Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility.

abstract：:Transposable elements (TEs) comprise a large proportion of long non-coding RNAs (lncRNAs). Here, we employed CRISPR to delete a short interspersed nuclear element (SINE) in Malat1, a cancer-associated lncRNA, to investigate its significance in cellular physiology. We show that Malat1 with a SINE deletion forms diffuse...

journal_title：Nucleic acids research

authors： Nguyen TM,Kabotyanski EB,Reineke LC,Shao J,Xiong F,Lee JH,Dubrulle J,Johnson H,Stossi F,Tsoi PS,Choi KJ,Ellis AG,Zhao N,Cao J,Adewunmi O,Ferreon JC,Ferreon ACM,Neilson JR,Mancini MA,Chen X,Kim J,Ma L,Li W,Ro

更新日期：2020-03-18 00:00:00

abstract：:We have determined the three-dimensional structure of a non-selfcomplementary nonanucleotide duplex which contains an abasic (apyrimidinic) site in the centre, i.e. a deoxyribose residue opposite an adenosine. The majority of the base and sugar proton resonances were assigned by NOESY, COSY and 2DQF spectra in D2O and...

journal_title：Nucleic acids research

authors： Cuniasse P,Sowers LC,Eritja R,Kaplan B,Goodman MF,Cognet JA,LeBret M,Guschlbauer W,Fazakerley GV

更新日期：1987-10-12 00:00:00

abstract：:We have characterized triple-helix-mediated inhibition of an artificial bacteriophage promoter with respect to relief of inhibition by incoming RNA polymerases that initiate upstream or downstream from the operator sequence. Whereas oligonucleotide-directed triple-helix formation inhibits the test promoter, promoter a...

journal_title：Nucleic acids research

authors： Skoog JU,Maher LJ 3rd

更新日期：1993-08-25 00:00:00

abstract：:PAX6 is a transcription factor that plays a major role in ocular morphogenesis. PAX6 is expressed in the eye, central nervous system and pancreas. Two alternative promoters, P0 and P1, which are differentially regulated during development, drive PAX6 transcription. We identified a 57 bp cis-regulatory element in exon ...

journal_title：Nucleic acids research

authors： Zheng JB,Zhou YH,Maity T,Liao WS,Saunders GF

更新日期：2001-10-01 00:00:00

abstract：:RNA molecules fold into characteristic secondary structures for their diverse functional activities such as post-translational regulation of gene expression. Searching homologs of a pre-defined RNA structural motif, which may be a known functional element or a putative RNA structural motif, can provide useful informat...

journal_title：Nucleic acids research

authors： Chang TH,Huang HD,Chuang TN,Shien DM,Horng JT

更新日期：2006-07-01 00:00:00

abstract：:We report here the first successful generation of a chromosome-enriched library from flow sorted plant chromosomes. Chromosomes with a characteristic DNA content (a peak) were sorted from a synchronized cell culture (TaKB1, derived from Triticum aestivum). A HpaII library was constructed from the sorted chromosomes an...

journal_title：Nucleic acids research

authors： Wang ML,Leitch AR,Schwarzacher T,Heslop-Harrison JS,Moore G

更新日期：1992-04-25 00:00:00

abstract：:The androgen receptor (AR) is a member of the nuclear hormone receptor family of transcription factors that plays a critical role in regulating expression of genes involved in prostate development and transformation. Upon hormone binding, the AR associates with numerous co-regulator proteins that regulate the activati...

journal_title：Nucleic acids research

authors： Gaughan L,Stockley J,Wang N,McCracken SR,Treumann A,Armstrong K,Shaheen F,Watt K,McEwan IJ,Wang C,Pestell RG,Robson CN

更新日期：2011-03-01 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

authors： Khare D,Orban J

更新日期：1992-10-11 00:00:00

abstract：:Translesional DNA synthesis past abasic sites proceeds with the preferential incorporation of dAMP opposite the lesion and, depending on the sequence context, one or two base deletions. High-resolution NMR spectroscopy and molecular dynamics simulations were used to determine the three-dimensional structure of a DNA h...

journal_title：Nucleic acids research

authors： Lin Z,Hung KN,Grollman AP,de los Santos C

更新日期：1998-05-15 00:00:00

abstract：:BmFTZ-F1 is a Bombyx mori homologue of FTZ-F1, a positive regulator of the fushi tarazu gene of Drosophila melanogaster. In order to determine the sequence recognized with this factor, we made three sets of oligonucleotide mixture which contain 4 possible nucleotides at different positions within the previously propos...

journal_title：Nucleic acids research

authors： Ueda H,Hirose S

更新日期：1991-07-11 00:00:00

abstract：:The yeast retrotransposon Ty encodes proteins that assemble into virus-like particles (Ty-VLPs) which can be readily purified. We have recently shown that expression of the pl protein encoded by the TYA gene of Ty is sufficient for particle formation. In this paper we show that when a heterologous coding sequence, hum...

journal_title：Nucleic acids research

authors： Malim MH,Adams SE,Gull K,Kingsman AJ,Kingsman SM

更新日期：1987-09-25 00:00:00

abstract：:We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillu...

journal_title：Nucleic acids research

authors： Price MN,Huang KH,Alm EJ,Arkin AP

更新日期：2005-02-08 00:00:00

abstract：:The conditions under which Drosophila melanogaster are grown markedly influence the amount of the hypermodified nucleoside Q found in certain tRNAs. This effect on Q biosynthesis was found in both the wild-type and the suppressor of sable [su(s)2] mutant. Suppressed vermilion flies [su(s)2v; bw] with 78% of the tyrosi...

journal_title：Nucleic acids research

authors： Wosnick MA,White BN

更新日期：1977-11-01 00:00:00

abstract：:We report the complete DNA sequence of the short repeat region in the genome of herpes simplex virus type 1, as 6633 base pairs of composition 79.5% G+C. This contains immediate early gene 3, encoding the IE175 protein, an important transcriptional activator of later virus genes. The IE175 coding region was identified...

journal_title：Nucleic acids research

authors： McGeoch DJ,Dolan A,Donald S,Brauer DH

更新日期：1986-02-25 00:00:00

abstract：:A non-enzymic protein factor that increases the in vitro rate of synthesis by HeLa DNA polymerase alpha 15- to 30-fold with denatured DNA as template has been partially purified from the cytoplasmic fraction of HeLa cells. The stimulatory effect is highly specific for HeLa DNA polymerase alpha and for DNA templates th...

journal_title：Nucleic acids research

authors： Novak B,Baril EF

更新日期：1978-01-01 00:00:00

abstract：:Signal transduction ATPases with numerous domains (STAND) get activated through inducer-dependent assembly into multimeric platforms. This switch relies on the conversion of their nucleotide-binding oligomerization domain (NOD) from a closed, ADP-bound form to an open, ATP-bound form. The NOD closed form is stabilized...

journal_title：Nucleic acids research

authors： Danot O

更新日期：2015-03-31 00:00:00

abstract：:From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently atta...

journal_title：Nucleic acids research

authors： Morten MJ,Lopez SG,Steinmark IE,Rafferty A,Magennis SW

更新日期：2018-11-30 00:00:00

abstract：:The TransTerm database of termination codon contexts has been extended to include sense codon usage, and initiation codon contexts. The database was constructed from 23,721 coding sequences from 93 organisms. The database contains: a) the sequence around the termination codon (-10, +10); b) the sequence around the ini...

journal_title：Nucleic acids research

authors： Brown CM,Stockwell PA,Dalphin ME,Tate WP

更新日期：1994-09-01 00:00:00

abstract：:Escherichia coli cells lacking the ribosomal RNA processing enzyme RNase III do no excise the normal RNA precursors p16a (17S) and p23a from nascent rRNA transcripts. These cells produce, instead, slightly larger p16b and p23b precursors. Digestion of p16b or p23b rRNA with RNases A plus T1 yields double-stranded frag...

journal_title：Nucleic acids research

authors： Gegenheimer P,Apirion D

更新日期：1980-04-25 00:00:00

abstract：:The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Stud...

journal_title：Nucleic acids research

authors： Mukherjee S,Stamatis D,Bertsch J,Ovchinnikova G,Verezemska O,Isbandi M,Thomas AD,Ali R,Sharma K,Kyrpides NC,Reddy TB

更新日期：2017-01-04 00:00:00

abstract：:Ribosome biogenesis is a dynamic multistep process, many features of which are still incompletely documented. Here, we show that changes in this pathway can be captured and annotated by means of a graphic set of pre-rRNA ratios, a technique we call Ratio Analysis of Multiple Precursors (RAMP). We find that knocking do...

journal_title：Nucleic acids research

authors： Wang M,Anikin L,Pestov DG

更新日期：2014-01-01 00:00:00

abstract：:Clustered damages are formed in DNA by ionising radiation and radiomimetic anticancer agents and are thought to be biologically severe. 7,8-dihydro-8-oxoguanine (8-oxoG), a major DNA damage resulting from oxidative attack, is highly mutagenic leading to a high level of G.C-->T.A transversions if not previously excised...

journal_title：Nucleic acids research

authors： David-Cordonnier MH,Boiteux S,O'Neill P

更新日期：2001-03-01 00:00:00

abstract：:OGG1 initiated base excision repair (BER) is the major pathway for repair of oxidative DNA base damage 8-oxoguanine (8-oxoG). Here, we report that RECQL4 DNA helicase, deficient in the cancer-prone and premature aging Rothmund-Thomson syndrome, physically and functionally interacts with OGG1. RECQL4 promotes catalytic...

journal_title：Nucleic acids research

authors： Duan S,Han X,Akbari M,Croteau DL,Rasmussen LJ,Bohr VA

更新日期：2020-07-09 00:00:00

abstract：:Chromatin immunoprecipitation (ChIP) has been used to detect binding of DNA-binding proteins to sites in nuclear and mitochondrial genomes. Here, we describe a method for detecting protein-binding sites on chloroplast DNA, using modifications to the nuclear ChIP procedures. The method was developed using the lac opera...

journal_title：Nucleic acids research

authors： Newell CA,Gray JC

更新日期：2010-08-01 00:00:00

abstract：:Interaction detection methods have led to the discovery of thousands of interactions between proteins, and discerning relevance within large-scale data sets is important to present-day biology. Here, a spectral method derived from graph theory was introduced to uncover hidden topological structures (i.e. quasi-cliques...

journal_title：Nucleic acids research

authors： Bu D,Zhao Y,Cai L,Xue H,Zhu X,Lu H,Zhang J,Sun S,Ling L,Zhang N,Li G,Chen R

更新日期：2003-05-01 00:00:00

abstract：:Basic region-leucine zipper (B-ZIP) proteins are a class of dimeric sequence-specific DNA-binding proteins unique to eukaryotes. We have identified 67 B-ZIP proteins in the Arabidopsis thaliana genome. No A.thaliana B-ZIP domains are homologous with any Homo sapiens B-ZIP domains. Here, we predict the dimerization spe...

journal_title：Nucleic acids research

authors： Deppmann CD,Acharya A,Rishi V,Wobbes B,Smeekens S,Taparowsky EJ,Vinson C

更新日期：2004-06-29 00:00:00

abstract：:A gene bank of Staphylococcus aureus strain Cowan I was established using an E. coli HB101/pBR327 host-vector system. Recombinants expressing staphylococcal protein A (SPA) were detected using an IgG-binding assay. A 3.2 Kb DNA fragment directing the synthesis of SPA in E. coli was identified. SPA produced by E. coli ...

journal_title：Nucleic acids research

authors： Duggleby CJ,Jones SA

更新日期：1983-05-25 00:00:00

abstract：:Our database on large ribosomal subunit RNA contained 334 sequences in July, 1995. All sequences in the database are aligned, taking into account secondary structure. The aligned sequences are provided, together with incorporated secondary structure information, in several computer-readable formats. These data can eas...

journal_title：Nucleic acids research

authors： De Rijk P,Van de Peer Y,De Wachter R

更新日期：1996-01-01 00:00:00

abstract：:We have sequenced the entire human S mu and S gamma 4 immunoglobulin heavy chain class switch regions, and have also completed the sequence of human S epsilon. S mu is composed predominantly of GAGCT and GGGCT pentameric repeats, with these units also being found in S epsilon at a much lower density. S mu-S gamma 4 ma...

journal_title：Nucleic acids research

authors： Mills FC,Brooker JS,Camerini-Otero RD

更新日期：1990-12-25 00:00:00

abstract：:ATF4 is a pro-oncogenic transcription factor whose translation is activated by eIF2 phosphorylation through delayed re-initiation involving two uORFs in the mRNA leader. However, in yeast, the effect of eIF2 phosphorylation can be mimicked by eIF5 overexpression, which turns eIF5 into translational inhibitor, thereby ...

journal_title：Nucleic acids research

authors： Kozel C,Thompson B,Hustak S,Moore C,Nakashima A,Singh CR,Reid M,Cox C,Papadopoulos E,Luna RE,Anderson A,Tagami H,Hiraishi H,Slone EA,Yoshino KI,Asano M,Gillaspie S,Nietfeld J,Perchellet JP,Rothenburg S,Masai H,W

更新日期：2016-10-14 00:00:00