Identification of members of several homeobox genes in a planarian using a ligation-mediated polymerase chain reaction technique.


:I have used a novel single-sided specific polymerase chain reaction (PCR) strategy inspired by ligation-mediated PCR to clone fragments of divergent homeobox genes from a flatworm, the planarian Polycelis nigra. Eight homeobox-containing fragments were amplified, belonging to the Hox, msh, NK-1 and NK-2 classes. Together with the results obtained from several genomes of platyhelminths, my screening shows the presence of the same array of homeodomain developmental regulators in planarians, traditionally regarded as primitive metazoans in terms of body plan, as in coelomate organisms. However, the presence of a Ubx/abd-A homolog may indicate that platyhelminths are more closely related to protostomes than to deuterostomes and supports the idea that flatworms have inherited an elaborate HOX cluster (seven or eight genes) from their ancestor. Likely homologs of the fly genes tinman, bagpipe and S59 suggest that the mesoderm might be patterned by the same genes in all bilaterally symmetrical animals. Finally, a msh-like gene, a family known to be involved in inductive mechanisms in vertebrates, has been found. These results support the hypothesis that the tremendous diversity of metazoan body plans is specified by a largely conserved array of homeobox-containing developmental genes.


Nucleic Acids Res


Nucleic acids research


Balavoine G




Has Abstract


1996-04-15 00:00:00














  • miRDB: an online database for prediction of functional microRNA targets.

    abstract::MicroRNAs (miRNAs) are small noncoding RNAs that act as master regulators in many biological processes. miRNAs function mainly by downregulating the expression of their gene targets. Thus, accurate prediction of miRNA targets is critical for characterization of miRNA functions. To this end, we have developed an online...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chen Y,Wang X

    更新日期:2020-01-08 00:00:00

  • Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum.

    abstract::Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (I...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lu XM,Batugedara G,Lee M,Prudhomme J,Bunnik EM,Le Roch KG

    更新日期:2017-07-27 00:00:00

  • Retroposons do jump: a B2 element recently integrated in an 18S rDNA gene.

    abstract::Several cDNA clones were isolated from cDNA libraries constructed with mRNA longer than 28S RNA from the murine cell line PYS-2/12. The plasmids have inserts containing 1-1.2 kb of the ribosomal 5' external transcribed spacer followed by nearly 700 nt of sequence for 18S rRNA and ending with a B2 element (retroposon)....

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Oberbäumer I

    更新日期:1992-02-25 00:00:00

  • Quantitation of DNA double-strand break resection intermediates in human cells.

    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


    authors: Zhou Y,Caron P,Legube G,Paull TT

    更新日期:2014-02-01 00:00:00

  • The modulation of topoisomerase I-mediated DNA cleavage and the induction of DNA-topoisomerase I crosslinks by crotonaldehyde-derived DNA adducts.

    abstract::Crotonaldehyde is a representative alpha,beta-unsaturated aldehyde endowed of mutagenic and carcinogenic properties related to its propensity to react with DNA. Cyclic crotonaldehyde-derived deoxyguanosine (CrA-PdG) adducts can undergo ring opening in duplex DNA to yield a highly reactive aldehydic moiety. Here, we de...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dexheimer TS,Kozekova A,Rizzo CJ,Stone MP,Pommier Y

    更新日期:2008-07-01 00:00:00

  • MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic {beta}-actin gene.

    abstract::Actin is a major cytoskeletal protein in eukaryotes. Recent studies suggest more diverse functional roles for this protein. Actin mRNA is known to be localized to neuronal synapses and undergoes rapid deadenylation during early developmental stages. However, its 3'-untranslated region (UTR) is not characterized and th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ghosh T,Soni K,Scaria V,Halimani M,Bhattacharjee C,Pillai B

    更新日期:2008-11-01 00:00:00

  • Degradation of initiator tRNAMet by Xrn1/2 via its accumulation in the nucleus of heat-treated HeLa cells.

    abstract::Stress response mechanisms that modulate the dynamics of tRNA degradation and accumulation from the cytoplasm to the nucleus have been studied in yeast, the rat hepatoma and human cells. In the current study, we investigated tRNA degradation and accumulation in HeLa cells under various forms of stress. We found that i...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Watanabe K,Miyagawa R,Tomikawa C,Mizuno R,Takahashi A,Hori H,Ijiri K

    更新日期:2013-04-01 00:00:00

  • Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs.

    abstract::Post-transcriptional regulation and the formation of mRNA 3' ends are crucial for gene expression in eukaryotes. Interspecies conservation of many sequences within 3'UTRs reveals selective constraint due to similar function. To study the pattern of conservation within 3'UTRs, we compiled and aligned 50 sets of complet...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shabalina SA,Ogurtsov AY,Lipman DJ,Kondrashov AS

    更新日期:2003-09-15 00:00:00

  • A novel RNA molecular signature for activation of 2'-5' oligoadenylate synthetase-1.

    abstract::Human 2'-5' oligoadenylate synthetase-1 (OAS1) is central in innate immune system detection of cytoplasmic double-stranded RNA (dsRNA) and promotion of host antiviral responses. However, the molecular signatures that promote OAS1 activation are currently poorly defined. We show that the 3'-end polyuridine sequence of ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Vachon VK,Calderon BM,Conn GL

    更新日期:2015-01-01 00:00:00

  • Recombinant hnRNP protein A1 and its N-terminal domain show preferential affinity for oligodeoxynucleotides homologous to intron/exon acceptor sites.

    abstract::The reported binding preference of human hnRNP protein A1 for the 3'-splice site of some introns (Swanson and Dreyfuss (1988) EMBO J. 7, 3519-3529; Mayrand and Pederson (1990) Nucleic Acids Res. 18, 3307-3318) was tested by assaying in vitro the binding of purified recombinant A1 protein (expressed in bacteria) to syn...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Buvoli M,Cobianchi F,Biamonti G,Riva S

    更新日期:1990-11-25 00:00:00

  • Updates of the HbVar database of human hemoglobin variants and thalassemia mutations.

    abstract::HbVar ( is one of the oldest and most appreciated locus-specific databases launched in 2001 by a multi-center academic effort to provide timely information on the genomic alterations leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records incl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Giardine B,Borg J,Viennas E,Pavlidis C,Moradkhani K,Joly P,Bartsakoulia M,Riemer C,Miller W,Tzimas G,Wajcman H,Hardison RC,Patrinos GP

    更新日期:2014-01-01 00:00:00

  • Detection of oligonucleotide hybridization at femtomolar level and sequence-specific gene analysis of the Arabidopsis thaliana leaf extract with an ultrasensitive surface plasmon resonance spectrometer.

    abstract::A flow-injection (FI) device is combined, through the use of a low-volume (4 microl) flow cell, with an ultrasensitive surface plasmon resonance (SPR) spectrometer equipped with a bi-cell photodiode detector. The application of this novel FI-SPR device for sequence-specific ultratrace analysis of oligodeoxynucleotides...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Song F,Zhou F,Wang J,Tao N,Lin J,Vellanoweth RL,Morquecho Y,Wheeler-Laidman J

    更新日期:2002-07-15 00:00:00

  • Recognition of base pairs by polar peptides in double stranded DNA.

    abstract::The resonance Raman spectrum of native DNA has been obtained using excitation at 257 nm. In a first part, the spectral lines are assigned to the different nucleotide bases which provide the resonance effect. In a second part, the interactions of DNA with basic peptides (Arginine Methylester, Lysine Methylester, Arginy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Laigle A,Chinsky L,Turpin PY

    更新日期:1982-03-11 00:00:00

  • The essential transcription factor Reb1p interacts with the CLB2 UAS outside of the G2/M control region.

    abstract::Regulation of CLB2 is important both for completion of the normal vegetative cell cycle in Saccharomyces cerevisiae and for departure from the vegetative cell cycle upon nitrogen deprivation. Cell cycle-regulated transcription of CLB2 in the G2/M phase is known to be brought about by a set of proteins including Mcm1p,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Van Slyke C,Grayhack EJ

    更新日期:2003-08-01 00:00:00

  • Ser-tRNAs from bovine mitochondrion form ternary complexes with bacterial elongation factor Tu and GTP.

    abstract::Transfer ribonucleic acids were isolated from mitochondria of bovine heart and aminoacylated in vitro by a crude mitochondrial enzyme. Ser-tRNASerUCN and Ser-tRNASerAGY were isolated and characterized by partial sequencing. Although these tRNAs possess unique structural features not found in any bacterial tRNA, they f...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gebhardt-Singh E,Sprinzl M

    更新日期:1986-09-25 00:00:00

  • A Tetrahymena thermophila ribozyme-based indicator gene to detect transposition of marked retroelements in mammalian cells.

    abstract::We devised an indicator gene for retrotransposition based on an autocatalytic ribozyme element--the Tetrahymena thermophila 23S rRNA group I intron--which can self-splice in vitro and does not require--at variance with nuclear mRNA introns--any specific pathway and cellular component for the completion of the splicing...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Esnault C,Casella JF,Heidmann T

    更新日期:2002-06-01 00:00:00

  • p53-mediated DNA renaturation can mimic strand exchange.

    abstract::The process of strand exchange is considered to be the hallmark of DNA recombination. Proteins known to carry out such exchange are believed to operate via one or the other of two mechanisms. RecA-like proteins promote the formation of a three-stranded or triplex synaptic intermediate in which strand exchange occurs, ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jean D,Gendron D,Delbecchi L,Bourgaux P

    更新日期:1997-10-15 00:00:00

  • The evolutionary scrambling and developmental unscrambling of germline genes in hypotrichous ciliates.

    abstract::Genes in the germline (micronuclear) genome of hypotrichous ciliates are interrupted by multiple, short, non-coding, AT-rich sequences called internal eliminated segments, or IESs. During conversion of a micronucleus to a somatic nucleus (macronucleus) after cell mating, all IESs are excised from the germline genes an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审


    authors: Prescott DM

    更新日期:1999-03-01 00:00:00

  • Compilation of tRNA sequences and sequences of tRNA genes.

    abstract::Sequences of 3279 sequences of tRNA genes and tRNAs published up to December 1996 are included in the compilation. Alignment of the sequences, which is most compatible with the tRNA phylogeny and known three-dimensional structures of tRNA, is used. Sequences and references are available under http://www.uni-bayreuth. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sprinzl M,Horn C,Brown M,Ioudovitch A,Steinberg S

    更新日期:1998-01-01 00:00:00

  • ECO, the Evidence & Conclusion Ontology: community standard for evidence information.

    abstract::The Evidence and Conclusion Ontology (ECO) contains terms (classes) that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). Capture of this inform...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Giglio M,Tauber R,Nadendla S,Munro J,Olley D,Ball S,Mitraka E,Schriml LM,Gaudet P,Hobbs ET,Erill I,Siegele DA,Hu JC,Mungall C,Chibucos MC

    更新日期:2019-01-08 00:00:00

  • Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number.

    abstract::Ribonucleic acids are highly conserved essential parts of cellular life. RNA function is determined to a large extent by its hydrodynamic behaviour. The presented study proposes a strategy to predict the hydrodynamic behaviour of RNA single strands on the basis of the polymer size. By atom-level shell-modelling of hig...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Werner A

    更新日期:2011-02-01 00:00:00

  • Conserved elements containing NF-E2 and tandem GATA binding sites are required for erythroid-specific chromatin structure reorganization within the human beta-globin locus control region.

    abstract::Proper expression of the genes of the human beta-globin gene locus requires the associated locus control region (LCR). Structurally, the LCR is defined by the presence of four domains of erythroid-specific chromatin structure. These domains, which have been characterized as DNase I hypersensitive sites (HSs), comprise...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pomerantz O,Goodwin AJ,Joyce T,Lowrey CH

    更新日期:1998-12-15 00:00:00

  • RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways.

    abstract::RegAnalyst is a user-friendly web interface that integrates MoPP (Motif Prediction Program), MyPatternFinder (pattern detection tool) and MycoRegDB (mycobacterial promoter and regulatory elements database). Since motif discovery is a challenging task, numerous tools have been developed over the past few years. Strikin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sharma D,Mohanty D,Surolia A

    更新日期:2009-07-01 00:00:00

  • Target sites for the transposition of rat long interspersed repeated DNA elements (LINEs) are not random.

    abstract::The long interspersed repeated DNA family of rats (LINE or L1Rn family) contains about 40,000 6.7-kilobase (kb) long members (1). LINE members may be currently mobile since their presence or absence causes allelic variation at three single copy loci (2, 3): insulin 1, Moloney leukemia virus integration 2 (Mlvi-2) (4),...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Furano AV,Somerville CC,Tsichlis PN,D'Ambrosio E

    更新日期:1986-05-12 00:00:00

  • Human Rad51 protein displays enhanced homologous pairing of DNA sequences resembling those at genetically unstable loci.

    abstract::DNA strand exchange, the central step of homologous recombination, is considered to occur approximately independently of DNA sequence content. However, certain prokaryotic and eukaryotic genomic loci display either an enhanced or reduced frequency of genetic exchange. Here we show that the Homo sapiens DNA strand exch...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Seitz EM,Kowalczykowski SC

    更新日期:2006-05-24 00:00:00

  • The Arabidopsis Information Resource (TAIR): gene structure and function annotation.

    abstract::The Arabidopsis Information Resource (TAIR, is the model organism database for the fully sequenced and intensively studied model plant Arabidopsis thaliana. Data in TAIR is derived in large part from manual curation of the Arabidopsis research literature and direct submissions from the research...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Swarbreck D,Wilks C,Lamesch P,Berardini TZ,Garcia-Hernandez M,Foerster H,Li D,Meyer T,Muller R,Ploetz L,Radenbaugh A,Singh S,Swing V,Tissier C,Zhang P,Huala E

    更新日期:2008-01-01 00:00:00

  • Reversible site-specific tagging of enzymatically synthesized RNAs using aldehyde-hydrazine chemistry and protease-cleavable linkers.

    abstract::The investigation of RNA structure, dynamics and biological function often requires the site-specific incorporation of non-natural moieties. Here we describe the functionalization of RNA transcripts by aldehyde-hydrazine chemistry using a simple initiator nucleotide that carries an acetal-protected aldehyde function. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pfander S,Fiammengo R,Kirin SI,Metzler-Nolte N,Jäschke A

    更新日期:2007-01-01 00:00:00

  • Some KpnI family members are associated with the Alu family in the human genome.

    abstract::The structures of the termini and their flanking regions of two human KpnI family members were investigated. The two differed in length, but the starting sequence at one terminal (defined as the 5' terminal) was found to be common to both members. The Alu family sequence was found in the 5' flanking regions. The KpnI ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Miyake T,Migita K,Sakaki Y

    更新日期:1983-10-11 00:00:00

  • Genome wide interactions of wild-type and activator bypass forms of σ54.

    abstract::Enhancer-dependent transcription involving the promoter specificity factor σ(54) is widely distributed amongst bacteria and commonly associated with cell envelope function. For transcription initiation, σ(54)-RNA polymerase yields open promoter complexes through its remodelling by cognate AAA+ ATPase activators. Since...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Schaefer J,Engl C,Zhang N,Lawton E,Buck M

    更新日期:2015-09-03 00:00:00

  • The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease.

    abstract::Extragenic sequences in genomes, such as microRNA and CRISPR, are vital players in the cell. Repetitive extragenic palindromic sequences (REPs) are a class of extragenic sequences, which form nucleotide stem-loop structures. REPs are found in many bacterial species at a high copy number and are important in regulation...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Messing SA,Ton-Hoang B,Hickman AB,McCubbin AJ,Peaslee GF,Ghirlando R,Chandler M,Dyda F

    更新日期:2012-10-01 00:00:00