Distinct roles of Pcf11 zinc-binding domains in pre-mRNA 3'-end processing.

abstract：:RNA G-quadruplexes (G4s) are secondary structures proposed to function as regulators of post-transcriptional mRNA localisation and translation. G4s within some neuronal mRNAs are known to control distal localisation and local translation, contributing to distinct local proteomes that facilitate the synaptic remodellin...

journal_title：Nucleic acids research

authors： Maltby CJ,Schofield JPR,Houghton SD,O'Kelly I,Vargas-Caballero M,Deinhardt K,Coldwell MJ

更新日期：2020-09-25 00:00:00

abstract：:The multifunctional HCV core protein consists of a hydrophilic RNA interacting D1 domain and a hydrophobic D2 domain interacting with membranes and lipid droplets. The core D1 domain was found to possess nucleic acid annealing and strand transfer properties. To further understand these chaperone properties, we investi...

journal_title：Nucleic acids research

authors： Sharma Kk,Didier P,Darlix JL,de Rocquigny H,Bensikaddour H,Lavergne JP,Pénin F,Lessinger JM,Mély Y

更新日期：2010-06-01 00:00:00

abstract：:The RecQ family of helicases is highly conserved both structurally and functionally from bacteria to humans. Defects in human RecQ helicases are associated with genetic diseases that are characterized by cancer predisposition and/or premature aging. RecQ proteins exhibit 3'-5' helicase activity and play critical roles...

journal_title：Nucleic acids research

authors： Choi S,Lee SW,Kim H,Ahn B

更新日期：2019-10-10 00:00:00

abstract：:Three clones of non-repetitive sequences and six clones containing repetitive sequences were obtained from micronuclear DNA of Tetrahymena thermophila. All the non-repetitive and three repetitive sequences had the same organization in micro- and macronuclear DNAs as revealed by blot hybridization. On the other hand, t...

journal_title：Nucleic acids research

authors： Iwamura Y,Sakai M,Muramatsu M

更新日期：1982-07-24 00:00:00

abstract：:A phage-display library of random peptides is a combinatorial experimental technique that can be harnessed for studying antibody-antigen interactions. In this technique, a phage peptide library is scanned against an antibody molecule to obtain a set of peptides that are bound by the antibody with high affinity. This s...

journal_title：Nucleic acids research

authors： Mayrose I,Shlomi T,Rubinstein ND,Gershoni JM,Ruppin E,Sharan R,Pupko T

更新日期：2007-01-01 00:00:00

abstract：:Nucleic acids possess the unique property of being enzymatically amplifiable, and have therefore been a popular choice for the combinatorial selection of functional sequences, such as aptamers or ribozymes. However, amplification typically requires known sequence segments that serve as primer binding sites, which can ...

journal_title：Nucleic acids research

authors： Wiesmayr A,Fournier P,Jäschke A

更新日期：2012-05-01 00:00:00

abstract：:The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification ex...

journal_title：Nucleic acids research

authors： Riffle M,Malmström L,Davis TN

更新日期：2005-01-01 00:00:00

abstract：:It has been postulated that a myriad of long noncoding RNAs (lncRNAs) contribute to gene regulation. In fission yeast, glucose starvation triggers lncRNA transcription across promoter regions of stress-responsive genes including fbp1 (fructose-1,6-bisphosphatase1). At the fbp1 promoter, this transcription promotes chr...

journal_title：Nucleic acids research

authors： Takemata N,Oda A,Yamada T,Galipon J,Miyoshi T,Suzuki Y,Sugano S,Hoffman CS,Hirota K,Ohta K

更新日期：2016-06-20 00:00:00

abstract：:p53 as an effector of nucleolar stress is well defined, but p53 independent mechanisms are largely unknown. Like p53, the NF-κB transcription factor plays a critical role in maintaining cellular homeostasis under stress. Many stresses that stimulate NF-κB also disrupt nucleoli. However, the link between nucleolar func...

journal_title：Nucleic acids research

authors： Chen J,Lobb IT,Morin P,Novo SM,Simpson J,Kennerknecht K,von Kriegsheim A,Batchelor EE,Oakley F,Stark LA

更新日期：2018-07-06 00:00:00

abstract：:The extrusion kinetics of two cruciforms derived from unrelated DNA sequences differ markedly. Kinetic barriers exist for both reactions, necessitating elevated temperatures before extrusion proceeds at measureable speeds, but the dependence upon temperature and ionic strength is quite different for the two sequences....

journal_title：Nucleic acids research

authors： Lilley DM

更新日期：1985-03-11 00:00:00

abstract：:The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the...

journal_title：Nucleic acids research

authors： Federhen S

更新日期：2012-01-01 00:00:00

abstract：:G-quadruplex (G4) DNA structures are linked to key biological processes and human diseases. Small molecules that target specific G4 DNA structures and signal their presence would therefore be of great value as chemical research tools with potential to further advance towards diagnostic and therapeutic developments. Ho...

journal_title：Nucleic acids research

authors： Kumar R,Chand K,Bhowmik S,Das RN,Bhattacharjee S,Hedenström M,Chorell E

更新日期：2020-02-20 00:00:00

abstract：:EMAGE (http://genex.hgu.mrc.ac.uk/Emage/database) is a database of in situ gene expression patterns in the developing mouse embryo. Domains of expression from raw data images are spatially integrated into a set of standard 3D virtual mouse embryos at different stages of development, allowing data interrogation by spat...

journal_title：Nucleic acids research

authors： Venkataraman S,Stevenson P,Yang Y,Richardson L,Burton N,Perry TP,Smith P,Baldock RA,Davidson DR,Christiansen JH

更新日期：2008-01-01 00:00:00

abstract：:The Dnd (DNA degradation) phenotype, reflecting a novel DNA modification by sulfur in Streptomyces lividans 1326, was strongly aggravated when one (dndB) of the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear change...

journal_title：Nucleic acids research

authors： Liang J,Wang Z,He X,Li J,Zhou X,Deng Z

更新日期：2007-01-01 00:00:00

abstract：:The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription factors whose binding sites are tightly clustered and form cis-regulatory modules. In this paper, we present a web serve...

journal_title：Nucleic acids research

authors： Sharan R,Ben-Hur A,Loots GG,Ovcharenko I

更新日期：2004-07-01 00:00:00

abstract：:Structural information on interacting proteins is important for understanding life processes at the molecular level. Genome-wide docking database is an integrated resource for structural studies of protein-protein interactions on the genome scale, which combines the available experimental data with models obtained by ...

journal_title：Nucleic acids research

authors： Kundrotas PJ,Zhu Z,Vakser IA

更新日期：2010-01-01 00:00:00

abstract：:Boundary elements partition eukaryotic chromatin into active and repressive domains, and can also block regulatory interactions between domains. Boundary elements act via diverse mechanisms making accurate feature-based computational predictions difficult. Therefore, we developed an unbiased algorithm that predicts th...

journal_title：Nucleic acids research

authors： Wang J,Lunyak VV,Jordan IK

更新日期：2012-01-01 00:00:00

abstract：:A newly designed cyclic bis-naphthyridine carbamate dimer CMBL4: with a limited conformational flexibility was synthesized and characterized. Absorption spectra revealed that two naphthyridines in CMBL4: were stacked on each other in aqueous solutions. The most efficient binding of CMBL4: to DNA was observed for the s...

journal_title：Nucleic acids research

authors： Mukherjee S,Dohno C,Asano K,Nakatani K

更新日期：2016-09-06 00:00:00

abstract：:The Escherichia coli RuvC protein is an endonuclease that resolves Holliday junctions. In vitro, the protein shows efficient structure-specific binding of Holliday junctions, yet the rate of junction resolution is remarkably low. We have mapped the sites of cleavage on a synthetic junction through which a crossover ca...

journal_title：Nucleic acids research

authors： Shah R,Bennett RJ,West SC

更新日期：1994-07-11 00:00:00

abstract：:UHRF1 plays multiple roles in regulating DNMT1-mediated DNA methylation maintenance during DNA replication. The UHRF1 C-terminal RING finger functions as an ubiquitin E3 ligase to establish histone H3 ubiquitination at Lys18 and/or Lys23, which is subsequently recognized by DNMT1 to promote its localization onto repli...

journal_title：Nucleic acids research

authors： Li T,Wang L,Du Y,Xie S,Yang X,Lian F,Zhou Z,Qian C

更新日期：2018-04-06 00:00:00

abstract：:As more and more high-throughput data has been produced by next-generation sequencing, it is still a challenge to classify RNA transcripts into protein-coding or non-coding, especially for poorly annotated species. We upgraded our original coding potential calculator, CNCI (Coding-Non-Coding Index), to CNIT (Coding-No...

journal_title：Nucleic acids research

authors： Guo JC,Fang SS,Wu Y,Zhang JH,Chen Y,Liu J,Wu B,Wu JR,Li EM,Xu LY,Sun L,Zhao Y

更新日期：2019-07-02 00:00:00

abstract：:Nucleosomes, a basic structural unit of eukaryotic chromatin, play a significant role in regulating gene expression. We have developed a web tool based on DNA sequences known from empirical and theoretical studies to influence DNA bending and flexibility, and to exclude nucleosomes. NXSensor (available at http://www.s...

journal_title：Nucleic acids research

authors： Luykx P,Bajić IV,Khuri S

更新日期：2006-07-01 00:00:00

abstract：:As protein-protein interactions are crucial in most biological processes, it is valuable to understand how and where protein pairs interact. We developed a web server HOMCOS (Homology Modeling of Complex Structure, http://biunit.naist.jp/homcos) to predict interacting protein pairs and interacting sites by homology mo...

journal_title：Nucleic acids research

authors： Fukuhara N,Kawabata T

更新日期：2008-07-01 00:00:00

abstract：:The alcohol dehydrogenase (Adh) gene of D. melanogaster is transcribed from two different promoters during fly development: the distal (adult) and the proximal (embryonic-larval). Certain aspects of Adh gene regulation are represented in Drosophila continuous cell lines. We have used Drosophila tissue culture cells in...

journal_title：Nucleic acids research

authors： Benyajati C,Ayer S,McKeon J,Ewel A,Huang J

更新日期：1987-10-12 00:00:00

abstract：:Pluripotency, the ability of embryonic stem cells to differentiate into specialized cell types, is determined by ESC-specific gene regulators such as transcription factors and chromatin modification factors. It is not well understood how ESCs are poised for differentiation, however, and methods are needed for prognosi...

journal_title：Nucleic acids research

authors： Ha M,Hong S

更新日期：2017-10-13 00:00:00

abstract：:The three dimensional crystal structure of T5 5'-3' exonuclease was compared with that of two other members of the 5'-3' exonuclease family: T4 ribonuclease H and the N-terminal domain of Thermus aquaticus DNA polymerase I. Though these structures were largely similar, some regions of these enzymes show evidence of si...

journal_title：Nucleic acids research

authors： Artymiuk PJ,Ceska TA,Suck D,Sayers JR

更新日期：1997-11-01 00:00:00

abstract：:Both Streptomyces lividans and Streptomyces avermitilis encode similar systems of post-replicative DNA modification which act site-specifically on closely opposed guanines on either strand. The modifications can be detected since they react in vitro with an oxidative derivative of Tris, resulting in strand cleavage. P...

journal_title：Nucleic acids research

authors： Boybek A,Ray TD,Evans MC,Dyson PJ

更新日期：1998-07-15 00:00:00

abstract：:The transcriptional silencing of one of the female X-chromosomes is a finely regulated process that requires accumulation in cis of the long non-coding RNA X-inactive-specific transcript (Xist) followed by a series of epigenetic modifications. Little is known about the molecular machinery regulating initiation and mai...

journal_title：Nucleic acids research

authors： Agostini F,Cirillo D,Bolognesi B,Tartaglia GG

更新日期：2013-01-07 00:00:00

abstract：:The binding kinetics of NF-kappaB p50 to the Ig-kappaB site and to a DNA duplex with no specific binding site were determined under varying conditions of potassium chloride concentration using a surface plasmonresonance biosensor. Association and dissociation rate constants were measured enabling calculation of the di...

journal_title：Nucleic acids research

authors： Hart DJ,Speight RE,Cooper MA,Sutherland JD,Blackburn JM

更新日期：1999-02-15 00:00:00

abstract：:DNA molecules with covalently sealed (hairpin) ends are probable intermediates in V(D)J recombination. According to current models hairpin ends are opened to produce short single-stranded extensions that are thought to be precursors of a particular type of extra nucleotides, termed P nucleotides, which are frequently ...

journal_title：Nucleic acids research

authors： Kabotyanski EB,Zhu C,Kallick DA,Roth DB

更新日期：1995-10-11 00:00:00