Abstract：
:We report here the discovery of HMBP, a protein in nuclei of human T-helper lymphocytes and other human cell types, which binds with enhanced affinity to a promoter element in the HIV-1 long terminal repeat when that element is methylated at CpGs, the target site of the human DNA methyltransferase. This promoter element contains three (degenerate) binding sites for Sp1, a general activator of transcription. Gel shift assays and footprinting experiments indicate that HMBP binding overlaps two of these methylated Sp1 sites. Although HMBP binds these methylated Sp1 sites, it does not bind consensus Sp1 sites. Competition studies, differences in binding site specificities, binding conditions, and, in some cases, chromatographic separation further distinguish HMBP from Sp1 and from each of four previously identified methylated-DNA binding proteins. HMBP binds hemimethylated DNA in a strand dependent manner. These binding characteristics suggest that HMBP may recognize newly replicated DNA and thereby play a role in differentiation. If HMBP is able to compete with Sp1 for binding at methylated, non-consensus Sp1 sites in vivo and repress transcription, it may play a role in AIDS latency.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Joel P,Shao W,Pratt Kdoi
10.1093/nar/21.24.5786subject
Has Abstractpub_date
1993-12-11 00:00:00pages
5786-93issue
24eissn
0305-1048issn
1362-4962journal_volume
21pub_type
杂志文章abstract：:Fragments of SP6 DNA generated by cleavage with Hpa II or Taq I were cloned into the Cla I site of pBR322 and the recombinant plasmids were screened for the presence of SP6 promoter activity by transcription in vitro with purified SP6 RNA polymerase. Three plasmids having promoter activity and small inserts of SP6 DNA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.8.3521
更新日期：1986-04-25 00:00:00
abstract：:In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding. DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt617
更新日期：2013-09-01 00:00:00
abstract：:The temperature-sensitive Neurospora nuclear mutant cyt18-1 is deficient in splicing many Group I mitochondrial introns when grown at its non-permissive temperature; however, splicing of intron 1 in the coI gene of the Adiopodoume (formerly called North Africa) strain is unaffected (R.A. Collins and A.M. Lambowitz, J....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.22.9087
更新日期：1989-11-25 00:00:00
abstract：:Synthesis and antisense activity of oligonucleotides modified with 2'-O-[2-[(N,N-dimethylamino)oxy] ethyl] (2'-O-DMAOE) are described. The 2'-O-DMAOE-modified oligonucleotides showed superior metabolic stability in mice. The phosphorothioate oligonucleotide 'gapmers', with 2'-O-DMAOE- modified nucleoside residues at t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh220
更新日期：2004-02-03 00:00:00
abstract：:We have isolated and characterized a S. pombe promoter using a functional heterologous gene product assay. Random S. pombe genomic fragments were cloned upstream from the promoterless 'lacZ gene and tested in vivo for their efficiency to promote expression of the beta-galactosidase protein in the fission yeast. An eff...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.17.8603
更新日期：1988-09-12 00:00:00
abstract：:In eukaryotes, the tRNA-mimicking polypeptide-chain release factor, eRF1, decodes stop codons on the ribosome in a complex with eRF3; this complex exhibits striking structural similarity to the tRNA-eEF1A-GTP complex. Although amino acid residues or motifs of eRF1 that are critical for stop codon discrimination have b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv376
更新日期：2015-05-19 00:00:00
abstract：:Purified 15 S globin mRNA-protein (mRNP) complexes obtained by EDTA dissociation of duck reticulocytes polyribosomes were digested with the calcium dependant Staphylococcus aureus nuclease (EC 3. 1. 4. 7.). 25% of the globin mRNA sequences were resistant to extensive nuclease digestion as determined by TCA precipitati...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.8.2787
更新日期：1979-06-25 00:00:00
abstract：:The HhaI methyltransferase recognizes the sequence GCGC and transfers a methyl group to C5 of the first cytosine residue. All m5C-methyltransferases contain a highly conserved sequence motif called the P-C motif. The cysteine residue of this motif is involved in catalysis by forming a covalent bond with the 6-position...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.10.2459
更新日期：1993-05-25 00:00:00
abstract：:Global run-on sequencing (GRO-seq) is a recent addition to the series of high-throughput sequencing methods that enables new insights into transcriptional dynamics within a cell. However, GRO-sequencing presents new algorithmic challenges, as existing analysis platforms for ChIP-seq and RNA-seq do not address the uniq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1237
更新日期：2014-02-01 00:00:00
abstract：:DNA polymerase delta (Pol δ) is responsible for the elongation and maturation of Okazaki fragments in eukaryotic cells. Proliferating cell nuclear antigen (PCNA) recruits Pol δ to the DNA and serves as a processivity factor. Here, we show that PCNA also stimulates the catalytic rate of Saccharomyces cerevisiae Pol δ b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1321
更新日期：2019-02-28 00:00:00
abstract：:Stacking self-association equilibria in aqueous solutions of m3uridine, m34,2',3',5'uridine, 2'-deoxyuridine, m13,4,4cytosine, m14,4,4,5cytosine, s2cytidine and s4thymidine were studied at various temperatures by vapour-pressure osmometry. Equilibrium constants Kst's were computed on the assumption of the isodesmic mo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.5.1295
更新日期：1976-05-01 00:00:00
abstract：:We have previously shown that in vivo estradiol-dependent dephosphorylation of MDBP-2-H1 (a member of the histone H1 family) correlates with the loss of in vitro preferential binding to methylated DNA. To study the effects of the phosphorylation/dephosphorylation of MDBP-2-H1 on the expression of the avian vitellogeni...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.10.1816
更新日期：1996-05-15 00:00:00
abstract：:Compounds that are covalent analogues of nucleic acid base pairs of normal, long, and short C1' to C1' dimensions [B. Devadas and N.J. Leonard (1990) J. Am. Chem. Soc., 112, 3125-3135.] have been added to the oligodeoxyribonucleotide d(A)6 with bacteriophage T4 RNA ligase as a prelude to placing them at defined loci w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.3.585
更新日期：1991-02-11 00:00:00
abstract：:We have developed a new COFACTOR webserver for automated structure-based protein function annotation. Starting from a structural model, given by either experimental determination or computational modeling, COFACTOR first identifies template proteins of similar folds and functional sites by threading the target structu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks372
更新日期：2012-07-01 00:00:00
abstract：:alpha2-Macroglobulin covalently linked to poly(L)-lysine can be used as a vehicle for receptor-mediated gene transfer. This modified alpha2-macroglobulin maintains its ability to bind to the alpha2-macroglobulin receptor, and was shown to introduce a luciferase reporter gene plasmid into HepG2 human hepatoma cells in ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.19.3873
更新日期：1996-10-01 00:00:00
abstract：:We examined the ability of the 5' flanking region sequences of a human U1 RNA gene to direct synthesis of functional mRNA. When fused to chloramphenicol acetyltransferase (CAT) coding region sequences, the upstream sequences of the U1 gene were able to stimulate the synthesis of functional CAT mRNA in 293 cells but no...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.13.5827
更新日期：1988-07-11 00:00:00
abstract：:Next-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression tha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz181
更新日期：2019-05-21 00:00:00
abstract：:Guanine-rich DNA sequences tend to form four-stranded G-quadruplex structures. Characteristic glycosidic conformational patterns along the G-strands, such as the 5'-syn-anti-syn-anti pattern observed with the Oxytricha nova telomeric G-quadruplexes, have been well documented. However, an explanation for these featured...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr031
更新日期：2011-05-01 00:00:00
abstract：:Thermophilic viruses represent a novel source of genetic material and enzymes with great potential for use in biotechnology. We have isolated a number of thermophilic viruses from geothermal areas in Iceland, and by combining high throughput genome sequencing and state of the art bioinformatics we have identified a nu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg914
更新日期：2003-12-15 00:00:00
abstract：:Molecules of single-stranded ribosomal RNA and double-stranded replicative form of phage f2 RNA (dsRNA) adopt a compact form in solutions, containing sufficiently high concentrations of salt (NaCl) and polymer (PEG). However, only in the cases of native dsRNA molecules the compact particles are characterized by a regu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.6.1533
更新日期：1976-06-01 00:00:00
abstract：:The precursor to the Euglena light harvesting chlorophyll a/b binding protein of photosystem II (LHCPII) is a polyprotein containing multiple copies of LHCPII covalently joined by a decapeptide linker. cDNA and genomic clones encoding the 5' and 3' end of a 6.6 kb LHCPII mRNA were sequenced. A 3.1 kb genomic region en...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.25.5737
更新日期：1994-12-25 00:00:00
abstract：:Using a combination of mathematical modelling, statistical simulation and large-scale data analysis we study the properties of linear regulatory chains (LRCs) within gene regulatory networks (GRNs). Our modelling indicates that downstream genes embedded within LRCs are highly insulated from the variation in expression...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx485
更新日期：2017-07-07 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
pub_type： 杂志文章
doi：10.1093/nar/gkz474
更新日期：2019-09-05 00:00:00
abstract：:The distribution and amount of 5-methylcytosine (5-MeCyt) in DNA was measured for early embryos of mouse strain CF1 (2 to 4 cell stage to blastocyst) and mouse teratocarcinoma cells. In each case, the pattern of methylation was examined by use of the restriction enzymes Hha I and HPA II HPA II, which cut DNA at the si...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/7.8.2369
更新日期：1979-12-20 00:00:00
abstract：:The effect of amino groups attached at positions 2 and 8 of the hypoxanthine moiety in the structure, reactivity and stability of DNA duplexes and triplexes is studied by means of quantum mechanical calculations, as well as extended molecular dynamics (MD) and thermodynamic integration (MD/TI) simulations. Theoretical...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.12.2522
更新日期：2001-06-15 00:00:00
abstract：:Recent research hints at an underappreciated complexity in pre-miRNA processing and regulation. Global profiling of pre-miRNA and its potential to increase understanding of the pre-miRNA landscape is impeded by overlap with highly expressed classes of other non coding (nc) RNA. Here, we present a data set excluding th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr903
更新日期：2012-02-01 00:00:00
abstract：:The replication control circuit of the FII plasmids R1, R100 and R6-5 involves a small untranslated RNA molecule of about 93 nucleotides. This RNA, designated CopA RNA in plasmid R1, acts in vivo as a post-transcriptional inhibitor of the expression of the RepA protein whose synthesis is required for each round of pla...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.6.2523
更新日期：1986-03-25 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
pub_type： 杂志文章
doi：10.1093/nar/25.21.4224
更新日期：1997-11-01 00:00:00
abstract：:Unoxidized crystalline silicon, characterized by high purity, high homogeneity, sturdiness and an atomically flat surface, offers many advantages for the construction of electronic miniaturized biosensor arrays upon attachment of biomolecules (DNA, proteins or small organic compounds). This allows to study the inciden...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnj034
更新日期：2006-02-28 00:00:00
abstract：:Previous work in predicting protein localization to the chloroplast organelle in plants led to the development of an artificial neural network-based approach capable of remarkable accuracy in its prediction (ChloroP). A common criticism against such neural network models is that it is difficult to interpret the criter...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.16.e82
更新日期：2001-08-15 00:00:00
