Pluralistic and stochastic gene regulation: examples, models and consistent theory.

abstract：:The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs Recursive Sampler, which has been developed specifically for locating multiple transcription factor binding sites for multip...

journal_title：Nucleic acids research

authors： Thompson W,Rouchka EC,Lawrence CE

更新日期：2003-07-01 00:00:00

abstract：:The DNA photosensitisers m-iodo Hoechst and m-iodo, p-methoxy Hoechst have been co-crystallised with the oligonucleotide d(CGCGAATTCGCG)(2)and their crystal structures determined. The crystals were then subjected to slow dehydration, which reduced their solvent contents from 40 (normal) to 30 (partially dehydrated) an...

journal_title：Nucleic acids research

authors： Squire CJ,Baker LJ,Clark GR,Martin RF,White J

更新日期：2000-03-01 00:00:00

abstract：:NF-IL6beta regulates gene expression and plays function roles in many tissues. The EGF-regulated cyclooxygenase-2 (cox-2) expression is mediated through p38(MAPK) signaling pathway and positively correlates with NF-IL6beta expression in A431 cells. NF-IL6beta coordinated with c-Jun on cox-2 transcriptional activation ...

journal_title：Nucleic acids research

authors： Wang JM,Ko CY,Chen LC,Wang WL,Chang WC

更新日期：2006-01-05 00:00:00

abstract：:A novel program suite was implemented for the functional interpretation of high-throughput gene expression data based on the identification of Gene Ontology (GO) nodes. The focus of the analysis lies on the interpretation of microarray data from prokaryotes. The three well established statistical methods of the thresh...

journal_title：Nucleic acids research

authors： Scheer M,Klawonn F,Münch R,Grote A,Hiller K,Choi C,Koch I,Schobert M,Härtig E,Klages U,Jahn D

更新日期：2006-07-01 00:00:00

abstract：:We have determined the sequence of 80 nucleotides adjacent to 3' poly(A) of both (middle and bottom component) cowpea mosaic virus RNAs, using dideoxynucleotide termination of reverse transcription. Sequence conservation is indicated, there being about 80% homology between the first 65 bases of each RNA. Although both...

journal_title：Nucleic acids research

authors： Davies JW,Stanley J,Van Kammen A

更新日期：1979-09-25 00:00:00

abstract：:RNA pseudoknots are functional structure elements with key roles in viral and cellular processes. Prediction of a pseudoknotted minimum free energy structure is an NP-complete problem. Practical algorithms for RNA structure prediction including restricted classes of pseudoknots suffer from high runtime and poor accura...

journal_title：Nucleic acids research

authors： Sperschneider J,Datta A

更新日期：2010-04-01 00:00:00

abstract：:Precursor tRNAAsp molecules, containing a 26-base 5' leader, were treated with diethylpyrocarbonate, 50% hydrazine or anhydrous hydrazine/3M NaCl and then subjected to processing by RNase P RNAs from Escherichia coli or Bacillus subtilis. Fully processed tRNAs and material not successfully cleaved by the catalytic RNA...

journal_title：Nucleic acids research

authors： Thurlow DL,Shilowski D,Marsh TL

更新日期：1991-02-25 00:00:00

abstract：:The cytosine base in DNA undergoes hydrolytic deamination at a considerable rate when UV radiation induces formation of a cyclobutane pyrimidine dimer (CPD) with an adjacent pyrimidine base. We have synthesized a phosphoramidite building block of a cis-syn cyclobutane thymine-uracil dimer (T[]U), which is the deaminat...

journal_title：Nucleic acids research

authors： Takasawa K,Masutani C,Hanaoka F,Iwai S

更新日期：2004-03-12 00:00:00

abstract：:IStrons are chimeric genetic elements composed of a group I intron associated with an insertion sequence (IS). The group I intron is a catalytic RNA providing the IStron with self-splicing ability, which renders IStron insertions harmless to the host genome. The IS element is a DNA transposon conferring mobility, and ...

journal_title：Nucleic acids research

authors： Tourasse NJ,Stabell FB,Kolstø AB

更新日期：2014-11-10 00:00:00

abstract：:5-methylcytosine (m5C) modifications of RNA are ubiquitous in nature and play important roles in many biological processes such as protein translational regulation, RNA processing and stress response. Aberrant expressions of RNA:m5C methyltransferases are closely associated with various human diseases including cancer...

journal_title：Nucleic acids research

authors： Liu RJ,Long T,Li J,Li H,Wang ED

更新日期：2017-06-20 00:00:00

abstract：:Significant differences are observed between the CD spectra of eu- and heterochromatin prepared by fractionating mechanically sheared rat liver chromatin on linear sucrose density gradients. Heterochromatin has a broad positive CD at 270--280 nm, a cross-over point at 256 nmn, and a negative shoulder at 248 nm. Euchro...

journal_title：Nucleic acids research

authors： Moyer GH,Kay E,Austin GE

更新日期：1979-04-01 00:00:00

abstract：:Mitochondrial DNA is a sensitive target of chemical carcinogens (Backer and Weinstein (1980) Science 209, 297-299), suggesting that mutations of the mitochondrial genome occur in tumor cells. We examined this point by comparing mitochondrial DNA sequences in four rat tumors with those of normal rat liver. Some novel m...

journal_title：Nucleic acids research

authors： Taira M,Yoshida E,Kobayashi M,Yaginuma K,Koike K

更新日期：1983-03-25 00:00:00

abstract：:Potential pathways that could account for observed rapid rates of transcription reinitiation were explored. A nuclear extract system was established in which reinitiation rates were observed to be kinetically facilitated and in which the rate was sensitive to TATA box mutation. Kinetic facilitation of functional compl...

journal_title：Nucleic acids research

authors： Yean D,Gralla JD

更新日期：1999-02-01 00:00:00

abstract：:Chemically modified siRNAs are expected to have resistance toward nuclease degradation and good thermal stability in duplex formation for in vivo applications. We have recently found that 2'-OMe-4'-thioRNA, a hybrid chemical modification based on 2'-OMeRNA and 4'-thioRNA, has high hybridization affinity for complement...

journal_title：Nucleic acids research

authors： Takahashi M,Nagai C,Hatakeyama H,Minakawa N,Harashima H,Matsuda A

更新日期：2012-07-01 00:00:00

abstract：:To understand how potential for G-quadruplex formation might influence regulation of gene expression, we examined the 2 kb spanning the transcription start sites (TSS) of the 18 217 human RefSeq genes, distinguishing contributions of template and nontemplate strands. Regions both upstream and downstream of the TSS are...

journal_title：Nucleic acids research

authors： Eddy J,Maizels N

更新日期：2008-03-01 00:00:00

abstract：:We have investigated the attachment of the DNA to the nuclear matrix during the division cycle of the plasmodial slime mold Physarum polycephalum. The DNA of plasmodia was pulse labelled at different times during the S phase and the label distribution was studied by graded DNase digestion of the matrix-DNA complexes p...

journal_title：Nucleic acids research

authors： Aelen JM,Opstelten RJ,Wanka F

更新日期：1983-02-25 00:00:00

abstract：:Sequential chromatin immunoprecipitation (SeqChIP) is a procedure in which formaldehyde-crosslinked, protein-DNA complexes from living cells are subjected to two sequential immunoprecipitations with antibodies of different specificity. SeqChIP has been used to address, in a qualitative manner, whether two proteins can...

journal_title：Nucleic acids research

authors： Geisberg JV,Struhl K

更新日期：2004-11-01 00:00:00

abstract：:The nucleotide sequence of the faeD gene of Escherichia coli and the amino acid sequence of its product is presented. The faeD product is an outer membrane protein required for transport of K88ab fimbrial subunits across the outer membrane. The protein is synthesized as a precursor containing a signal peptide, and the...

journal_title：Nucleic acids research

authors： Mooi FR,Claassen I,Bakker D,Kuipers H,de Graaf FK

更新日期：1986-03-25 00:00:00

abstract：:Termination of protein synthesis is promoted in ribosomes by proper stop codon discrimination by class 1 polypeptide release factors (RFs). A large set of prokaryotic RFs differing in stop codon specificity, RF1 for UAG and UAA, and RF2 for UGA and UAA, was analyzed by means of a recently developed computational metho...

journal_title：Nucleic acids research

authors： Oparina NJ,Kalinina OV,Gelfand MS,Kisselev LL

更新日期：2005-09-14 00:00:00

abstract：:Cell specific expression of the insulin gene is achieved through transcriptional mechanisms operating on 5' flanking DNA elements. In the enhancer of rat I insulin gene, two elements, the Nir and Far boxes, located at positions -104 and -233 respectively and containing the same octameric motif are essential for B cell...

journal_title：Nucleic acids research

authors： Reibel L,Besnard C,Lores P,Jami J,Gacon G

更新日期：1993-04-11 00:00:00

abstract：:More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of re...

journal_title：Nucleic acids research

authors： Braun CM,Hackert P,Schmid CE,Bohnsack MT,Bohnsack KE,Perez-Fernandez J

更新日期：2020-01-10 00:00:00

abstract：:We recently identified a region of preferential replication initiation, oriGNAI3, near the 3' end of the Chinese hamster GNAI3 gene. oriGNAI3 is co-amplified in mutants selected for AMPD2 amplification, a process generating chromosomal rearrangements. In this report we have taken advantage of cell lines with truncated...

journal_title：Nucleic acids research

authors： Toledo F,Lachagès AM,Mayau V,Debatisse M

更新日期：1999-04-01 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：:Oxoguanine DNA glycosylase (OGG1) initiates the repair of 8-oxoguanine (8-oxoG), a major oxidative DNA base modification that has been directly implicated in cancer and aging. OGG1 functions in the base excision repair pathway, for which a molecular hand-off mechanism has been proposed. To date, only one functional an...

journal_title：Nucleic acids research

authors： Hu J,Imam SZ,Hashiguchi K,de Souza-Pinto NC,Bohr VA

更新日期：2005-06-07 00:00:00

abstract：:Escherichia coli has long been regarded as a model organism in the study of codon usage bias (CUB). However, most studies in this organism regarding this topic have been computational or, when experimental, restricted to small datasets; particularly poor attention has been given to genes with low CUB. In this work, co...

journal_title：Nucleic acids research

authors： dos Reis M,Wernisch L,Savva R

更新日期：2003-12-01 00:00:00

abstract：:The availability of a draft human genome sequence and ability to monitor the transcription of thousands of genes with DNA microarrays has necessitated the need for new computational tools that can analyze cis-regulatory elements controlling genes that display similar expression patterns. We have developed a tool desig...

journal_title：Nucleic acids research

authors： Zhang H,Ramanathan Y,Soteropoulos P,Recce ML,Tolias PP

更新日期：2002-11-01 00:00:00

abstract：:Since its discovery in 1979, left-handed Z-DNA has evolved from an in vitro curiosity to a challenging DNA structure with crucial roles in gene expression, regulation and recombination. A fundamental question that has puzzled researchers for decades is how the transition from B-DNA, the prevalent right-handed form of ...

journal_title：Nucleic acids research

authors： Moradi M,Babin V,Roland C,Sagui C

更新日期：2013-01-07 00:00:00

abstract：:In vitro compartmentalization (IVC) was employed for the first time to select for novel bacteriophage lambda integrase variants displaying significantly enhanced recombination activity on a non-cognate target DNA sequence. These variants displayed up to 9-fold increased recombination activity over the parental enzyme,...

journal_title：Nucleic acids research

authors： Tay Y,Ho C,Droge P,Ghadessy FJ

更新日期：2010-03-01 00:00:00

abstract：:This report documents the error rate in a commercially distributed subset of the IMAGE Consortium mouse cDNA clone collection. After isolation of plasmid DNA from 1189 bacterial stock cultures, only 62. 2% were uncontaminated and contained cDNA inserts that had significant sequence identity to published data for the o...

journal_title：Nucleic acids research

authors： Halgren RG,Fielden MR,Fong CJ,Zacharewski TR

更新日期：2001-01-15 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