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Review
. 2006 Sep;18(9):2101-11.
doi: 10.1105/tpc.105.037572.

Unraveling the dynamic transcriptome

Siobhan M Brady  1 , Terri A Long, Philip N Benfey
Affiliations
Review

Unraveling the dynamic transcriptome

Siobhan M Brady et al. Plant Cell. 2006 Sep.
No abstract available

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Figures

Figure 1.
Figure 1.
Elucidation of the Transcriptional Regulatory Code under Drought Conditions. Clustering analysis of microarrays identifies a series of transcription factors that are upregulated or downregulated in response to mild and severe drought. (A) Integration of data to determine what upstream regulators act to control the expression of these transcription factors (TF). Bioinformatic analysis, analysis of phylogenetic conservation between upstream regulatory sequences, and transcription factor binding data by chromatin immunoprecipation are integrated to identify transcription factor binding sites present in the upstream sequences of each transcription factor. The resulting binding site architecture provides clues to its regulatory logic. (A) A binding site motif for a single regulator suggests a single input. (B) A repetitive binding site motif suggests increased binding strength of the transcription factor or the potential for a graded transcriptional response. (C) Multiple regulator architecture suggests combinatorial logic. (D) Co-occurring regulator architecture suggests that these transcriptional regulators may interact together. (B) Analysis of binding conditions provides information about the downstream targets of a regulator and the behavior of a regulator. Microarray analysis coupled to chromatin immunoprecipitation is used to identify targets of two of the transcription factors that were identified as being upregulated under drought conditions. Transcription factor A shows condition-invariant behavior. This transcription factor binds to the same set of promoters in both drought conditions. Transcription factor B shows condition-expanded behavior. The regulator binds to a core set of target promoters under mild drought and binds to an expanded set of promoters under severe drought. (Based on Harbison et al., 2004.)
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