Home LiteratureArticle Details
PMID: 12827523 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes.

Functional & integrative genomics ·Vol. 3 ·No. 3 ·2003-07-00 ·Pages 125-34

Sandelin A, Höglund A, Lenhard B, Wasserman WW

Abstract

Dramatic progress in deciphering the regulatory controls in Saccharomyces cerevisiae has been enabled by the fusion of high-throughput genomics technologies with advanced sequence analysis algorithms. Sets of genes likely to function together and with similar expression profiles have been identified in diverse studies. By fusing an advanced pattern recognition algorithm for identification of transcription factor binding sites with a new method for the quantitative comparison of binding properties of transcription factors, we provide an integrated means to move from expression data to biological insights. The Yeast Regulatory Sequence Analysis system, YRSA, combines standard functions with a novel pattern characterization procedure in an intuitive interface designed for use by a broad range of scientists. The features of the system include automated retrieval of user-defined promoter sequences, binding site discovery by pattern recognition, graphical displays of the observed pattern and positions of similar sequences in the specified genes, and comparison of the new pattern against a collection of binding patterns for characterized transcription factors. The comprehensive YRSA system was used to study the regulatory mechanisms of yeast regulons. Analysis of the regulatory controls of a battery of genes induced by DNA damaging agents supports a putative mediating role for the cell-cycle checkpoint regulatory element MCB. YRSA is available at http://yrsa.cgb.ki.se. [YRSA: ancient Scandinavian name meaning old she-bear (Latin Ursus arctos = brown bear/grizzly).]

MeSH Terms
Algorithms Binding Sites Cell Cycle/physiology DNA Damage Multigene Family Promoter Regions, Genetic Saccharomyces cerevisiae/genetics Sequence Analysis, DNA/methods Transcription Factors/metabolism
Chemicals
Transcription Factors
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Sandelin Albin
Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden.
Höglund Annette
Lenhard Boris
Wasserman Wyeth W
References (53)
53 references, click to expand
  1. Regulatory element detection using correlation with expression.
    Nat Genet. 2001 Feb;27(2):167-71 PMID: 11175784
  2. Cell cycle checkpoints: preventing an identity crisis.
    Science. 1996 Dec 6;274(5293):1664-72 PMID: 8939848
  3. Inferring subnetworks from perturbed expression profiles.
    Bioinformatics. 2001;17 Suppl 1:S215-24 PMID: 11473012
  4. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.
    J Mol Biol. 1998 Sep 4;281(5):827-42 PMID: 9719638
  5. Genome-wide location and function of DNA binding proteins.
    Science. 2000 Dec 22;290(5500):2306-9 PMID: 11125145
  6. DNA binding sites: representation and discovery.
    Bioinformatics. 2000 Jan;16(1):16-23 PMID: 10812473
  7. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
    Mol Biol Cell. 1998 Dec;9(12):3273-97 PMID: 9843569
  8. Functional organization of the yeast proteome by systematic analysis of protein complexes.
    Nature. 2002 Jan 10;415(6868):141-7 PMID: 11805826
  9. A web site for the computational analysis of yeast regulatory sequences.
    Yeast. 2000 Jan 30;16(2):177-87 PMID: 10641039
  10. Separating real motifs from their artifacts.
    Bioinformatics. 2001;17 Suppl 1:S30-8 PMID: 11472990
  11. Life with 6000 genes.
    Science. 1996 Oct 25;274(5287):546, 563-7 PMID: 8849441
  12. The DNA repair genes RAD54 and UNG1 are cell cycle regulated in budding yeast but MCB promoter elements have no essential role in the DNA damage response.
    Nucleic Acids Res. 1995 Jun 25;23 (12 ):2147-52 PMID: 7610042
  13. A comprehensive two-hybrid analysis to explore the yeast protein interactome.
    Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4569-74 PMID: 11283351
  14. The DNA replication and damage checkpoint pathways induce transcription by inhibition of the Crt1 repressor.
    Cell. 1998 Sep 4;94(5):595-605 PMID: 9741624
  15. Adaptability at the protein-DNA interface is an important aspect of sequence recognition by bZIP proteins.
    Proc Natl Acad Sci U S A. 1993 May 15;90(10):4513-7 PMID: 8506292
  16. Genome-wide discovery of transcriptional modules from DNA sequence and gene expression.
    Bioinformatics. 2003;19 Suppl 1:i273-82 PMID: 12855470
  17. Discovering regulatory and signalling circuits in molecular interaction networks.
    Bioinformatics. 2002;18 Suppl 1:S233-40 PMID: 12169552
  18. Information content of binding sites on nucleotide sequences.
    J Mol Biol. 1986 Apr 5;188(3):415-31 PMID: 3525846
  19. The nuclear hormone receptor gene superfamily.
    Annu Rev Med. 1995;46:443-53 PMID: 7598477
  20. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae.
    J Mol Biol. 2000 Mar 10;296(5):1205-14 PMID: 10698627
  21. Fluorescence-based expression monitoring using microarrays.
    Methods Enzymol. 1999;306:3-18 PMID: 10432445
  22. The role of DSC1 components cdc10+, rep1+ and rep2+ in MCB gene transcription at the mitotic G1-S boundary in fission yeast.
    Curr Genet. 2001 Dec;40(4):251-9 PMID: 11795845
  23. MIPS: a database for genomes and protein sequences.
    Nucleic Acids Res. 2002 Jan 1;30(1):31-4 PMID: 11752246
  24. Recognition of multiple patterns of DNA sites by Drosophila homeodomain protein Bicoid.
    J Biochem. 1999 Apr;125(4):809-17 PMID: 10101296
  25. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p.
    Mol Biol Cell. 2001 Oct;12(10):2987-3003 PMID: 11598186
  26. Genome-wide studies on the nuclear PDR3-controlled response to mitochondrial dysfunction in yeast.
    FEBS Lett. 2002 Mar 27;515(1-3):25-8 PMID: 11943188
  27. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy.
    Nat Genet. 1996 Dec;14(4):450-6 PMID: 8944025
  28. TFBS: Computational framework for transcription factor binding site analysis.
    Bioinformatics. 2002 Aug;18(8):1135-6 PMID: 12176838
  29. An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences.
    Proteins. 1990;7(1):41-51 PMID: 2184437
  30. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.
    Science. 1993 Oct 8;262(5131):208-14 PMID: 8211139
  31. SCPD: a promoter database of the yeast Saccharomyces cerevisiae.
    Bioinformatics. 1999 Jul-Aug;15(7-8):607-11 PMID: 10487868
  32. Discovery of novel transcription factor binding sites by statistical overrepresentation.
    Nucleic Acids Res. 2002 Dec 15;30(24):5549-60 PMID: 12490723
  33. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
    Nature. 2002 Jan 10;415(6868):180-3 PMID: 11805837
  34. Rich probabilistic models for gene expression.
    Bioinformatics. 2001;17 Suppl 1:S243-52 PMID: 11473015
  35. New mode of DNA binding of multi-zinc finger transcription factors: deltaEF1 family members bind with two hands to two target sites.
    EMBO J. 1999 Sep 15;18(18):5073-84 PMID: 10487759
  36. Functional profiling of the Saccharomyces cerevisiae genome.
    Nature. 2002 Jul 25;418(6896):387-91 PMID: 12140549
  37. Transcription. Of chips and ChIPs.
    Science. 2002 Apr 26;296(5568):666-9 PMID: 11976432
  38. Searching databases of conserved sequence regions by aligning protein multiple-alignments.
    Nucleic Acids Res. 1996 Oct 1;24(19):3836-45 PMID: 8871566
  39. The Bioperl toolkit: Perl modules for the life sciences.
    Genome Res. 2002 Oct;12(10):1611-8 PMID: 12368254
  40. Predicting the sub-cellular location of proteins from text using support vector machines.
    Pac Symp Biocomput. 2002;:374-85 PMID: 11928491
  41. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.
    Nature. 2000 Feb 10;403(6770):623-7 PMID: 10688190
  42. Transcriptional regulatory networks in Saccharomyces cerevisiae.
    Science. 2002 Oct 25;298(5594):799-804 PMID: 12399584
  43. A general method applicable to the search for similarities in the amino acid sequence of two proteins.
    J Mol Biol. 1970 Mar;48(3):443-53 PMID: 5420325
  44. Approaches to the automatic discovery of patterns in biosequences.
    J Comput Biol. 1998 Summer;5(2):279-305 PMID: 9672833
  45. Quantitative discrimination of MEF2 sites.
    Mol Cell Biol. 1996 Jan;16(1):437-41 PMID: 8524326
  46. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.
    Nature. 2001 Jan 25;409(6819):533-8 PMID: 11206552
  47. Exploring genetic regulatory networks in metazoan development: methods and models.
    Physiol Genomics. 2002 Sep 03;10(3):131-43 PMID: 12209016
  48. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.
    Genome Res. 2001 Jul;11(7):1175-86 PMID: 11435399
  49. A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes.
    J Comput Biol. 2002;9(2):447-64 PMID: 12015892
  50. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.
    Nat Biotechnol. 1998 Oct;16(10 ):939-45 PMID: 9788350
  51. A genome-wide transcriptional analysis of the mitotic cell cycle.
    Mol Cell. 1998 Jul;2(1):65-73 PMID: 9702192
  52. Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles.
    Bioinformatics. 2001;17 Suppl 1:S49-55 PMID: 11472992
  53. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
Article Info
Journal
Functional & integrative genomics
Abbr.
Funct Integr Genomics
ISSN
1438-793X
DOI
10.1007/s10142-003-0086-6
Published
2003-07-00
Epub
2003-00-25
Pages
125-34
Language
English
Region
Germany
NLM ID
100939343
Subset
IM
External Links
PubMed source DOI: 10.1007/s10142-003-0086-6 View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2