Identification in silico of putative damage responsive elements (DRE) in promoter regions of the yeast genome

Genetics and Molecular Biology

Volumn 28, Issue 4, 2005, Pages 814-820

  de Santana Silva, Walkiria Luckwu ^a   de Oliveira Cavalcanti, Andre Ricardo ^a   Guimarães, Katia Silva ^a   de Morais Jr , Marcos Antonio ^b  

^a FEDERAL UNIVERSITY OF PERNAMBUCO   (Brazil)

^b DEPARTAMENTO DE MICOLOGIA   (Brazil)

Author keywords

DNA binding site; DNA repair; Gene promoter; Gene regulation; Transfac; Weight matrix

Indexed keywords

FUNGAL DNA; MUTAGENIC AGENT; REGULATOR PROTEIN;

ARTICLE; BINDING SITE; COMPUTER MODEL; DNA REPAIR; FUNGAL GENETICS; GENE INDUCTION; GENETIC DATABASE; GENETIC REGULATION; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PROMOTER REGION; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 31444454347     PISSN: 14154757     EISSN: 16784685     Source Type: Journal    
DOI: 10.1590/s1415-47572005000500025     Document Type: Article

References (27)

1. Dong YX, Sueda S , Nikawa J and Kondo H (2004) Characterization of the products of the genes SNO1 and SNZ1 involved in pyridoxine synthesis in Saccharomyces cerevisiae. Eur J Biochem 271:745-52.
2. Elledge SJ and Davis RW (1989) Identification of the DNA damage responsive element of RNR2 and evidence that four distinct cellular factors bind it. Mol Cell Biol 9:5373-5386.
3. Errede B and Ammerer G (1989) STE12, a protein involved in cell-type-specific transcription and signal transduction in yeast, is part of protein-DNA complexes. Genes Develop 3:1349-1361.
4. Ettwiller LM, Rung J and Birney E (2003) Discovering novel cis-regulatory motifs using regulatory networks. Genome Res 13:883-895.
5. Friedberg EC (1991) Yeast genes involved in DNA repair process: New looks on old faces. Mol Microbiol 5:2303-2310.
6. Gasch AP, Huang M, Metzner S, Botstein D, Elledge SJ and Brown PO (2001) Genomic expression responses to DNA-damage agents and the regulatory role of the yeast ATR homolog Meclp. Mol Cell Biol 12:2987-3003.
7. Harrison H and DeLisi C (2001) Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae. Bioinformatics 18:1289-1296.
8. Henriques JAP and Brendel M (1990) The role of PSO and SNM genes in DNA repair of the yeast Saccharomyces cerevisiae. Curr Genet 18:387-393.
9. Hughes JD, Estep PW, Tavazoie S and Church GM (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296:1205-1214.
10. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M and Brown PO (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409:533-538.
11. Jelinsky S, Estep P, Church G and Samson L (2000) Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: RPN4 links base excision repair with proteasomes. Mol Cell Biol 20:8157-8167.
12. Kiser GL and Weinert TA (1996) Distinct roles of yeast MEC and RAD checkpoint genes in transcriptional induction after DNA damage and implications for function. Mol Cell Biol 7:703-718.
13. Lowndes NF and Murguia JR (2000) Sensing and responding to DNA damage. Curr Opin Genet Dev 10:17-25.
14. McClanahan T and McEntee K (1984) Specific transcripts are elevated in Saccharomyces cerevisiae in response to DNA damage. Mol Cell Biol 4:2356-2363.
15. Mercier G, Denis Y, Marc P, Picard L and Dutriex M (2001) Transcriptional induction of repair genes during slowing of replication in irradiated Saccharomyces cerevisiae. Mut Res 487:157-172.
16. Quandt K, Frech K, Karas H, Wingender E and Werner T (1995) MatInd and MatInspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucl Acids Res 23:4878-4884.
17. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP and Young RA (2000) Genome-wide location and function of DNA binding proteins. Science 290:2306-2309.
18. Ruby SW and Szostak JW (1985) Specific Saccharomyces cerevisiae genes are expressed in response to DNA-damaging agents. Mol Cell Biol 5:75-84.
19. Sakurai H and Fukasawa T (2001) A novel domain of the yeast heat shock factor that regulates its activation function. Biochem Biophys Res Common 285:696-701.
20. Siede W and Friedberg EC (1992) Regulation of the yeast RAD2 gene: DNA damage-dependent induction correlates with protein binding to regulatory sequences and their deletion influences survival. Mo Gen Genet 232:247-256.
21. Simon JR, Treger JM and McEntee K (1998). Multiple independent regulatory pathways control UBI4 expression after heat shock in Saccharomyces cerevisiae. Mol Microbiol 31:823-832.
22. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ and Church GM (1999) Systematic determination of genetic network architecture. Nat Genet 22:281-285.
23. Treger JM, Schmitt AP, Simon JR and McEntee K (1998). Transcriptional factor mutations reveal regulatory complexities of heat shock and newly identified stress genes in Saccharomyces cerevisiae. J Biol Chem 273:26875-26879.
24. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Prüß M, Reuter I and Schacherer F (2000) TRANSFAC: An integrated system for gene expression regulation. Nucl Acids Res 28:316-319.
25. Wolter R, Siede W and Brendel M (1996) Regulation of SNM1, an inducible Saccharomyces cerevisiae gene required for repair of DNA cross-links. Mol Gen Genet 250:162-168.
26. Xiao W, Singh KK, Chen B and Samson L (1993) A common element involved in transcriptional regulation of two DAN alkylation repairgenes (MAG and MGTI) of Saccharomyces cerevisiae. Mol Cell Biol 13:7213-7221.
27. Zhu J and Zhang MQ (1999) SCPD: A promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15:607-611.