Abstract:
:The chromatin structure of yeast ribosomal DNA was analyzed in vivo by crosslinking intact cells with psoralen. We found that in exponentially growing cultures the regions coding for the 35S rRNA precursor fall into two distinct classes. One class was highly accessible to psoralen and associated with nascent RNAs, characteristic for transcriptionally active rRNA genes devoid of nucleosomes, whereas the other class showed a crosslinking pattern indistinguishable from that of bulk chromatin and was interpreted to represent the inactive rRNA gene copies. By crosslinking the same strain growing in complex or minimal medium, we have shown that yeast cells can modulate the proportion of active (non-nucleosomal) and inactive (nucleosomal) rRNA gene copies in response to variations in environmental conditions which suggests that yeast can regulate rRNA synthesis by varying the number of active gene copies, in contrast to the vertebrate cells studied so far. Whereas intergenic spacers flanking inactive rRNA gene copies are packaged in a regular nucleosomal array, spacers flanking active genes show an unusual crosslinking pattern suggesting a complex interaction of regulatory factors and histones with DNA.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Dammann R,Lucchini R,Koller T,Sogo JMdoi
10.1093/nar/21.10.2331subject
Has Abstractpub_date
1993-05-25 00:00:00pages
2331-8issue
10eissn
0305-1048issn
1362-4962journal_volume
21pub_type
杂志文章abstract::We have used temperature gradient gel electrophoresis (TGGE) to measure the progress of local denaturation in closed circular topoisomer DNA as a function of temperature and superhelicity (sigma). We describe the versatility of this method as a tool for detecting various conformational modifications of plasmid DNAs. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.11.e51
更新日期:2000-06-01 00:00:00
abstract::The stability of chromosome ends, the telomeres, is dependent on the ribonucleoprotein telomerase. In vitro, telomerase requires at least one RNA molecule and a reverse transcriptase-like protein. However, for telomere homeostasis in vivo, additional proteins are required. Telomerase RNAs of different species vary in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt514
更新日期:2013-09-01 00:00:00
abstract::Tcf/Lef family transcription factors are the downstream effectors of the Wingless/Wnt signal transduction pathway. Upon Wingless/Wnt signalling, beta-catenin translocates to the nucleus, interacts with Tcf (1-3) and thus activates transcription of target genes (4,5). Tcf factors also interact with members of the Grouc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.7.1410
更新日期:2001-04-01 00:00:00
abstract::The small subunit (SSU) processome is a large ribonucleoprotein that is required for maturation of the 18S rRNA of the ribosome. Recently, a missense mutation in the C-terminus of an SSU processome protein, Utp4/Cirhin, was reported to cause North American Indian childhood cirrhosis (NAIC). In this study, we use Sacch...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq185
更新日期:2010-08-01 00:00:00
abstract::More and more evidences demonstrate that the long non-coding RNAs (lncRNAs) play many key roles in diverse biological processes. There is a critical need to annotate the functions of increasing available lncRNAs. In this article, we try to apply a global network-based strategy to tackle this issue for the first time. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks967
更新日期:2013-01-01 00:00:00
abstract::In the process of establishing more and more complete annotations of eukaryotic genomes, a constantly growing number of alternative splicing (AS) events has been reported over the last decade. Consequently, the increasing transcript coverage also revealed the real complexity of some variations in the exon-intron struc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm311
更新日期:2007-07-01 00:00:00
abstract::With the high number of sequences and structures streaming in from genomic projects, there is a need for more powerful and sophisticated annotation tools. Most problematic of the annotation efforts is predicting gene and protein function. Over the past few years there has been considerable progress in automated protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl045
更新日期:2006-07-01 00:00:00
abstract::The deoxyoligonucleotide 5' AATCGGGCATGGATT (15-mer) was synthesized containing 12 phosphoramidate linkages derived from 2 primary and 2 secondary amines. The oligonucleotides were purified by reverse phase HPLC and characterized by PAGE. The thermal stability of the duplexes derived from these compounds, when hybridi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.11.4831
更新日期:1988-06-10 00:00:00
abstract::DNA polymerases alpha and delta are essential enzymes believed to play critical roles in initiation and replication of chromosome DNA. In this study, we show that the genes for Schizosaccharomyces pombe (S.pombe) DNA polymerase alpha and delta (pol alpha+ and pol delta+) are essential for cell viability. Disruption of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.16.3821
更新日期:1993-08-11 00:00:00
abstract::Post-transcriptional regulation and the formation of mRNA 3' ends are crucial for gene expression in eukaryotes. Interspecies conservation of many sequences within 3'UTRs reveals selective constraint due to similar function. To study the pattern of conservation within 3'UTRs, we compiled and aligned 50 sets of complet...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg751
更新日期:2003-09-15 00:00:00
abstract::Within a single infected individual, a virus population can have a high genomic variability. In the case of HIV, several mutations can be present even in a small genomic window of 20-30 nucleotides. For diagnostics purposes, it is often needed to resequence genomic subsets where crucial mutations are known to occur. I...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt682
更新日期:2013-10-01 00:00:00
abstract::The structural gene and the regulatory DNA sequence of the yeast Hansenula polymorpha methanol oxidase have been isolated. According to the nucleotide sequence data obtained, the structural gene encodes a 664 amino acids long protein, contains no intervening sequences, and the 5'- and 3'-non-coding region contains sev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.9.3063
更新日期:1985-05-10 00:00:00
abstract::To investigate the mechanisms by which oligonucleotides hybridize to target molecules, the binding of two oligodeoxynucleotide probes to RNA targets was measured over a broad range of temperatures. Mutations were then scanned across each DNA/RNA hybrid to map, at single base resolution, sequences important for hybridi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn134
更新日期:2008-05-01 00:00:00
abstract::We present the sequences of five additional human U2 pseudogenes which are very similar to the U2.13 pseudogene reported previously [Van Arsdell et al. (1981) Cell 26, 11-17]. All six U2 pseudogenes preserve the 5' end of the mature U2 snRNA sequence, and all six are flanked by nearly perfect direct repeats that diffe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.3.1463
更新日期:1984-02-10 00:00:00
abstract::The sequence of 110 nucleotides adjacent to the 3'-end of Neurospora crassa 25S-rRNA has been derived by chemical sequencing methods. Sequences present between 40 and 85 nucleotides of the 3'-end were found to complement sequences at the 3'- and 5'-ends of 5.8S-rRNA. Interaction was shown to occur between 5.8S-rRNA an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.5.1111
更新日期:1981-03-11 00:00:00
abstract::This paper examines theoretically the effects that restraints on the tertiary structure of a superhelical DNA domain exert on the energetics of linking and the onset of conformational transitions. The most important tertiary constraint arises from the nucleosomal winding of genomic DNA in vivo. Conformational transiti...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/15.23.9985
更新日期:1987-12-10 00:00:00
abstract::The chemical synthesis of backbone deuterium labelled [r(CGCGAAU*U*CGCG)]2 (U* = [5'-2H]U) is described. An efficient purification procedure was developed using a polymeric reverse phase (PRP) HPLC column at 60 degrees C. This procedure provided pure RNA dodecamer in the multi-milligram quantities (39% overall yield) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.19.5131
更新日期:1992-10-11 00:00:00
abstract::Previous work has demonstrated that the yeast SPT3 gene is required for transcription from delta sequences, the long terminal repeats that flank yeast Ty elements. In spt3 null mutants, transcription fails to initiate in delta sequences and instead initiates farther downstream. Null mutations in SPT3 cause other mutan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.17.6885
更新日期:1986-09-11 00:00:00
abstract::The nucleotide sequence of the Anacystis nidulans 23S rRNA gene, including the 5'- and 3'-flanking regions has been determined. The gene is 2876 nucleotides long and shows higher primary sequence homology to the 23S rRNAs of plastids (84.5%) than to that of E. coli (79%). The predicted rRNA transcript also shares many...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.7.3373
更新日期:1984-04-11 00:00:00
abstract::Analysis of 41 histone homologous clones from an isogenic gene library of Drosophila melanogaster showed that non-histone fragments interrupt the histone repetitive clusters at several sites. Long (L) and short (S) forms of the repeating units are distinguished by the insertion of 240 bp into the spacer between H1 and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.1.225
更新日期:1989-01-11 00:00:00
abstract::The Saccharomyces cerevisiae viruses are non-infectious double-stranded (ds) RNA viruses present in most laboratory strains of yeast. Their genome consists of one or more dsRNAs separately encapsidated in particles composed mainly of one polypeptide, which has a Mr of 88 kdaltons in the best-studied viral subtype. A l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.5.1575
更新日期:1985-03-11 00:00:00
abstract::DNA polymerase lambda (pol lambda) is a member of the X family DNA polymerases and is endowed with multiple enzymatic activities. In this work we investigated the in vitro miscoding properties of full-length, human pol lambda either in the absence or in the presence of the human auxiliary proteins proliferating cell n...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl032
更新日期:2006-03-06 00:00:00
abstract::Thermal elution poly(U)-Sepharose chromatography was utilized to fractionate yeast mRNA based on poly(A) size. Analysis of the in vitro translation products of the fractionated RNAs in a wheat-embryo cell-free protein synthesis system shows a heterogeneous but equal distribution of these abundant translatable mRNAs in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.17.3841
更新日期:1980-09-11 00:00:00
abstract::By screening a rabbit reticulocyte library, an alternative 15-LOX transcript of 3.6 kb (15-LOX mRNA2) was detected containing a 1019 nt longer 3'-untranslated region (UTR2) than the main 2.6 kb mRNA (15-LOX mRNA1). In anaemic animals, northern blotting showed that 15-LOX mRNA2 was predominantly expressed in non-erythr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.8.1828
更新日期:1999-04-15 00:00:00
abstract::Previous studies have shown that (i) several RNAs induced by heat shock of Drosophila melanogaster cells are homologous to tandemly repeated alpha beta units found in cloned segments of D. melanogaster DNA, and (ii) the alpha beta sequences are present both at a major heat shock locus, 87Cl, and the chromocenter of po...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.20.5297
更新日期:1981-10-24 00:00:00
abstract::RNA-protein complexes are essential in mediating important fundamental cellular processes, such as transport and localization. In particular, ncRNA-protein interactions play an important role in post-transcriptional gene regulation like mRNA localization, mRNA stabilization, poly-adenylation, splicing and translation....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv020
更新日期:2015-02-18 00:00:00
abstract::Cadmium (Cd2+) is a known carcinogen that inactivates the DNA mismatch repair (MMR) pathway. In this study, we have tested the effect of Cd2+ exposure on the enzymatic activity of the mismatch binding complex MSH2-MSH6. Our results indicate that Cd2+ is highly inhibitory to the ATP binding and hydrolysis activities of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki291
更新日期:2005-03-03 00:00:00
abstract::The frequencies of occurrence of four bases in the first, second and third codon positions and in the total coding sequences have been calculated by the codon usage table published in 1990 by Ikemura et al. The distribution of frequencies are further analysed in detail by a graphic technique presented recently by us. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.22.6313
更新日期:1991-11-25 00:00:00
abstract::Mitochondrial DNA from human tissue culture cells contains heterogeneous sequences located within a previously identified, evolutionarily conserved region termed CSB-2. CSB-2 is located near the origin of heavy-strand mitochondrial DNA synthesis and the major transcriptional promoters for each strand of human mitochon...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.22.8093
更新日期:1985-11-25 00:00:00
abstract::Double-stranded soybean leghemoglobin DNA was synthesized from leghemoglobin mRNA isolated from soybean nodules. The dsDNA was inserted into the Bam H1 site of plasmid pBR322 using the poly-dAT-joiner method. A cloned DNA fragment of one recombinant plasmid was isolated and characterized by restriction endonuclease di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.9.3061
更新日期:1979-07-11 00:00:00