Abstract：
:High mobility group protein B1 (HMGB1) binds to the internucleosomal linker DNA in chromatin and abuts the nucleosome. Bending and untwisting of the linker DNA results in transmission of strain to the nucleosome core, disrupting histone/DNA contacts. An interaction between H3 and HMGB1 has been reported. Here we confirm and characterize the interaction of HMGB1 with H3, which lies close to the DNA entry/exit points around the nucleosome dyad, and may be responsible for positioning of HMGB1 on the linker DNA. We show that the interaction is between the N-terminal unstructured tail of H3 and the C-terminal unstructured acidic tail of HMGB1, which are presumably displaced from DNA and the HMG boxes, respectively, in the HMGB1-nucleosome complex. We have characterized the interaction by nuclear magnetic resonance spectroscopy and show that it is extensive for both peptides, and appears not to result in the acquisition of significant secondary structure by either partner.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Watson M,Stott K,Fischl H,Cato L,Thomas JOdoi
10.1093/nar/gkt950subject
Has Abstractpub_date
2014-01-01 00:00:00pages
848-59issue
2eissn
0305-1048issn
1362-4962pii
gkt950journal_volume
42pub_type
杂志文章abstract：:At the DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usua...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.8.1395
更新日期：1996-04-15 00:00:00
abstract：:We have examined the ability of a cationic planar chromophore, ethidium bromide, to intercalate into a short, defined triple helix. Using UV absorption, fluorescence spectroscopy and a gel retardation assay we demonstrate that ethidium bromide is able to bind to a triple helix with a lower affinity than to the corresp...
journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：1991-04-11 00:00:00
abstract：:The Central glycolytic genes Repressor (CggR) from Bacillus subtilis belongs to the SorC family of transcription factors that control major carbohydrate metabolic pathways. Recent studies have shown that CggR binds as a tetramer to its tandem operator DNA sequences and that the inducer metabolite, fructose 1,6-bisphos...
journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2010-09-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1305
更新日期：2012-05-01 00:00:00
abstract：:A 12 bp long GCN4-binding, self-complementary duplex DNA d(CATGACGTCATG)(2) has been investigated by NMR spectroscopy to study the structure and dynamics of the molecule in aqueous solution. The NMR structure of the DNA obtained using simulated annealing and iterative relaxation matrix calculations compares quite clos...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.2.499
更新日期：2001-01-15 00:00:00
abstract：:Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding the DNA double strand. Interestingly, the number of MCM hexamers greatly exceeds the number of firing origins suggesting additional roles of MCMs. Here we show a hitherto unanticipated function of MCM2 in cilia formatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky945
更新日期：2019-01-10 00:00:00
abstract：:Ribosomes transit between two conformational states, non-rotated and rotated, through the elongation cycle. Here, we present evidence that an internal loop in the essential yeast ribosomal protein rpL10 is a central controller of this process. Mutations in this loop promote opposing effects on the natural equilibrium ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1107
更新日期：2014-02-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt977
更新日期：2014-01-01 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
pub_type： 杂志文章
doi：10.1093/nar/gks968
更新日期：2013-01-07 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1195
更新日期：2021-01-11 00:00:00
abstract：:Aside from classical loops among G-quadruplexes, the unique leaped V-shape scaffold spans over three G-tetrads, without any intervening residues. This scaffold enables a sharp reversal of two adjacent strand directions and simultaneously participates in forming the G-tetrad core. These features make this scaffold itse...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1167
更新日期：2019-02-20 00:00:00
abstract：:GenBank is a comprehensive database that contains publicly available DNA sequences for more than 140 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin program an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh045
更新日期：2004-01-01 00:00:00
abstract：:The BRENDA enzyme database (https://www.brenda-enzymes.org), established in 1987, has evolved into the main collection of functional enzyme and metabolism data. In 2018, BRENDA was selected as an ELIXIR Core Data Resource. BRENDA provides reliable data, continuous curation and updates of classified enzymes, and the in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1025
更新日期：2021-01-08 00:00:00
abstract：:We have isolated an eight kilobase fragment of Bacillus subtilis DNA by specific integration and excision of a plasmid containing a sequence adjacent to ribosomal operon rrn O. The genetic locus of the cloned fragment was verified by linkage of the integrated vector to nearby genetic markers using both transduction an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.15.6307
更新日期：1984-08-10 00:00:00
abstract：:Pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that ha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1065
更新日期：2012-01-01 00:00:00
abstract：:The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. The Entrez system provides search and re...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkaa892
更新日期：2021-01-08 00:00:00
abstract：:Protein classification by machine learning algorithms is now widely used in structural and functional annotation of proteins. The Protein Classification Benchmark collection (http://hydra.icgeb.trieste.it/benchmark) was created in order to provide standard datasets on which the performance of machine learning methods ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl812
更新日期：2007-01-01 00:00:00
abstract：:Ribosomal recruitment of cellular mRNAs depends on binding of eIF4F to the mRNA's 5'-terminal 'cap'. The minimal 'cap0' consists of N7-methylguanosine linked to the first nucleotide via a 5'-5' triphosphate (ppp) bridge. Cap0 is further modified by 2'-O-methylation of the next two riboses, yielding 'cap1' (m7GpppNmN) ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1321
更新日期：2014-03-01 00:00:00
abstract：:An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx598
更新日期：2017-09-19 00:00:00
abstract：:The disappearance of defined restriction fragments of the beta 1-globin, an albumin and the A1 vitellogenin gene was quantitated after DNase I digestion and expressed by a sensitivity factor defined by a mathematical model. Analysis of naked DNA showed that the gene fragments have similar but not identical sensitivity...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.11.2455
更新日期：1981-06-11 00:00:00
abstract：:Many tools are available to analyse genomes but are often challenging to use in a cell type-specific context. We have developed a method similar to the isolation of nuclei tagged in a specific cell type (INTACT) technique [Deal,R.B. and Henikoff,S. (2010) A simple method for gene expression and chromatin profiling of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks671
更新日期：2012-10-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.1.22
更新日期：2001-01-01 00:00:00
abstract：:Alternative splicing is widespread in mammalian gene expression, and variant splice patterns are often specific to different stages of development, particular tissues or a disease state. There is a need to systematically collect data on alternatively spliced exons, introns and splice isoforms, and to annotate this dat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh030
更新日期：2004-01-01 00:00:00
abstract：:Signal transducer and activator of transcription 6 (STAT6) is a regulator of transcription for interleukin-4 (IL-4)-induced genes. The ability of STAT6 to activate transcription depends on functional interaction with other transcription factors and coactivators. We have characterized the mechanism of STAT6-mediated tr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl539
更新日期：2006-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.17.4689
更新日期：1991-09-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.23.4653
更新日期：1996-12-01 00:00:00
abstract：:Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1236
更新日期：2016-01-04 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv312
更新日期：2015-05-19 00:00:00
abstract：:Naturally occurring hammerhead ribozymes are produced by rolling circle replication followed by self-cleavage. This results in monomer-length catalytic RNAs which have self-complementary sequences that can occupy their trans -binding domains and potentially block their ability to cleave other RNA strands. Here we show...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.3.776
更新日期：2000-02-01 00:00:00
abstract：:A short histone-like fusion RNA, generated when the RNA 3' processing signal from a mouse histone H4 gene is inserted into a heterologous transcription unit, becomes correctly down-regulated in G1-arrested cells of a temperature-sensitive mouse mastocytoma cell cycle mutant (21-Tb; Stauber et al., EMBO J. 5, 3297-3303...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.20.9399
更新日期：1988-10-25 00:00:00
