Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step-by-Step Guided Analysis.
Transcriptional regulation is one of the key steps in the control of gene expression, with huge impact on the survival, adaptation, and fitness of all organisms. However, it is becoming increasingly clear that transcriptional regulation is far more complex than initially foreseen. In model organisms such as the yeast Saccharomyces cerevisiae evidence has been piling up showing that the expression of each gene can be controlled by several transcription factors, in the close dependency of the environmental conditions. Furthermore, transcription factors work in intricate networks, being themselves regulated at the transcriptional, post-transcriptional, and post-translational levels, working in cooperation or antagonism in the promoters of their target genes.In this chapter, a step-by-step guide using the YEASTRACT database is provided, for the prediction and ranking of the transcription factors required for the regulation of the expression a single gene and of a genome-wide response. These analyses are illustrated with the regulation of the PDR18 gene and of the transcriptome-wide changes induced upon exposure to the herbicide 2,4-Dichlorophenoxyacetic acid (2,4-D), respectively. The newest potentialities of this information system are explored, and the various results obtained in the dependency of the querying criteria are discussed in terms of the knowledge gathered on the biological responses considered as case studies.
Biological Sciences Research Group, Department of Bioengineering, Instituto Superior Técnico, IBB - Institute for Bioengineering and Biosciences, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal. mnpct@tecnico.ulisboa.pt.
Miguel C
MC
Teixeira
INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisbon, Portugal.
Pedro T
PT
Monteiro
Biological Sciences Research Group, Department of Bioengineering, Instituto Superior Técnico, IBB - Institute for Bioengineering and Biosciences, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
Isabel
I
Sá-Correia
D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D023281:Genomics; D020407:Internet; D012441:Saccharomyces cerevisiae / Q000235:genetics; D014158:Transcription, Genetic
Saccharomyces cerevisiae; Transcription regulatory networks; Transcriptional regulation prediction; Transcriptomic data analysis; YEASTRACT