Comparative analysis of non-autonomous effects of tasiRNAs and miRNAs in Arabidopsis thaliana.

Abstract:

:In plants, small interfering RNAs (siRNAs) can trigger a silencing signal that may spread within a tissue to adjacent cells or even systemically to other organs. Movement of the signal is initially limited to a few cells, but in some cases the signal can be amplified and travel over larger distances. How far silencing initiated by other classes of plant small RNAs (sRNAs) than siRNAs can extend has been less clear. Using a system based on the silencing of the CH42 gene, we have tracked the mobility of silencing signals initiated in phloem companion cells by artificial microRNAs (miRNA) and trans-acting siRNA (tasiRNA) that have the same primary sequence. In this system, both the ta-siRNA and the miRNA act at a distance. Non-autonomous effects of the miRNA can be triggered by several different miRNA precursors deployed as backbones. While the tasiRNA also acts non-autonomously, it has a much greater range than the miRNA or hairpin-derived siRNAs directed against CH42, indicating that biogenesis can determine the non-autonomous effects of sRNAs. In agreement with this hypothesis, the silencing signals initiated by different sRNAs differ in their genetic requirements.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

de Felippes FF,Ott F,Weigel D

doi

10.1093/nar/gkq1240

subject

Has Abstract

pub_date

2011-04-01 00:00:00

pages

2880-9

issue

7

eissn

0305-1048

issn

1362-4962

pii

gkq1240

journal_volume

39

pub_type

杂志文章
  • Biochemical analysis of the N-terminal domain of human RAD54B.

    abstract::The human RAD54B protein is a paralog of the RAD54 protein, which plays important roles in homologous recombination. RAD54B contains an N-terminal region outside the SWI2/SNF2 domain that shares less conservation with the corresponding region in RAD54. The biochemical roles of this region of RAD54B are not known, alth...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn516

    authors: Sarai N,Kagawa W,Fujikawa N,Saito K,Hikiba J,Tanaka K,Miyagawa K,Kurumizaka H,Yokoyama S

    更新日期:2008-10-01 00:00:00

  • Zinc ions are differentially required for the transcription of ribosomal 5S RNA and tRNA in a HeLa-cell extract.

    abstract::Chelation of divalent cations by 5 mM EDTA and subsequent removal by dialysis from a cytoplasmic HeLa cell extract leads to a complete loss of 5S rRNA transcription without affecting tRNA synthesis. Transcription complexes for 5S RNA can no longer be assembled in such a zinc-depleted extract and this ability can be fu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.23.8971

    authors: Wingender E,Dilloo D,Seifart KH

    更新日期:1984-12-11 00:00:00

  • Regulatory modules function in a non-autonomous manner to control transcription of the mbp gene.

    abstract::Multiple regulatory modules contribute to the complex expression programs realized by many loci. Although long thought of as isolated components, recent studies demonstrate that such regulatory sequences can physically associate with promoters and with each other and may localize to specific sub-nuclear transcription ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1160

    authors: Dib S,Denarier E,Dionne N,Beaudoin M,Friedman HH,Peterson AC

    更新日期:2011-04-01 00:00:00

  • NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.

    abstract::Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are involved in binding to the DNA and how they interact with the bases and sugar-phosphate backbone of nucleic acids. Here...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.24.4940

    authors: Luscombe NM,Laskowski RA,Thornton JM

    更新日期:1997-12-15 00:00:00

  • TcSNP: a database of genetic variation in Trypanosoma cruzi.

    abstract::The TcSNP database (http://snps.tcruzi.org) integrates information on genetic variation (polymorphisms and mutations) for different stocks, strains and isolates of Trypanosoma cruzi, the causative agent of Chagas disease. The database incorporates sequences (genes from the T. cruzi reference genome, mRNAs, ESTs and ge...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn874

    authors: Ackermann AA,Carmona SJ,Agüero F

    更新日期:2009-01-01 00:00:00

  • Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli.

    abstract::Recognition of genomic binding sites by transcription factors can occur through base-specific recognition, or by recognition of variations within the structure of the DNA macromolecule. In this article, we investigate what information can be retrieved from local DNA structural properties that is relevant to transcript...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1071

    authors: Meysman P,Dang TH,Laukens K,De Smet R,Wu Y,Marchal K,Engelen K

    更新日期:2011-01-01 00:00:00

  • PRMT1 loss sensitizes cells to PRMT5 inhibition.

    abstract::PRMT5 is an arginine methyltransferase that accounts for the vast majority of the symmetric methylation in cells. PRMT5 exerts its function when complexed with MEP50/WDR77. This activity is often elevated in cancer cells and correlates with poor prognosis, making PRMT5 a therapeutic target. To investigate the PRMT5 si...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz200

    authors: Gao G,Zhang L,Villarreal OD,He W,Su D,Bedford E,Moh P,Shen J,Shi X,Bedford MT,Xu H

    更新日期:2019-06-04 00:00:00

  • Skeletal muscle actin mRNA. Characterization of the 3' untranslated region.

    abstract::Plasmids p749, p106, and p150 contain cDNA inserts complementary to rat skeletal muscle actin mRNA. Nucleotide sequence analysis indicates the following sequence relationships: p749 specifies codons 171 to 360; p150 specifies codons 357 to 374 together with 120 nucleotides of the 3'-non-translated region; p106 specifi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/9.3.579

    authors: Shani M,Nudel U,Zevin-Sonkin D,Zakut R,Givol D,Katcoff D,Carmon Y,Reiter J,Frischauf AM,Yaffe D

    更新日期:1981-02-11 00:00:00

  • The Saccharomyces cerevisiae RAD9 cell cycle checkpoint gene is required for optimal repair of UV-induced pyrimidine dimers in both G(1) and G(2)/M phases of the cell cycle.

    abstract::Cells respond to DNA damage by activating both cellular growth arrest and DNA repair processes. In Saccharomyces cerevesiae the RAD9 gene controls DNA damage-mediated cell cycle arrest that is known to allow efficient repair. To ascertain whether RAD9 plays a role in DNA repair per se, the removal of UV-induced photol...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.10.2020

    authors: Al-Moghrabi NM,Al-Sharif IS,Aboussekhra A

    更新日期:2001-05-15 00:00:00

  • Novel internucleotide 3'-NH-P(CH3)(O)-O-5' linkage. Oligo(deoxyribonucleoside methanephosphonamidates); synthesis, structure and hybridization properties.

    abstract::Diastereomeric dithymidine methanephosphonamidates (TnpmT) were synthesized by reaction of 3'-amino-3'-deoxythymidine with 3'- O -acetylthymidin-5-yl-methanephosphonochloridate. Separated dinucleotide TnpmT(fast) and TnpmT(slow) diastereomers were used as building blocks to prepare chimeric dodecathy-midylates, posses...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.11.2650

    authors: Nawrot B,Boczkowska M,Wójcik M,Sochacki M,Kazmierski S,Stec WJ

    更新日期:1998-06-01 00:00:00

  • PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

    abstract::The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main nove...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw300

    authors: Floden EW,Tommaso PD,Chatzou M,Magis C,Notredame C,Chang JM

    更新日期:2016-07-08 00:00:00

  • CRISPR interference and priming varies with individual spacer sequences.

    abstract::CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR inter...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv1259

    authors: Xue C,Seetharam AS,Musharova O,Severinov K,Brouns SJ,Severin AJ,Sashital DG

    更新日期:2015-12-15 00:00:00

  • Electronic fingerprinting of RNA.

    abstract::Software has been developed to assist RNA fingerprinting analysis. One program generates, from a DNA sequence data file, the oligonucleotides resulting from digestion of an RNA transcript labeled with any specified nucleotide(s). Oligonucleotides are sorted according to their position on the fingerprint. Expected mola...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.5.1799

    authors: Gegenheimer P

    更新日期:1988-03-11 00:00:00

  • A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3.

    abstract::Reverse transcription in retroviruses and retrotransposons requires nucleic acid chaperones, which drive the rearrangement of nucleic acid conformation. The nucleic acid chaperone properties of the human immunodeficiency virus type-1 (HIV-1) nucleocapsid (NC) protein have been extensively studied, and nucleic acid agg...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr726

    authors: Chaurasiya KR,Geertsema H,Cristofari G,Darlix JL,Williams MC

    更新日期:2012-01-01 00:00:00

  • 3did Update: domain-domain and peptide-mediated interactions of known 3D structure.

    abstract::The database of 3D interacting domains (3did) is a collection of protein interactions for which high-resolution 3D structures are known. 3did exploits structural information to provide the crucial molecular details necessary for understanding how protein interactions occur. Besides interactions between globular domain...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn690

    authors: Stein A,Panjkovich A,Aloy P

    更新日期:2009-01-01 00:00:00

  • From head to toes: the multiple facets of Sox proteins.

    abstract::Sox proteins belong to the HMG box superfamily of DNA-binding proteins and are found throughout the animal kingdom. They are involved in the regulation of such diverse developmental processes as germ layer formation, organ development and cell type specifi-cation. Hence, deletion or mutation of Sox proteins often resu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审

    doi:10.1093/nar/27.6.1409

    authors: Wegner M

    更新日期:1999-03-15 00:00:00

  • Cyclic mismatch binding ligand CMBL4 binds to the 5'-T-3'/5'-GG-3' site by inducing the flipping out of thymine base.

    abstract::A newly designed cyclic bis-naphthyridine carbamate dimer CMBL4: with a limited conformational flexibility was synthesized and characterized. Absorption spectra revealed that two naphthyridines in CMBL4: were stacked on each other in aqueous solutions. The most efficient binding of CMBL4: to DNA was observed for the s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw672

    authors: Mukherjee S,Dohno C,Asano K,Nakatani K

    更新日期:2016-09-06 00:00:00

  • Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA.

    abstract::DNA predominantly contains Watson-Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif at any time. In HG, the purine is rotated ∼180° relative to the WC motif. The transitions between WC and HG may play a role in recognition and replication, but are diffi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz837

    authors: Vreede J,Pérez de Alba Ortíz A,Bolhuis PG,Swenson DWH

    更新日期:2019-12-02 00:00:00

  • A sequence-specific core promoter-binding transcription factor recruits TRF2 to coordinately transcribe ribosomal protein genes.

    abstract::Ribosomal protein (RP) genes must be coordinately expressed for proper assembly of the ribosome yet the mechanisms that control expression of RP genes in metazoans are poorly understood. Recently, TATA-binding protein-related factor 2 (TRF2) rather than the TATA-binding protein (TBP) was found to function in transcrip...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx676

    authors: Baumann DG,Gilmour DS

    更新日期:2017-10-13 00:00:00

  • PSSweb: protein structural statistics web server.

    abstract::With the increasing number of protein structures available, there is a need for tools capable of automating the comparison of ensembles of structures, a common requirement in structural biology and bioinformatics. PSSweb is a web server for protein structural statistics. It takes as input an ensemble of PDB files of p...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw332

    authors: Gaillard T,Stote RH,Dejaegere A

    更新日期:2016-07-08 00:00:00

  • Elk-1 can recruit SRF to form a ternary complex upon the serum response element.

    abstract::The initial genomic response to serum growth factors is the transcriptional activation of a set of immediate-early genes. Serum-induced transcriptional activation of several of these genes involves the formation of a ternary complex that includes the serum response factor (SRF), a 62 kDa ternary complex factor (TCF) a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.7.1345

    authors: Latinkić BV,Zeremski M,Lau LF

    更新日期:1996-04-01 00:00:00

  • The stability of oligodeoxyribonucleotide duplexes containing degenerate bases.

    abstract::Oligodeoxyribonucleotides containing N4-methoxycytosine (mo4C), N4-methoxy-5-methylcytosine (mo4m5C) and other base-analogues were synthesised and used to compare the stabilities of duplexes containing mo4C.A and mo4C.G base pairs with those containing normal and mismatch pairs. The Tm values and other thermodynamic p...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/15.20.8167

    authors: Anand NN,Brown DM,Salisbury SA

    更新日期:1987-10-26 00:00:00

  • Database resources of the National Center for Biotechnology Information.

    abstract::In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utili...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkj158

    authors: Wheeler DL,Barrett T,Benson DA,Bryant SH,Canese K,Chetvernin V,Church DM,DiCuccio M,Edgar R,Federhen S,Geer LY,Helmberg W,Kapustin Y,Kenton DL,Khovayko O,Lipman DJ,Madden TL,Maglott DR,Ostell J,Pruitt KD,Schuler G

    更新日期:2006-01-01 00:00:00

  • The production of PCR products with 5' single-stranded tails using primers that incorporate novel phosphoramidite intermediates.

    abstract::We have prepared several novel phosphoramidites and have synthesised oligonucleotides incorporating them internally. The presence of these residues in an oligonucleotide template presents an impossible barrier to primed synthesis by Taq DNA polymerase. When extended as polymerase chain reaction products, these oligonu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.5.1155

    authors: Newton CR,Holland D,Heptinstall LE,Hodgson I,Edge MD,Markham AF,McLean MJ

    更新日期:1993-03-11 00:00:00

  • Molecular cloning and characterization of the gene encoding the adenine methyltransferase M.CviRI from Chlorella virus XZ-6E.

    abstract::The gene encoding the DNA methyltransferase M.CviRI from Chlorella virus XZ-6E was cloned and expressed in Escherichia coli. M.CviRI methylates adenine in TGCA sequences. DNA containing the M.CviRI gene was sequenced and a single open reading frame of 1137 bp was identified which could code for a polypeptide of 379 am...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.2.307

    authors: Stefan C,Xia YN,Van Etten JL

    更新日期:1991-01-25 00:00:00

  • Termination of DNA synthesis by N6-alkylated, not 3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates.

    abstract::The Human Genome Project has facilitated the sequencing of many species, yet the current Sanger method is too expensive, labor intensive and time consuming to accomplish medical resequencing of human genomes en masse. Of the 'next-generation' technologies, cyclic reversible termination (CRT) is a promising method with...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm689

    authors: Wu W,Stupi BP,Litosh VA,Mansouri D,Farley D,Morris S,Metzker S,Metzker ML

    更新日期:2007-01-01 00:00:00

  • Different strategies of differential display: areas of application.

    abstract::The main goal of this review is to provide some guide-lines for choosing a proper method when searching for differentially expressed transcripts. The choice of an approach should depend upon particular features of the experiment and project requirements. We outline some general considerations to help decide between di...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审

    doi:10.1093/nar/26.24.5537

    authors: Matz MV,Lukyanov SA

    更新日期:1998-12-15 00:00:00

  • BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases.

    abstract::SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public web servers available...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg535

    authors: Bimpikis K,Budd A,Linding R,Gibson TJ

    更新日期:2003-07-01 00:00:00

  • Detection of platinum-DNA adducts by 32P-postlabelling.

    abstract::We developed a sensitive 32P-postlabeling method for the detection of bifunctional intrastrand crosslinks d(Pt-GpG) and d(Pt-ApG) in DNA in vitro and in vivo. After enzymatic digestion of DNA the positively charged platinum adducts were purified from unplatinated products, using strong cation exchange chromatography. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.8.1300

    authors: Blommaert FA,Saris CP

    更新日期:1995-04-25 00:00:00

  • Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands.

    abstract::Mutations in mammalian and Drosophila Hel308 and PolQ paralogues cause genome instability but their helicase functions are mysterious. By in vivo and in vitro analysis, we show that Hel308 from archaea (Hel308a) may act at stalled replication forks. Introducing hel308a into Escherichia coli dnaE strains that condition...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki685

    authors: Guy CP,Bolt EL

    更新日期:2005-06-30 00:00:00