WormBase: a modern Model Organism Information Resource.

abstract：:Maintenance of stem-cell identity requires proper regulation of enhancer activity. Both transcription factors OCT4/SOX2/NANOG and histone methyltransferase complexes MLL/SET1 were shown to regulate enhancer activity, but how they are regulated in embryonic stem cells (ESCs) remains further studies. Here, we report a t...

journal_title：Nucleic acids research

authors： Niu C,Wang S,Guo J,Wei X,Jia M,Chen Z,Gong W,Qin Y,Wang X,Zhi X,Lu M,Chen S,Gu M,Zhang J,Han JJ,Lan F,Meng D

更新日期：2021-01-27 00:00:00

abstract：:We describe a rapid fluorescence indicator displacement assay (R-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal c...

journal_title：Nucleic acids research

authors： Del Villar-Guerra R,Gray RD,Trent JO,Chaires JB

更新日期：2018-04-20 00:00:00

abstract：:In silico screening based on the structures of the ligands or of the receptors has become an essential tool to facilitate the drug discovery process but compound collections are needed to carry out such in silico experiments. It has been recognized that absorption, distribution, metabolism, excretion and toxicity (ADM...

journal_title：Nucleic acids research

authors： Miteva MA,Violas S,Montes M,Gomez D,Tuffery P,Villoutreix BO

更新日期：2006-07-01 00:00:00

abstract：:DNA predominantly contains Watson-Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif at any time. In HG, the purine is rotated ∼180° relative to the WC motif. The transitions between WC and HG may play a role in recognition and replication, but are diffi...

journal_title：Nucleic acids research

authors： Vreede J,Pérez de Alba Ortíz A,Bolhuis PG,Swenson DWH

更新日期：2019-12-02 00:00:00

abstract：:The human mitochondrial translation apparatus, which synthesizes the core subunits of the oxidative phosphorylation system, is of central interest as mutations in several genes encoding for mitoribosomal proteins or translation factors cause severe human diseases. Little is known, how this complex machinery assembles ...

journal_title：Nucleic acids research

authors： Lavdovskaia E,Kolander E,Steube E,Mai MM,Urlaub H,Richter-Dennerlein R

更新日期：2018-09-19 00:00:00

abstract：:Detection of cancer-associated somatic mutations has broad applications for oncology and precision medicine. However, this becomes challenging when cancer-derived DNA is in low abundance, such as in impure tissue specimens or in circulating cell-free DNA. Next-generation sequencing (NGS) is particularly prone to techn...

journal_title：Nucleic acids research

authors： Wang TT,Abelson S,Zou J,Li T,Zhao Z,Dick JE,Shlush LI,Pugh TJ,Bratman SV

更新日期：2019-09-05 00:00:00

abstract：:Ribosomal DNA (rDNA) from Xenopus laevis contains several heterogeneities in all three transcribed spacers, as revealed by analysis of cloned and uncloned amplified rDNA from oocytes and cloned chromosomal rDNA from erythrocytes. Heterogeneities include single base changes and length variants of one to several nucleot...

journal_title：Nucleic acids research

authors： Stewart MA,Hall LM,Maden BE

更新日期：1983-02-11 00:00:00

abstract：:Three databases that provide data on transcriptional regulation are described. TRANSFAC is a database on transcription factors and their DNA binding sites. TRRD (Transcription Regulatory Region Database) collects information about complete regulatory regions, their regulation properties and architecture. COMPEL compri...

journal_title：Nucleic acids research

authors： Wingender E,Kel AE,Kel OV,Karas H,Heinemeyer T,Dietze P,Knüppel R,Romaschenko AG,Kolchanov NA

更新日期：1997-01-01 00:00:00

abstract：:A long-range physical map of the centromeric region of human chromosome 7 has been constructed in order to define the region containing sequences with potential involvement in centromere function. The map is centered around alpha satellite DNA, a family of tandemly repeated DNA forming arrays of hundreds to thousands ...

journal_title：Nucleic acids research

authors： Wevrick R,Willard HF

更新日期：1991-05-11 00:00:00

abstract：:A minizyme is a hammerhead ribozyme with short oligonucleotide linkers instead of stem-loop II. In a previous study we demonstrated that a minizyme with high activity forms a dimeric structure with a common stem II. Because of their dimeric structure, minizymes are potentially capable of cleaving a substrate at two di...

journal_title：Nucleic acids research

authors： Kuwabara T,Amontov SV,Warashina M,Ohkawa J,Taira K

更新日期：1996-06-15 00:00:00

abstract：:ADAR enzymes, adenosine deaminases that act on RNA, form a family of RNA editing enzymes that convert adenosine to inosine within RNA that is completely or largely double-stranded. Site-selective A-->I editing has been detected at specific sites within a few structured pre-mRNAs of metazoans. We have analyzed the edit...

journal_title：Nucleic acids research

authors： Källman AM,Sahlin M,Ohman M

更新日期：2003-08-15 00:00:00

abstract：:We have previously reported that transcription from a distal promoter (promoter B) of the estrogen receptor alpha (ERalpha) gene is responsible for the increased expression of ERalpha in human breast carcinomas. This paper first characterized the promoter B region in terms of transient transfection experiments with lu...

journal_title：Nucleic acids research

authors： Tanimoto K,Eguchi H,Yoshida T,Hajiro-Nakanishi K,Hayashi S

更新日期：1999-02-01 00:00:00

abstract：:Microarrays are an effective tool for monitoring genome-wide gene expression levels. In current microarray analyses, the majority of genes on arrays are frequently eliminated for further analysis because the changes in their expression levels (ratios) are considered to be not significant. This strategy risks failure t...

journal_title：Nucleic acids research

authors： Yano K,Imai K,Shimizu A,Hanashita T

更新日期：2006-03-14 00:00:00

abstract：:The ability of histone chaperone Anti-silencing factor 1 (Asf1) to direct acetylation of lysine 56 of histone H3 (H3K56ac) represents an important regulatory step in genome replication and DNA repair. In Saccharomyces cerevisiae, Asf1 interacts functionally with a second chaperone, Vps75, and the lysine acetyltransfer...

journal_title：Nucleic acids research

authors： Cote JM,Kuo YM,Henry RA,Scherman H,Krzizike DD,Andrews AJ

更新日期：2019-08-22 00:00:00

abstract：:We have determined the nucleotide sequence at the 3' end of the vesicular stomatitis virus (VSV) polymerase or L gene and compared it to that obtained from a defective interfering particle (DI) RNA generated by this virus. The latter (DI 0.50) contains a large internal deletion within this gene. The deletion begins ex...

journal_title：Nucleic acids research

authors： De BK,Perrault J

更新日期：1982-11-11 00:00:00

abstract：:The structure-specific Mus81-Eme1/Mms4 endonuclease contributes importantly to DNA repair and genome integrity maintenance. Here, using budding yeast, we have studied its function and regulation during the cellular response to DNA damage and show that this endonuclease is necessary for successful chromosome replicatio...

journal_title：Nucleic acids research

authors： Saugar I,Vázquez MV,Gallo-Fernández M,Ortiz-Bazán MÁ,Segurado M,Calzada A,Tercero JA

更新日期：2013-10-01 00:00:00

abstract：:5' strand resection at DNA double strand breaks (DSBs) is critical for homologous recombination (HR) and genomic stability. Here we develop a novel method to quantitatively measure single-stranded DNA intermediates in human cells and find that the 5' strand at endonuclease-generated break sites is resected up to 3.5 k...

journal_title：Nucleic acids research

authors： Zhou Y,Caron P,Legube G,Paull TT

更新日期：2014-02-01 00:00:00

abstract：:Several restriction endonuclease fragments isolated from highly repetitive satellite DNA of the chromatin eliminating nematode Ascaris lumbricoides var. suum have been cloned. Each type of restriction fragment corresponds to a different variant of the same related ancestral sequence. These variants differ by small del...

journal_title：Nucleic acids research

authors： Müller F,Walker P,Aeby P,Neuhaus H,Felder H,Back E,Tobler H

更新日期：1982-12-11 00:00:00

abstract：:The effect of several rifamycin derivatives on poly(A) synthesis in vitro was tested using purified rat liver mitochondrial poly(A) polymerase assayed with an exogenous primer. When used at a concentration of 300 mug/ml, derivatives AF/013, PR/19, AF/AETP, M/88 and AF/ABDP completely inhibited activity corresponding t...

journal_title：Nucleic acids research

authors： Jacob ST,Rose KM

更新日期：1974-11-01 00:00:00

abstract：:Mitochondrial DNA (mtDNA) is entirely dependent on nuclear genes for its transcription and replication. One of these genes is TOP1MT, which encodes the mitochondrial DNA topoisomerase IB, involved in mtDNA relaxation. To elucidate TOP1MT regulation, we performed genome-wide profiling across the 60-cell line panel (the...

journal_title：Nucleic acids research

authors： Zoppoli G,Douarre C,Dalla Rosa I,Liu H,Reinhold W,Pommier Y

更新日期：2011-08-01 00:00:00

abstract：:Bisulfite genomic sequencing is the most widely used technique to analyze the 5-methylation of cytosines, the prevalent covalent DNA modification in mammals. The process is based on the selective transformation of unmethylated cytosines to uridines. Then, the investigated genomic regions are PCR amplified, subcloned a...

journal_title：Nucleic acids research

authors： Tusnády GE,Simon I,Váradi A,Arányi T

更新日期：2005-01-13 00:00:00

abstract：:Backscattering interferometry (BSI) has been used to successfully monitor molecular interactions without labeling and with high sensitivity. These properties suggest that this approach might be useful for detecting biomarkers of infection. In this report, we identify interactions and characteristics of nucleic acid pr...

journal_title：Nucleic acids research

authors： Adams NM,Olmsted IR,Haselton FR,Bornhop DJ,Wright DW

更新日期：2013-05-01 00:00:00

abstract：:In Euplotes crassus millions of telomeres are synthesized during the sexual phase of the life cycle. Since these newly synthesized telomeres are longer than normal macronuclear telomeres, they must be trimmed to the mature size. We have examined the timing and mechanism of this trimming step. We have shown that a sudd...

journal_title：Nucleic acids research

authors： Vermeesch JR,Williams D,Price CM

更新日期：1993-11-25 00:00:00

abstract：:Expression of the rpoBC genes encoding the beta and beta' RNA polymerase subunits of Escherichia coli is autogenously regulated. Although previous studies have demonstrated a post-transcriptional feedback mechanism, complex transcriptional controls of rpoBC expression may also contribute. We show that an attenuator (r...

journal_title：Nucleic acids research

authors： Steward KL,Linn T

更新日期：1992-09-25 00:00:00

abstract：:Multivalent cations are known to condense DNA into higher ordered structures, including toroids and rods. Here we report that solid supports treated with monovalent or multivalent cationic silanes, followed by removal of soluble molecules, can condense DNA. The mechanism of this surface-directed condensation depends o...

journal_title：Nucleic acids research

authors： Fang Y,Hoh JH

更新日期：1998-01-15 00:00:00

abstract：:In highly oncogenic adenovirus (Ad) 12-transformed cells, major histocompatibility complex (MHC) class I gene expression is down-regulated by the products of the viral E1A oncogene at the level of initiation of transcription. However, class I gene expression is unaltered or elevated in non-oncogenic Ad2- or Ad5-transf...

journal_title：Nucleic acids research

authors： Proffitt JL,Sharma E,Blair GE

更新日期：1994-11-11 00:00:00

abstract：:TFIIH is a multisubunit factor essential for transcription initiation and promoter escape of RNA polymerase II and for the opening of damaged DNA double strands in nucleotide excision repair (NER). In this study, we have analyzed at which step of the transcription cycle TFIIH is essential for transcription by RNA poly...

journal_title：Nucleic acids research

authors： Assfalg R,Lebedev A,Gonzalez OG,Schelling A,Koch S,Iben S

更新日期：2012-01-01 00:00:00

abstract：:1731, a Drosophila retrotransposon was first described as having a transcription activity which was negatively regulated by 20-hydroxyecdysone (20-OH), the steroid molting hormone of insects. Using constructions expressing the bacterial chloramphenicol-acetyltransferase (CAT) gene under the control of the entire or de...

journal_title：Nucleic acids research

authors： Ziarczyk P,Best-Belpomme M

更新日期：1991-10-25 00:00:00

abstract：:The abundance and complexity of total poly(A)+RNA of human normal unstimulated lymphocytes, PHA-stimulated and leukemic lymphocytes were examined using the cDNA-poly(A)+ RNA hybridization technique. It was found that in both PHA-stimulated and leukemic lymphocytes the complexity of total poly(A)+RNA is strongly reduce...

journal_title：Nucleic acids research

authors： Torelli G,Ferrari S,Donelli A,Cadossi R,Ferrari S,Bosi P,Torelli U

更新日期：1981-12-21 00:00:00

abstract：:The ever growing number of completely sequenced prokaryotic genomes facilitates cross-species comparisons by genomic annotation algorithms. This paper introduces a new probabilistic framework for comparative genomic analysis and demonstrates its utility in the context of improving the accuracy of prokaryotic gene star...

journal_title：Nucleic acids research

authors： Walker M,Pavlovic V,Kasif S

更新日期：2002-07-15 00:00:00