Lin Lin, Benjamin Holmes, Max W. Shen, Darnell Kammeron, Niels Geijsen et al.
Gene expression is controlled by the collective binding of transcription factors to cis-regulatory regions. Deciphering gene-centered regulatory networks is vital to understanding and controlling gene misexpression in human disease; however, systematic approaches to uncovering regulatory networks have been lacking. Here we present high-throughput interrogation of gene-centered activation networks (HIGAN), a pipeline that employs a suite of multifaceted genomic approaches to connect upstream signaling inputs, trans-acting TFs, and cis-regulatory elements. We apply HIGAN to understand the aberrant activation of the cytidine deaminase APOBEC3B, an intrinsic source of cancer hypermutation. We reveal that nuclear factor κB (NF-κB) and AP-1 pathways are the most salient trans-acting inputs, with minor roles for other inflammatory pathways. We identify a cis-regulatory architecture dominated by a major intronic enhancer that requires coordinated NF-κB and AP-1 activity with secondary inputs from distal regulatory regions. Our data demonstrate how integration of cis and trans genomic screening platforms provides a paradigm for building gene-centered regulatory networks.
Lin Lin, Benjamin Holmes, Max W. Shen, Darnell Kammeron, Niels Geijsen, David K. Gifford, Richard I. Sherwood. Comprehensive Mapping of Key Regulatory Networks that Drive Oncogene Expression. 2020-11-24. https://doi.org/10.1016/j.celrep.2020.108426
An episomal mutant-tiled STARR-seq library tested 150-bp wild-type oligos and internal-deletion constructs spanning 91 prioritized APOBEC3B regulatory regions plus two negative-control regions. HCT116 cells were assayed with DMSO vehicle in two biological replicates.
An episomal mutant-tiled STARR-seq library tested 150-bp wild-type oligos and internal-deletion constructs spanning 91 prioritized APOBEC3B regulatory regions plus two negative-control regions. U2OS cells were assayed in two biological replicates under the basal condition.
An episomal mutant-tiled STARR-seq library tested 150-bp wild-type oligos and internal-deletion constructs spanning 91 prioritized APOBEC3B regulatory regions plus two negative-control regions. HCT116 cells were assayed after 2 µM gemcitabine treatment in two biological replicates.
An episomal mutant-tiled STARR-seq library tested 150-bp wild-type oligos and internal-deletion constructs spanning 91 prioritized APOBEC3B regulatory regions plus two negative-control regions. DLD-1 cells were assayed in two biological replicates under the basal condition.
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