Abstract
Chromatin-based mechanisms significantly contribute to the regulation of many developmentally regulated genes, including Notch target genes. After specific ligand binding, the intracellular part of the Notch receptor is cleaved off and translocates to the nucleus, where it binds to the transcription factor CSL (encoded by the RBPJ gene in mammals), in order to activate transcription. In the absence of a Notch signal, CSL represses Notch target genes by recruiting a co-repressor complex. Both NICD co-activator and CSL co-repressor complexes contain chromatin modifiers such as histone acetyltransferases and methyltransferases, which dynamically regulate chromatin marks at Notch target genes.
Here we provide protocols for ChIP (chromatin immunoprecipitation) to analyze the chromatin status of dynamically regulated Notch target genes. Furthermore, an example is presented how to perform a primary analysis of ChIP-Seq data at Notch target genes using the Cistrome platform.
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Acknowledgments
We thank Drs. K. Hein and B.D. Giaimo for critical reading of the manuscript and testing the bioinformatics guide. This work was supported by the Heisenberg program (BO 1639/5-1) of the DFG, the Max-Planck society, and the Excellence Cluster Cardio-Pulmonary System (ECCPS) to T.B. R.L. has been supported by a DFG postdoctoral fellowship (LI 2057/1-1).
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Liefke, R., Borggrefe, T. (2014). Probing the Epigenetic Status at Notch Target Genes. In: Bellen, H., Yamamoto, S. (eds) Notch Signaling. Methods in Molecular Biology, vol 1187. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1139-4_20
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DOI: https://doi.org/10.1007/978-1-4939-1139-4_20
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