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Transcription regulation: a genomic network

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The transcriptional regulatory system plays a central role in directing gene expression changes in response to internal and external stimuli. In this talk, I will present our group's computational studies on transcription regulation in yeast, ranging from large-scale experimental studies to computational analyses of regulatory networks. In the first half I will introduce results from ChIp-chip experiments that identify genome-wide DNA-binding sites of transcription factors, particularly focusing on the cell cycle regulatory system. In the second half I will discuss how these observations fit in with the idea of a genomic regulatory network, and examine the effects of such networks on gene expression levels. Finally, I will introduce the concept of dynamic network usage in the context of transcription regulation, and how specific regulatory pathways are employed to bring about these transitions.

References

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    Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M: Genomic analysis of regulatory network dynamics. Nature, in press.

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    Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA: Structure and evolution of transcriptional regulatory networks. Current Opinions in Structural Biology 14: 283–291. 10.1016/j.sbi.2004.05.004

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    Yu H, Luscombe NM, Qian J, Gerstein M: Genome-wide analysis of gene expression relationships in transcriptional regulatory networks. Trend in Genetics 19: 422–427. 10.1016/S0168-9525(03)00175-6

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    Horak CE, Luscombe NM, Qian J, Bertone P, Piccirillo S, Gerstein M, Snyder M: Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes and Development 2002, 16: 3017–3033. 10.1101/gad.1039602

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Correspondence to Nicholas Luscombe.

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Luscombe, N. Transcription regulation: a genomic network. BMC Bioinformatics 6, S1 (2005). https://doi.org/10.1186/1471-2105-6-S3-S1

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Keywords

  • Regulatory Network
  • Gene Expression Level
  • Regulatory System
  • External Stimulus
  • Computational Study