AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome

Gene expression is controlled mainly by the binding of transcription factors to regulatory sequences. To generate a genomic map for regulatory sequences, the Arabidopsis thaliana genome was screened for putative transcription factor binding sites. Using publicly available data from the TRANSFAC database and from publications, alignment matrices for 23 transcription factors of 13 different factor families were used with the pattern search program Patser to determine the genomic positions of more than 2.4 x 10(6) putative binding sites. Due to the dense clustering of genes and the observation that regulatory sequences are not restricted to upstream regions, the prediction of binding sites was performed for the whole genome. The genomic positions and the underlying data were imported into the newly developed AthaMap database. This data can be accessed by positional information or the Arabidopsis Genome Initiative identification number. Putative binding sites are displayed in the defined region. Data on the matrices used and on the thresholds applied in these screens are given in the database. Considering the high density of sites it will be a valuable resource for generating models on gene expression regulation. The data are available at http://www.athamap.de.

[1]  D. Bastola,et al.  Alfin1, a novel zinc-finger protein in alfalfa roots that binds to promoter elements in the salt-inducible MsPRP2 gene , 1998, Plant Molecular Biology.

[2]  Kathleen Marchal,et al.  PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences , 2002, Nucleic Acids Res..

[3]  Yan Wang,et al.  DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro , 2004, Plant Molecular Biology.

[4]  Alexander E. Kel,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[5]  Yuko Ohashi,et al.  DNA binding and dimerization specificity and potential targets for the TCP protein family. , 2002, The Plant journal : for cell and molecular biology.

[6]  Jacques van Helden,et al.  Regulatory Sequence Analysis Tools , 2003, Nucleic Acids Res..

[7]  E Wingender,et al.  Database-assisted promoter analysis. , 2001, Trends in plant science.

[8]  Jungwon Yoon,et al.  The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community , 2003, Nucleic Acids Res..

[9]  R. Solano,et al.  MYB.Ph3 transcription factor from Petunia hybrida induces similar DNA-bending/distortions on its two types of binding site. , 1995, The Plant journal : for cell and molecular biology.

[10]  T. Werner,et al.  MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. , 1995, Nucleic acids research.

[11]  S. Kosugi,et al.  Cloning and DNA-binding properties of a tobacco Ethylene-Insensitive3 (EIN3) homolog. , 2000, Nucleic acids research.

[12]  C. Dean,et al.  Sequences downstream of translation start regulate quantitative expression of two petunia rbcS genes. , 1989, The Plant cell.

[13]  J. Memelink,et al.  Characterization of a zinc-dependent transcriptional activator from Arabidopsis. , 1996, Nucleic acids research.

[14]  S. Yanagisawa,et al.  Diversity and similarity among recognition sequences of Dof transcription factors. , 1999, The Plant journal : for cell and molecular biology.

[15]  Xin Chen,et al.  TRANSFAC: an integrated system for gene expression regulation , 2000, Nucleic Acids Res..

[16]  D. Weigel,et al.  Regulatory Elements of the Floral Homeotic Gene AGAMOUS Identified by Phylogenetic Footprinting and Shadowing Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.009548. , 2003, The Plant Cell Online.

[17]  H. Ma,et al.  Isolation and characterization of the binding sequences for the product of the Arabidopsis floral homeotic gene AGAMOUS. , 1993, Nucleic acids research.

[18]  R. Schmidt,et al.  Opaque-2 is a transcriptional activator that recognizes a specific target site in 22-kD zein genes. , 1992, The Plant cell.

[19]  R. Dixon,et al.  Silencer region of a chalcone synthase promoter contains multiple binding sites for a factor, SBF-1, closely related to GT-1 , 1991, Plant Molecular Biology.

[20]  R. Solano,et al.  Dual DNA binding specificity of a petal epidermis‐specific MYB transcription factor (MYB.Ph3) from Petunia hybrida. , 1995, The EMBO journal.

[21]  K. Yoshida,et al.  Functional analysis of tobacco LIM protein Ntlim1 involved in lignin biosynthesis. , 2000, The Plant journal : for cell and molecular biology.

[22]  D. Twell,et al.  Novel anther-specific myb genes from tobacco as putative regulators of phenylalanine ammonia-lyase expression. , 2001, Plant physiology.

[23]  Yoshihiro Ugawa,et al.  Plant cis-acting regulatory DNA elements (PLACE) database: 1999 , 1999, Nucleic Acids Res..

[24]  A. Cashmore,et al.  TGA1 and G-box binding factors: two distinct classes of Arabidopsis leucine zipper proteins compete for the G-box-like element TGACGTGG. , 1992, The Plant cell.

[25]  B. Krizek,et al.  DNA binding properties of the Arabidopsis floral development protein AINTEGUMENTA. , 2000, Nucleic acids research.

[26]  C. Steindler,et al.  The Arabidopsis Athb-8, -9 and genes are members of a small gene family coding for highly related HD-ZIP proteins , 1998, Plant Molecular Biology.

[27]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[28]  W. Peacock,et al.  Evidence for a role for AtMYB2 in the induction of the Arabidopsis alcohol dehydrogenase gene (ADH1) by low oxygen. , 1998, Genetics.

[29]  F. Gubler,et al.  Target genes and regulatory domains of the GAMYB transcriptional activator in cereal aleurone. , 1999, The Plant journal : for cell and molecular biology.

[30]  K. Ohmiya,et al.  RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. , 1999, Nucleic acids research.

[31]  E. Grotewold,et al.  The myb-homologous P gene controls phlobaphene pigmentation in maize floral organs by directly activating a flavonoid biosynthetic gene subset , 1994, Cell.

[32]  K. Shinozaki,et al.  A cdc5+ homolog of a higher plant, Arabidopsis thaliana. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[33]  L. Sieburth,et al.  Molecular dissection of the AGAMOUS control region shows that cis elements for spatial regulation are located intragenically. , 1997, The Plant cell.

[34]  S. H. Lee,et al.  A novel cold-inducible zinc finger protein from soybean, SCOF-1, enhances cold tolerance in transgenic plants. , 2001, The Plant journal : for cell and molecular biology.

[35]  E. Wingender,et al.  MATCH: A tool for searching transcription factor binding sites in DNA sequences. , 2003, Nucleic acids research.

[36]  Alexander E. Kel,et al.  MATCHTM: a tool for searching transcription factor binding sites in DNA sequences , 2003, Nucleic Acids Res..

[37]  L. Krusell,et al.  DNA binding sites recognised in vitro by a knotted class 1 homeodomain protein encoded by the hooded gene, k, in barley (Hordeum vulgare) , 1997, FEBS letters.

[38]  John M. Hancock,et al.  PlantProm: a database of plant promoter sequences , 2003, Nucleic Acids Res..

[39]  Nils Ole Steffens,et al.  Isolation and Analysis of Gene Regulatory Sequences , 2004 .

[40]  Xin Chen,et al.  The TRANSFAC system on gene expression regulation , 2001, Nucleic Acids Res..

[41]  Gary D. Stormo,et al.  Identifying DNA and protein patterns with statistically significant alignments of multiple sequences , 1999, Bioinform..

[42]  Ramana V. Davuluri,et al.  AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors , 2003, BMC Bioinformatics.