Abstract
Run-on and sequencing assays like GRO-seq, PRO-seq, and ChRO-seq allow for joint profiling of transcription activity of transcriptional regulatory elements (TREs), i.e., promoters and active enhancers, and target genes. Variation in biological conditions, such as treated vs. control, results in changes in the activity of transcription factors (TFs), which induces concerted changes in TREs and target genes. By modeling the differences between two biological conditions, we developed the computational pipeline known as tfTarget that predicts a set of putative TREs and target genes responding to each TF under the biological condition of interest. In this chapter, we demonstrate the use of the new web-based tfTarget in mapping transcription regulation using run-on sequencing data.
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Acknowledgments
Work in this publication was supported by R01-HG009309 (NHGRI) to C.G.D.
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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
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Wang, N., Wang, Z., Danko, C.G., Chu, T. (2023). Mapping Transcription Regulation with Run-on and Sequencing Data Using the Web-Based tfTarget Gateway. In: Simoes-Costa, M. (eds) DNA-Protein Interactions. Methods in Molecular Biology, vol 2599. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2847-8_15
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DOI: https://doi.org/10.1007/978-1-0716-2847-8_15
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