Histone demethylase KDM3A is required for enhancer activation of hippo target genes in colorectal cancer.

abstract：:N-nitrosation of glycine and its derivatives generates potent alkylating agents that can lead to the formation of O(6)-carboxymethylguanine (O(6)-CMG) in DNA. O(6)-CMG has been identified in DNA derived from human colon tissue, and its occurrence has been linked to diets high in red and processed meats. By analogy to ...

journal_title：Nucleic acids research

authors： Zhang F,Tsunoda M,Suzuki K,Kikuchi Y,Wilkinson O,Millington CL,Margison GP,Williams DM,Czarina Morishita E,Takénaka A

更新日期：2013-05-01 00:00:00

abstract：:A gene encoding a putative DNA helicase from Staphylococcus aureus USA300 was cloned and expressed in Escherichia coli. The protein was purified to over 90% purity by chromatography. The purified enzyme, SauUSI, predominantly cleaves modified DNA containing 5mC and 5-hydroxymethylcytosine. Cleavage of 5mC-modified pla...

journal_title：Nucleic acids research

authors： Xu SY,Corvaglia AR,Chan SH,Zheng Y,Linder P

更新日期：2011-07-01 00:00:00

abstract：:The topoisomerase I (TOP1) inhibitor irinotecan triggers cell death by trapping TOP1 on DNA, generating cytotoxic protein-linked DNA breaks (PDBs). Despite its wide application in a variety of solid tumors, the mechanisms of cancer cell resistance to irinotecan remains poorly understood. Here, we generated colorectal ...

journal_title：Nucleic acids research

authors： Meisenberg C,Ashour ME,El-Shafie L,Liao C,Hodgson A,Pilborough A,Khurram SA,Downs JA,Ward SE,El-Khamisy SF

更新日期：2017-02-17 00:00:00

abstract：:The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www....

journal_title：Nucleic acids research

authors： Tatusov RL,Natale DA,Garkavtsev IV,Tatusova TA,Shankavaram UT,Rao BS,Kiryutin B,Galperin MY,Fedorova ND,Koonin EV

更新日期：2001-01-01 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

authors： Wang TT,Abelson S,Zou J,Li T,Zhao Z,Dick JE,Shlush LI,Pugh TJ,Bratman SV

更新日期：2019-09-05 00:00:00

abstract：:Actinomycin D (ActD) is a small molecule with strong antibiotic and anticancer activity. However, its biologically relevant DNA-binding mechanism has never been resolved, with some studies suggesting that the primary binding mode is intercalation, and others suggesting that single-stranded DNA binding is most importan...

journal_title：Nucleic acids research

authors： Paramanathan T,Vladescu I,McCauley MJ,Rouzina I,Williams MC

更新日期：2012-06-01 00:00:00

abstract：:One-Block CYRCA is an automated procedure for identifying multiple-block alignments from single block queries (http://bioinfo.weizmann.ac.il/blocks/OneCYRCA). It is based on the LAMA and CYRCA block-to-block alignment methods. The procedure identifies whether the query blocks can form new multiple-block alignments (bl...

journal_title：Nucleic acids research

authors： Frenkel-Morgenstern M,Singer A,Bronfeld H,Pietrokovski S

更新日期：2005-07-01 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：:Tcf/Lef family transcription factors are the downstream effectors of the Wingless/Wnt signal transduction pathway. Upon Wingless/Wnt signalling, beta-catenin translocates to the nucleus, interacts with Tcf (1-3) and thus activates transcription of target genes (4,5). Tcf factors also interact with members of the Grouc...

journal_title：Nucleic acids research

authors： Brantjes H,Roose J,van De Wetering M,Clevers H

更新日期：2001-04-01 00:00:00

abstract：:We present NetCore, a novel network propagation approach based on node coreness, for phenotype-genotype associations and module identification. NetCore addresses the node degree bias in PPI networks by using node coreness in the random walk with restart procedure, and achieves improved re-ranking of genes after propag...

journal_title：Nucleic acids research

authors： Barel G,Herwig R

更新日期：2020-09-25 00:00:00

abstract：:The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads has become an important yet challenging probl...

journal_title：Nucleic acids research

authors： Rho M,Tang H,Ye Y

更新日期：2010-11-01 00:00:00

abstract：:The nucleotide sequence of the Klebsiella pneumoniae ntrA gene has been determined. NtrA encodes a 53,926 Dalton acidic polypeptide; a calculated molecular weight which is significantly lower than that determined by SDS polyacrylamide gel analysis. NtrA is followed by another open-reading frame (orf) of at least 75 am...

journal_title：Nucleic acids research

authors： Merrick MJ,Gibbins JR

更新日期：1985-11-11 00:00:00

abstract：:Sodium is one of the most abundant metals in the environment and in biology, playing critical ecological and physiological roles. Na+ is also the most common buffer salt for nucleic acids research, while its specific interaction with DNA has yet to be fully studied. Herein, we probe a highly selective and robust Na+ a...

journal_title：Nucleic acids research

authors： Zhou W,Ding J,Liu J

更新日期：2016-12-01 00:00:00

abstract：:Abasic substitutions in the non-template strand and promoter sequence changes were made to assess the roles of various promoter features in sigma70 holoenzyme interactions with fork junction probes. Removal of -10 element non-template single strand bases, leaving the phosphodiester backbone intact, did not interfere w...

journal_title：Nucleic acids research

authors： Fenton MS,Gralla JD

更新日期：2003-06-01 00:00:00

abstract：:DNA polymerase lambda (pol lambda) is a member of the X family DNA polymerases and is endowed with multiple enzymatic activities. In this work we investigated the in vitro miscoding properties of full-length, human pol lambda either in the absence or in the presence of the human auxiliary proteins proliferating cell n...

journal_title：Nucleic acids research

authors： Maga G,Shevelev I,Villani G,Spadari S,Hübscher U

更新日期：2006-03-06 00:00:00

abstract：:The integrases are a diverse family of tyrosine recombinases which rearrange DNA duplexes by means of conservative site-specific recombination reactions. Members of this family, of which the well-studied lambda Int protein is the prototype, were previously found to share four strongly conserved residues, including an ...

journal_title：Nucleic acids research

authors： Esposito D,Scocca JJ

更新日期：1997-09-15 00:00:00

abstract：:Despite the great potential of RNAi, ectopic expression of shRNA or siRNAs holds the inherent risk of competition for critical RNAi components, thus altering the regulatory functions of some cellular microRNAs. In addition, specific siRNA sequences can potentially hinder incorporation of other siRNAs when used in a co...

journal_title：Nucleic acids research

authors： Castanotto D,Sakurai K,Lingeman R,Li H,Shively L,Aagaard L,Soifer H,Gatignol A,Riggs A,Rossi JJ

更新日期：2007-01-01 00:00:00

abstract：:Protein structures often show similarities to another which would not be seen at the sequence level. Given the coordinates of a protein chain, the SALAMI server at www.zbh.uni-hamburg.de/salami will search the protein data bank and return a set of similar structures without using sequence information. The results page...

journal_title：Nucleic acids research

authors： Margraf T,Schenk G,Torda AE

更新日期：2009-07-01 00:00:00

abstract：:A cross index is presented for using the improved selectivity offered by the Hung and Wensink (Nucl. Acids Res. 12, 1863-1874, 1984) method of partially filling in 5'-extensions produced by type II restriction endonucleases. After this treatment, DNA fragments which normally cannot be ligated to one another, can be jo...

journal_title：Nucleic acids research

authors： Korch C

更新日期：1987-04-24 00:00:00

abstract：:A previously elaborated technique for fixing a chosen partially melted state of DNA with glyoxal was used in a study of the melting process of the replicative form (RF III) of phi X174 DNA. Electron-microscopic maps corresponding to five points of the melting curve of RF III were obtained and compared with the theoret...

journal_title：Nucleic acids research

authors： Lyubchenko YuL,Kalambet YuA,Lyamichev VI,Borovik AS

更新日期：1982-03-25 00:00:00

abstract：:Many DNA modification and repair enzymes require access to DNA bases and therefore flip nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within or in the vicinity of the target recognition site and do not require base extrusion for the sequence readout and catalysis. Therefore, the...

journal_title：Nucleic acids research

authors： Tamulaitis G,Zaremba M,Szczepanowski RH,Bochtler M,Siksnys V

更新日期：2007-01-01 00:00:00

abstract：:Analysis of the human protein-tyrosine phosphatase (PTP) PTPRJ mRNA detected three in-frame AUGs at the 5'-end (starting at nt +14, +191 and +356) with no intervening stop codons. This tandem AUG arrangement is conserved between humans and the mouse and is unique among the genes of the classical PTPs. Until now it was...

journal_title：Nucleic acids research

authors： Karagyozov L,Godfrey R,Böhmer SA,Petermann A,Hölters S,Ostman A,Böhmer FD

更新日期：2008-08-01 00:00:00

abstract：:ProtoNet is an automatic hierarchical classification of the protein sequence space. In 2004, the ProtoNet (version 4.0) presents the analysis of over one million proteins merged from SwissProt and TrEMBL databases. In addition to rich visualization and analysis tools to navigate the clustering hierarchy, we incorporat...

journal_title：Nucleic acids research

authors： Kaplan N,Sasson O,Inbar U,Friedlich M,Fromer M,Fleischer H,Portugaly E,Linial N,Linial M

更新日期：2005-01-01 00:00:00

abstract：:Recent studies have employed cross-species comparisons of transcription factor binding, reporting significant regulatory network 'rewiring' between species. Here, we address how a transcriptional repressor targets and regulates neural genes differentially between human and mouse embryonic stem cells (ESCs). We find th...

journal_title：Nucleic acids research

authors： Rockowitz S,Zheng D

更新日期：2015-07-13 00:00:00

abstract：:The RESID Database is a comprehensive collection of annotations and structures for protein post-translational modifications including N-terminal, C-terminal and peptide chain cross-link modifications. The RESID Database includes systematic and frequently observed alternate names, Chemical Abstracts Service registry nu...

journal_title：Nucleic acids research

authors： Garavelli JS,Hou Z,Pattabiraman N,Stephens RM

更新日期：2001-01-01 00:00:00

abstract：:We present a study of how substituent groups of naturally occurring and modified nucleotide bases affect the degree of hydration of right-handed B-DNA and left-handed Z-DNA. A comparison of poly(dG-dC) and poly(dG-dm5C) titrations with the lipotropic salts of the Hofmeister series infers that the methyl stabilization ...

journal_title：Nucleic acids research

authors： Kagawa TF,Howell ML,Tseng K,Ho PS

更新日期：1993-12-25 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：:The sequencing of the full transcriptome (RNA-seq) has become the preferred choice for the measurement of genome-wide gene expression. Despite its widespread use, challenges remain in RNA-seq data analysis. One often-overlooked aspect is normalization. Despite the fact that a variety of factors or 'batch effects' can ...

journal_title：Nucleic acids research

authors： Peixoto L,Risso D,Poplawski SG,Wimmer ME,Speed TP,Wood MA,Abel T

更新日期：2015-09-18 00:00:00

abstract：:A soluble enzyme system that specifically initiates lambda dv plasmid DNA replication at a bacteriophage lambda replication origin [Wold et al. (1982) Proc. Natl. Acad. Sci. USA 79, 6176-6180] is also capable of replicating the single-stranded circular chromosomes of phages M13 and phi X174 to a duplex form. This chai...

journal_title：Nucleic acids research

authors： LeBowitz JH,McMacken R

更新日期：1984-04-11 00:00:00

abstract：:The noncoding RNA database (ncRNAdb) was created as a source of information on RNA molecules, which do not possess protein-coding capacity. It is now widely accepted that, in addition to constitutively expressed, housekeeping or infrastructural RNAs, there is a wide variety of RNAs participating in mechanisms involved...

journal_title：Nucleic acids research

authors： Szymanski M,Erdmann VA,Barciszewski J

更新日期：2007-01-01 00:00:00