Belle A. Moyers1, E. Christopher Partridge1, Mark Mackiewicz1, Michael J. Betti2, Roshan Darji1, Sarah K. Meadows1, Kimberly M. Newberry1, Laurel A. Brandsmeier1, Barbara J. Wold3, Eric M. Mendenhall1 and Richard M. Myers1 1HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA; 2Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA; 3Merkin Institute for Translational Research, California Institute of Technology, Pasadena, California 91125, USA Corresponding authors: rmyershudsonalpha.org, emendenhallhudsonalpha.org Abstract

Transcription factors (TFs) are trans-acting proteins that bind cis-regulatory elements (CREs) in DNA to control gene expression. Here, we analyzed the genomic localization profiles of 529 sequence-specific TFs and 151 cofactors and chromatin regulators in the human cancer cell line HepG2, for a total of 680 broadly termed DNA-associated proteins (DAPs). We used this deep collection to model each TF's impact on gene expression, and identified a cohort of 26 candidate transcriptional repressors. We examine high occupancy target (HOT) sites in the context of three-dimensional genome organization and show biased motif placement in distal-promoter connections involving HOT sites. We also found a substantial number of closed chromatin regions with multiple DAPs bound, and explored their properties, finding that a MAFF/MAFK TF pair correlates with transcriptional repression. Altogether, these analyses provide novel insights into the regulatory logic of the human cell line HepG2 genome and show the usefulness of large genomic analyses for elucidation of individual TF functions.

Footnotes

[Supplemental material is available for this article.]

Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.278205.123.

Freely available online through the Genome Research Open Access option.

Received July 3, 2023. Accepted October 13, 2023.