Abstract:
:In silico prediction of transcription factor binding sites (TFBSs) is central to the task of gene regulatory network elucidation. Genomic DNA sequence information provides a basis for these predictions, due to the sequence specificity of TF-binding events. However, DNA sequence alone is an impoverished source of information for the task of TFBS prediction in eukaryotes, as additional factors, such as chromatin structure regulate binding events. We show that incorporating high-throughput chromatin modification estimates can greatly improve the accuracy of in silico prediction of in vivo binding for a wide range of TFs in human and mouse. This improvement is superior to the improvement gained by equivalent use of either transcription start site proximity or phylogenetic conservation information. Importantly, predictions made with the use of chromatin structure information are tissue specific. This result supports the biological hypothesis that chromatin modulates TF binding to produce tissue-specific binding profiles in higher eukaryotes, and suggests that the use of chromatin modification information can lead to accurate tissue-specific transcriptional regulatory network elucidation.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Whitington T,Perkins AC,Bailey TLdoi
10.1093/nar/gkn866subject
Has Abstractpub_date
2009-01-01 00:00:00pages
14-25issue
1eissn
0305-1048issn
1362-4962pii
gkn866journal_volume
37pub_type
杂志文章abstract::Three clones of non-repetitive sequences and six clones containing repetitive sequences were obtained from micronuclear DNA of Tetrahymena thermophila. All the non-repetitive and three repetitive sequences had the same organization in micro- and macronuclear DNAs as revealed by blot hybridization. On the other hand, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.14.4279
更新日期:1982-07-24 00:00:00
abstract::Alu elements have repeatedly been found involved in gene rearrangements in humans. Although these elements have been suggested to stimulate gene rearrangements, sparse information is available for the possible mechanism(s) of these events. Here we present a compilation of Alu elements that have been involved in recomb...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.2.256
更新日期:1995-01-25 00:00:00
abstract::We previously reported the isolation of PRP28, a gene in Saccharomyces cerevisiae whose activity is required for the first step of nuclear mRNA splicing in vivo. Sequence analysis revealed that PRP28 is included in the 'DEAD-box' gene family, members of which are thought to function as ATP-dependent RNA helicases. Gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.15.3187
更新日期:1994-08-11 00:00:00
abstract::We developed an integrated method to identify aptamers with only 10 fixed nucleotides through ligation and removal of primer binding sites within the systematic evolution of ligands by exponential enrichment (SELEX) process. This Tailored-SELEX approach was validated by identifying a Spiegelmer ('mirror-image aptamer'...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng130
更新日期:2003-11-01 00:00:00
abstract::Synthesis of 8-phosphorus substituted isosteres of purine [pyrimidino (4,5-d)-1,3,2-diazaphosphole], 1-deazapurine [pyridino (2,3-d)-1,3,2-diazaphosphole] and 3-deazapurine [pyridino (4,5-d)-1,3,2-diazaphosphole] has been achieved by the reaction of equimolar amounts of triphenylphosphite and 4,5-diaminopyrimidine, 2,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.1.251
更新日期:1979-09-11 00:00:00
abstract::The thermodynamics of 13 hybridization reactions between 10 base DNA sequences of design 5'-ATGCXYATGC-3' with X, Y = A, C, G, T and their complementary PNA and DNA sequences were determined from isothermal titration calorimetry (ITC) measurements at ambient temperature. For the PNA/DNA hybridization reactions, the bi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.24.4792
更新日期:1999-12-15 00:00:00
abstract::A small family of DNA sequences is rearranged during the development of the somatic nucleus in Tetrahymena. The family is defined by 266 bp of highly conserved sequence which restriction mapping, hybridization and sequence analysis have shown is shared by a cloned micronuclear fragment and three sequences which consti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.20.8007
更新日期:1986-10-24 00:00:00
abstract::The nucleotide excision repair pathway removes ultraviolet (UV) photoproducts from the human genome in the form of short oligonucleotides ∼ 30 nt in length. Because there are limitations to many of the currently available methods for investigating UV photoproduct repair in vivo, we developed a convenient non-radioisot...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1179
更新日期:2014-02-01 00:00:00
abstract::Controllable gene delivery via vector-based systems remains a formidable challenge in mammalian synthetic biology and a desirable asset in gene therapy applications. Here, we introduce a methodology to control the copies and residence time of a gene product delivered in host human cells but also selectively disrupt fr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1326
更新日期:2015-01-01 00:00:00
abstract::The database of molecular motions, MolMovDB (http://molmovdb.org), has been in existence for the past decade. It classifies macromolecular motions and provides tools to interpolate between two conformations (the Morph Server) and predict possible motions in a single structure. In 2005, we expanded the services offered...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj046
更新日期:2006-01-01 00:00:00
abstract::Primer extension studies have shown that the Y-family DNA polymerase IV (Dpo4) from Sulfolobus solfataricus P2 can preferentially insert C opposite N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) [F. Boudsocq, S. Iwai, F. Hanaoka and R. Woodgate (2001) Nucleic Acids Res., 29, 4607-4616]. Our goal is to elucidate...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj479
更新日期:2006-02-01 00:00:00
abstract::In this paper, we describe a new method for selecting RNA aptamers that cooperatively bind to two specific sites within a target RNA. We designed a selection system in which two RNAs, a target RNA and a RNA pool, were assembled by employing a pre-organized GAAA tetraloop-11-nt receptor interaction. This allows us to s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1012
更新日期:2009-02-01 00:00:00
abstract::Alternative splicing and polyadenylation were observed pervasively in eukaryotic messenger RNAs. These alternative isoforms could either be consequences of physiological regulation or stochastic noise of RNA processing. To quantify the extent of stochastic noise in splicing and polyadenylation, we analyzed the alterna...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1271
更新日期:2013-02-01 00:00:00
abstract::Transcription initiation complexes formed by bacterial RNA polymerases (RNAPs) exhibit dramatic species-specific differences in stability, leading to different strategies of transcription regulation. The molecular basis for this diversity is unclear. Promoter complexes formed by RNAP from Thermus aquaticus (Taq) are c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks973
更新日期:2012-12-01 00:00:00
abstract::Adaptive Laboratory Evolution (ALE) has emerged as an experimental approach to discover causal mutations that confer desired phenotypic functions. ALE not only represents a controllable experimental approach to systematically discover genotype-phenotype relationships, but also allows for the revelation of the series o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky983
更新日期:2019-01-08 00:00:00
abstract::In vivo and in vitro RNA splicing experiments have demonstrated that the intron splicing machineries are not interchangeable in all organisms. These differences have prevented the efficient in vivo expression of monocot genes containing introns in dicot plants and the in vitro excision of some plant introns in HeLa ce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.14.7159
更新日期:1988-07-25 00:00:00
abstract::CRISPR/Cas9 is a powerful genome editing system but uncontrolled Cas9 nuclease expression triggers off-target effects and even in vivo immune responses. Inspired by synthetic biology, here we built a synthetic switch that self-regulates Cas9 expression not only in the transcription step by guide RNA-aided self-cleavag...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1165
更新日期:2019-02-20 00:00:00
abstract::The fine structure of the melting curve for the linear colE1 DNA has been obtained. To find the ColE1 DNA regions corresponding to peaks in the melting curve's fine structure, we fixed the melted DNA regions with glyoxal /12/. Electron-microscopic denaturation maps were obtained for nine temperature points within the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.18.4165
更新日期:1980-09-25 00:00:00
abstract::The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3' tail that is critical for their retrotransposition. The predicted secondary structure of the conserved 3' tail of UnaL2 RNA contains a stem region with a putative internal loop. Deletion of the putativ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl664
更新日期:2006-01-01 00:00:00
abstract::RNA polymerase III recognizes and pauses at its terminator, an oligo(dT) tract in non-template DNA, terminates 3' oligo(rU) synthesis within this sequence, and releases the RNA. The pol III subunit Rpc11p (C11) mediates RNA 3'-5' cleavage in the catalytic center of pol III during pausing. The amino and carboxyl region...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr182
更新日期:2011-08-01 00:00:00
abstract::To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1273
更新日期:2014-03-01 00:00:00
abstract::An enzyme activity introducing an alkali-labile site at 2-hydroxyadenine (2-OH-A) in double-stranded oligonucleotides was detected in nuclear extracts of Jurkat cells. This activity co-eluted with activities toward adenine paired with guanine and 8-oxo-7,8-dihydroguanine (8-oxoG) as a single peak corresponding to a 55...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.6.1355
更新日期:2000-03-15 00:00:00
abstract::Variable (diversity) joining [V(D)J] recombination of immune gene loci proceeds in an ordered manner with D to J portions recombining first and then an upstream V joins that recombinant. We present evidence that the non-core domain of recombination activating gene (RAG) protein 2 is involved in the regulation of recom...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn553
更新日期:2008-10-01 00:00:00
abstract::Use of antisense oligonucleotides is a versatile strategy for achieving control of gene expression. Unfortunately, the interpretation of antisense-induced phenotypes is sometimes difficult, and chemical modifications that improve the potency and specificity of antisense action would be useful. The introduction of lock...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf651
更新日期:2002-12-01 00:00:00
abstract::We describe a new, broadly applicable methodology for screening in parallel interactions of RNA-binding proteins (RBPs) with large numbers of microRNA (miRNA) precursors and for determining their affinities in native form in the presence of cellular factors. The assays aim at identifying pre-miRNAs that are potentiall...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1197
更新日期:2013-02-01 00:00:00
abstract::Many enzymes acting on DNA require Mg(2+) ions not only for catalysis but also to bind DNA. Binding studies often employ Ca(2+) as a substitute for Mg(2+), to promote DNA binding whilst disallowing catalysis. The SfiI endonuclease requires divalent metal ions to bind DNA but, in contrast to many systems where Ca(2+) m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp569
更新日期:2009-09-01 00:00:00
abstract::Differences between species have been suggested to largely reside in the network of connections among the genes. Nevertheless, the rate at which these connections evolve has not been properly quantified. Here, we measure the extent to which co-regulation between pairs of genes is conserved over large phylogenetic dist...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh815
更新日期:2004-09-07 00:00:00
abstract::The covalent attachment of thiol-modified DNA oligomers; to self-assembled monolayer silane films on fused silica and oxidized silicon substrates is described. A heterobifunctional crosslinking molecule bearing both thiol- and amino-reactive moieties was used to tether a DNA oligomer (modified at its terminus with a t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.15.3031
更新日期:1996-08-01 00:00:00
abstract::Engineered nucleases, which incise the genome at predetermined sites, have a number of laboratory and clinical applications. There is, however, a need for better methods for controlled intracellular delivery of nucleases. Here, we demonstrate a method for ligand-mediated delivery of zinc finger nucleases (ZFN) protein...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt710
更新日期:2013-10-01 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
pub_type: 杂志文章
doi:10.1093/nar/gnh148
更新日期:2004-11-01 00:00:00