Genome-Wide Identification and Characterization of Notch Transcriptional Complex-Binding Sequence Paired Sites in Leukemia Cells
Severson, Eric A.
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CitationSeverson, Eric A. 2016. Genome-Wide Identification and Characterization of Notch Transcriptional Complex-Binding Sequence Paired Sites in Leukemia Cells. Master's thesis, Harvard Medical School.
AbstractNotch transcription complexes (NTCs) drive target gene expression by binding two distinct types of genomic response elements, NTC monomer sites and sequence-paired sites (SPSs) that bind NTC dimers. SPSs are conserved and linked to rapid responses to Notch in a few genes, but their overall contribution to Notch-dependent gene regulation is unknown. To address this issue, we determined the DNA sequence requirements for NTC dimerization using a fluorescence resonance energy transfer (FRET) assay, and applied insights from these in vitro studies to Notch-“addicted” leukemia cells. We find that at least 16% of functional NTC binding sites are SPSs. While originally described in promoters, SPSs are present mainly in enhancers and contribute to regulation of both coding and non-coding RNAs. Our work provides a general method for identifying sequence-paired sites in genome-wide data sets and highlights the widespread role of NTC dimerization in mammalian gene regulation.
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