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Methods Mol Biol. 2012;786:131-49. doi: 10.1007/978-1-61779-292-2_8.

Genome-wide dissection of posttranscriptional and posttranslational interactions.

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Joint Centers for Systems Biology, Columbia University, New York, NY, USA.


Transcriptional interactions in the cell are modulated by a variety of posttranscriptional and posttranslational mechanisms that make them highly dependent on the molecular context of the specific cell. These include, among others, microRNA-mediated control of transcription factor (TF) mRNA translation and degradation, transcription factor activation by phosphorylation and acetylation, formation of active complexes with one or more cofactors, and mRNA/protein degradation and stabilization processes. Thus, the ability of a transcription factor to regulate its targets depends on a variety of genetic and epigenetic mechanisms, resulting in highly context-dependent regulatory networks. In this chapter, we introduce a step-by-step guide on how to use the MINDy systems biology algorithm (Modulator Inference by Network Dynamics) that we recently developed, for the genome-wide, context-specific identification of posttranscriptional and posttranslational modulators of transcription factor activity.

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