

abstract：:The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problema...

journal_title：Nucleic acids research

authors： Tweedie S,Braschi B,Gray K,Jones TEM,Seal RL,Yates B,Bruford EA

更新日期：2021-01-08 00:00:00

abstract：:The NusA protein is a universally conserved bacterial transcription elongation factor that binds RNA polymerase (RNAP). When functioning independently, NusA enhances intrinsic termination. Paradoxically, NusA stimulates the function of the N and Q antiterminator proteins of bacteriophage λ. The mechanistic basis for N...

journal_title：Nucleic acids research

authors： Wells CD,Deighan P,Brigham M,Hochschild A

更新日期：2016-06-20 00:00:00