Abstract：
:Granulocyte macrophage-colony stimulating factor (GM-CSF) is produced by T cells, but not B cells, in response to immune signals. GM-CSF gene activation in response to T-cell stimulation requires remodelling of chromatin associated with the gene promoter, and these changes do not occur in B cells. While the CpG methylation status of the murine GM-CSF promoter shows no correlation with the ability of the gene to respond to activation, we find that the basal chromatin environment of the gene promoter influences its ability to respond to immune signals. In unstimulated T cells but not B cells, the GM-CSF promoter is selectively marked by enrichment of histone acetylation, and association of the chromatin-remodelling protein BRG1. BRG1 is removed from the promoter upon activation concomitant with histone depletion and BRG1 is required for efficient chromatin remodelling and transcription. Increasing histone acetylation at the promoter in T cells is paralleled by increased BRG1 recruitment, resulting in more rapid chromatin remodelling, and an associated increase in GM-CSF mRNA levels. Furthermore, increasing histone acetylation in B cells removes the block in chromatin remodelling and transcriptional activation of the GM-CSF gene. These data are consistent with a model in which histone hyperacetylation and BRG1 enrichment at the GM-CSF promoter, generate a chromatin environment competent to respond to immune signals resulting in gene activation.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Brettingham-Moore KH,Sprod OR,Chen X,Oakford P,Shannon MF,Holloway AFdoi
10.1093/nar/gkn117subject
Has Abstractpub_date
2008-05-01 00:00:00pages
2639-53issue
8eissn
0305-1048issn
1362-4962pii
gkn117journal_volume
36pub_type
杂志文章abstract：:ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky420
更新日期：2018-07-02 00:00:00
abstract：:The cause of 50S ribosomal subunit collapse reportedly triggered by hybridization of a 14-base cDNA probe to the alpha-sarcin region of 23S rRNA was investigated by physical measurement of probe-subunit complexes in varying buffer conditions. The results reported here show that this probe was unable to hybridize to it...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.22.10817
更新日期：1988-11-25 00:00:00
abstract：:PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa971
更新日期：2021-01-08 00:00:00
abstract：:We describe a dedicated RNA motif search program and web server to identify RNA riboswitches. The Riboswitch finder analyses a given sequence using the web interface, checks specific sequence elements and secondary structure, calculates and displays the energy folding of the RNA structure and runs a number of tests in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh352
更新日期：2004-07-01 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
pub_type： 杂志文章
doi：10.1093/nar/gks1003
更新日期：2013-01-07 00:00:00
abstract：:Inspection of the structure of the C-terminal domain of ribosomal protein L7/L12 (1) reveals a helix-turn-helix motif similar to the one found in many DNA-binding regulatory proteins (2-5). The 19 alpha-carbon atoms of the L7/L12 alpha-helices superimpose on the DNA binding helices of CAP and cro with root-mean-square...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.10.3757
更新日期：1989-05-25 00:00:00
abstract：:The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. The information is obtained by manual extraction from primary literature, text...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1068
更新日期：2015-01-01 00:00:00
abstract：:Unfolding of the nucleosomes in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3 and permits the selective recovery of the unfolded nucleosomes by mercury-affinity chromatography. This new technique has been used to compare the nucleosomal proteins and their postsynthetic modifications i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.11.4375
更新日期：1987-06-11 00:00:00
abstract：:This work presents the Apo-Holo DataBase (AH-DB, http://ahdb.ee.ncku.edu.tw/ and http://ahdb.csbb.ntu.edu.tw/), which provides corresponding pairs of protein structures before and after binding. Conformational transitions are commonly observed in various protein interactions that are involved in important biological f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr940
更新日期：2012-01-01 00:00:00
abstract：:Population-scale sequencing is increasingly uncovering large numbers of rare single-nucleotide variants (SNVs) in coding regions of the genome. The rarity of these variants makes it challenging to evaluate their deleteriousness with conventional phenotype-genotype associations. Protein structures provide a way of addr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw927
更新日期：2016-12-01 00:00:00
abstract：:In order to study the effects of DNA structure on cellular processes such as transcription, we have made a series of plasmids that locate several different kinds of DNA structure (stiff, flexible or curved) near the sites of cleavage by commonly-used restriction enzymes. One can use these plasmids to place any DNA reg...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.22.9447
更新日期：1989-11-25 00:00:00
abstract：:Most human genes generate multiple transcript isoforms. The differential expression of these isoforms can help specify cell types. Diverse transcript isoforms arise from the use of alternative transcription start sites, polyadenylation sites and splice sites; however, the relative contribution of these processes to is...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1165
更新日期：2018-01-25 00:00:00
abstract：:BZ junctions, which connect B-DNA to Z-DNA, are necessary for local transformation of B-DNA to Z-DNA in the genome. However, the limited information on the junction-forming sequences and junction structures has led to a lack of understanding of the structural diversity and sequence preferences of BZ junctions. We dete...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky784
更新日期：2018-11-02 00:00:00
abstract：:Complete genomes of three closely related Gram-positive bacteria Streptococcus pyogenes, Streptococcus pneumoniae and Lactococcus lactis are analyzed for abundances of short DNA sequence motifs (frequent words). The character and extent of frequent words are strikingly different among these genomes. The frequent words...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf534
更新日期：2002-10-01 00:00:00
abstract：:The mRNA encoding repressor cI of phage lambda is the only known E. coli message which starts directly with the initiation AUG codon. The ability of in vitro synthesized cI mRNA fragments (150 or 400 nts) to form ternary initiation complexes has been studied using the toeprint method. In the presence of tRNA(Met)f, th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.3.563
更新日期：1992-02-11 00:00:00
abstract：:Gene duplications are a major source of evolutionary innovations. Understanding the functional divergence of duplicates and their role in genetic robustness is an important challenge in biology. Previously, analyses of genetic robustness were primarily focused on duplicates essentiality and epistasis in several labora...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1200
更新日期：2014-02-01 00:00:00
abstract：:A method is presented for the purification of mRNAs and the identification of structural gene sequences in recombinant DNA molecules. RNA is hybridized to double-stranded linear DNA such that R-loops are formed between most DNAs and their complementary RNA sequences. These R-loops are purified from unhybridized RNAs b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.7.2483
更新日期：1979-06-11 00:00:00
abstract：:SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv351
更新日期：2015-07-01 00:00:00
abstract：:We report here the construction of engineered endonuclease database (EENdb) (http://eendb.zfgenetics.org/), a searchable database and knowledge base for customizable engineered endonucleases (EENs), including zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). EENs are artificial...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1144
更新日期：2013-01-01 00:00:00
abstract：:Phage display technology involves the display of proteins or peptides, as coat protein fusions, on the surface of a phage or phagemid particles. Using standard technology, helper phage are essential for the replication and assembly of phagemid particles, during library production and biopanning. We have eliminated the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl772
更新日期：2006-01-01 00:00:00
abstract：:Toxic metals are part of our environment, and undue exposure to them leads to a variety of pathologies. In response, most organisms adapt their metabolism and have evolved systems to limit this toxicity and to acquire tolerance. Ribosome biosynthesis being central for protein synthesis, we analyzed in yeast the effect...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt335
更新日期：2013-07-01 00:00:00
abstract：:Escherichia coli DNA polymerase III holoenzyme is composed of 10 different subunits linked by noncovalent interactions. The polymerase activity resides in the alpha-subunit. The epsilon-subunit, which contains the proofreading exonuclease site within its N-terminal 185 residues, binds to alpha via a segment of 57 addi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn489
更新日期：2008-09-01 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
pub_type： 杂志文章
doi：10.1093/nar/gkt1309
更新日期：2014-02-01 00:00:00
abstract：:According to recent models, as yet poorly studied architectural proteins appear to be required for local regulation of enhancer-promoter interactions, as well as for global chromosome organization. Transcription factors ZIPIC, Pita and Zw5 belong to the class of chromatin insulator proteins and preferentially bind to ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw371
更新日期：2016-09-06 00:00:00
abstract：:Reverse gyrase is a peculiar DNA topoisomerase, specific of hyperthermophilic Archaea and Bacteria, which has the unique ability of introducing positive supercoiling into DNA molecules. Although the function of the enzyme has not been established directly, it has been suggested to be involved in DNA protection and rep...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl115
更新日期：2006-04-14 00:00:00
abstract：:Gene rewiring is a common evolutionary phenomenon in nature that may lead to extinction for living organisms. Recent studies on synthetic biology demonstrate that cells can survive genetic rewiring. This survival (adaptation) is often linked to the stochastic expression of rewired genes with random transcriptional cha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1366
更新日期：2015-01-01 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：:Natural oligopeptides may regulate nearly all vital processes. To date, the chemical structures of nearly 6000 oligopeptides have been identified from >1000 organisms representing all the biological kingdoms. We have compiled the known physical, chemical and biological properties of these oligopeptides--whether synthe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj008
更新日期：2006-01-01 00:00:00
abstract：:Numerous RNA-binding proteins have modular structures, comprising one or several copies of a selective RNA-binding domain generally coupled to an auxiliary domain that binds RNA non-specifically. We have built and compared homology-based models of the cold-shock domain (CSD) of the Xenopus protein, FRGY2, and of the t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.11.2223
更新日期：2001-06-01 00:00:00
abstract：:This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is di...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.9.2951
更新日期：1982-05-11 00:00:00
