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Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

Abstract

The ability of a transcription factor (TF) to regulate its targets is modulated by a variety of genetic and epigenetic mechanisms, resulting in highly context-dependent regulatory networks. However, high-throughput methods for the identification of proteins that affect TF activity are still largely unavailable. Here we introduce an algorithm, modulator inference by network dynamics (MINDy), for the genome-wide identification of post-translational modulators of TF activity within a specific cellular context. When used to dissect the regulation of MYC activity in human B lymphocytes, the approach inferred novel modulators of MYC function, which act by distinct mechanisms, including protein turnover, transcription complex formation and selective enzyme recruitment. MINDy is generally applicable to study the post-translational modulation of mammalian TFs in any cellular context. As such it can be used to dissect context-specific signaling pathways and combinatorial transcriptional regulation.

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Figure 1: MINDy algorithm.
Figure 2: STK38 regulates the stability of MYC protein.
Figure 3: BHLHB2 antagonizes MYC activity in B cells.
Figure 4: MEF2B enhances MYC activity via protein-protein interaction.
Figure 5: MYC selectively recruits HDAC1 to its targets as co-repressor.

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Acknowledgements

This work was supported by the US National Cancer Institute (R01CA109755), the National Institute of Allergy and Infectious Diseases (R01AI066116) and the National Centers for Biomedical Computing NIH Roadmap Initiative (U54CA121852). I.N. was supported in part by the National Institute for General Medical Sciences (R21GM080216). A.A.M. was supported by an IBM PhD fellowship.

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Contributions

K.W. and A.C. designed the algorithm and the computational analysis procedures. I.N. and A.A.M. assisted in algorithm design and computational analysis. M.S. experimentally validated BHLHB2, MEF2B and HDAC1. B.C.B. experimentally validated STK38. M.J.A. and W.K.L. performed the analysis and validation of TFs other than MYC. I.N. and K.W. studied the information theoretic properties of the algorithm. P.R., Q.S., K.B. and U.K. assisted with the experimental validation and microarray expression profile generation. A.C., R.D.-F., M.S., BC.B., K.W. and K.B. designed the experimental assays. A.C., R.D.-F., K.W. and M.S. wrote the manuscript.

Corresponding author

Correspondence to Andrea Califano.

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Competing interests

A.C. is a cofounder of Therasis, a company engaged in the discovery of combination therapy for cancer using systems biology approaches, and W.K.L. is currently employed by Therasis. MINDy is one of several algorithms that the company has licensed from Columbia University.

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Wang, K., Saito, M., Bisikirska, B. et al. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol 27, 829–837 (2009). https://doi.org/10.1038/nbt.1563

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