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Epioncogene Networks: Identification of Epigenomic and Transcriptomic Cooperation by Multi-omics Integration of ChIP-Seq and RNA-Seq Data

  • Fabian Volker Filipp
Chapter
Part of the RNA Technologies book series (RNATECHN)

Abstract

Next generation sequencing and systems biology have changed our understanding of oncogenesis. Master regulators at the transcriptional and epigenomic level have the ability to affect how an entire network of cancer genes behaves, and thereby taking on an oncogenic role. Further, epigenetic factors cooperate and team up with transcription factors to control specific gene target networks. Transcriptomics in combination with epigenomic profiling and measurement of chromatin accessibility enables global detection of epigenetic modifications and characterization of transcriptional and epigenetic footprints. Chromatin remodelers and transcription factors are in close communication via recognition of posttranslational histone modifications, DNA methylation marks, and sequence motifs to coordinate dynamic exchange of chromatin between open transcriptionally active conformations and compacted silences ones. Integration of complementary high-throughput sequencing platforms (HiC, DNAseI-Seq, MNase-Seq, FAIRE-Seq, ATAC-Seq, ChIP-Seq, ChIA-PET, TBS-Seq, WGBS-Seq, RNA-Seq, GRID-Seq) including chromatin higher-order structures, DNase hypersensitive sites, chromatin accessibility, histone modification, chromatin binding, and DNA methylation enables identification of cooperation and gene target networks. In cancer, due to the ability to team up with transcription factors, epigenetic factors concert mitogenic and metabolic gene networks claiming the role of a cancer master regulators or epioncogenes.

Keywords

ATAC-Seq Cancer systems biology ChIA-PET ChIP-Seq Chromatin accessibility Coactivation Cooperation CpG DNAseI-Seq Epigenetics Epigenome Epigenomics Epioncogene FAIRE-Seq Gene set enrichment GRID-Seq HAT HDAC HiC Histone modification KDM KMT Master regulator MNase-Seq Motif enrichment Multi-omics Omics Precision medicine PRMT Regulome Resistance Rewiring RNA-Seq Target gene TBS-Seq Transcription factor target Transcriptomics Upstream regulator WGBS-Seq 

Notes

Acknowledgements

The power of systems biology comprises that information content of a network is greater than the sum of all individual nodes. The same principle applies to a team and highlights why teamwork is so valuable. To all students of the Systems Biology and Cancer Metabolism Laboratory, who taught me about friendship, selflessness, and—above all—unwavering loyalty. This work on cancer systems biology is generously supported by the National Institutes of Health and the National Science Foundation. F.V.F. is grateful for the support of grants CA154887 from the National Institutes of Health, National Cancer Institute, CRN-17-427258 by the University of California, Office of the President, Cancer Research Coordinating Committee, the Goethe Institute, Washington, DC, USA, and the Federal Foreign Office, Berlin, Germany.

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© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Systems Biology and Cancer MetabolismUniversity of California MercedMercedUSA

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