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Occupancy patterns of 208 DNA-associated proteins in a single human cell type

Partridge, E. Christopher and Chhetri, Surya B. and Prokop, Jeremy W. and Ramaker, Ryne C. and Jansen, Camden S. and Goh, Say-Tar and Mackiewicz, Mark and Newberry, Kimberly M. and Brandsmeier, Laurel A. and Meadows, Sarah K. and Messer, C. Luke and Hardigan, Andrew A. and Dean, Emma C. and Jiang, Shan and Savic, Daniel and Mortazavi, Ali and Wold, Barbara J. and Myers, Richard M. and Mendenhall, Eric M. (2018) Occupancy patterns of 208 DNA-associated proteins in a single human cell type. . (Unpublished) http://resolver.caltech.edu/CaltechAUTHORS:20181128-093527238

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Abstract

Genome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes, but only a small fraction of the >1,600 transcription factors (TFs) encoded in the human genome has been assayed. Here we present data and analyses of ChIP-seq experiments for 208 DNA-associated proteins (DAPs) in the HepG2 hepatocellular carcinoma line, spanning nearly a quarter of its expressed TFs, transcriptional co-factors, and chromatin regulator proteins. The DAP binding profiles classify into major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalog of DNA sequence motifs; 77 factors showed similar motifs to those previously described using in vivo and/or in vitro methods, and 17 yielded novel motifs. We also describe motifs corresponding to other TFs that co-enrich with the primary ChIP target. FOX family motifs are, for example, significantly enriched in ChIP-seq peaks of 37 other DAPs. We show that promoters and enhancers can be discriminated based on motif content and occupancy patterns. This large catalog reveals High Occupancy Target (HOT) regions at which many DAPs associate, although each contains motifs for only a minority of the numerous associated DAPs. These analyses provide a deeper and more complete overview of the gene regulatory networks that define this cell type.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/464800DOIDiscussion Paper
ORCID:
AuthorORCID
Ramaker, Ryne C.0000-0001-8666-4841
Mortazavi, Ali0000-0002-4259-6362
Wold, Barbara J.0000-0003-3235-8130
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. Research reported in this publication was supported by the National Human Genome Research Institute of the National Institutes of Health under Award Number U54HG006998 to R.M.M. and E.M.M.. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. This work was also supported by funds from The HudsonAlpha Institute for Biotechnology. We thank Rosy Nguyen, Dianna Moore, and Megan McEown for their outstanding technical efforts in this study. We thank Brian S. Roberts and Gregory M. Cooper for helpful comments, HudsonAlpha’s Genomic Services Laboratory led by Dr. Shawn Levy for the high-throughput sequencing of much of the data used in this paper, and members of the ENCODE Consortium for public deposition of data generated by other Consortium groups.
Funders:
Funding AgencyGrant Number
NIHU54HG006998
HudsonAlpha Institute for BiotechnologyUNSPECIFIED
Record Number:CaltechAUTHORS:20181128-093527238
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20181128-093527238
Official Citation:Occupancy patterns of 208 DNA-associated proteins in a single human cell type E. Christopher Partridge, Surya B. Chhetri, Jeremy W. Prokop, Ryne C. Ramaker, Camden S. Jansen, Say-Tar Goh, Mark Mackiewicz, Kimberly M. Newberry, Laurel A. Brandsmeier, Sarah K. Meadows, C. Luke Messer, Andrew A. Hardigan, Emma C. Dean, Shan Jiang, Daniel Savic, Ali Mortazavi, Barbara J. Wold, Richard M. Myers, Eric M. Mendenhall bioRxiv 464800; doi: https://doi.org/10.1101/464800
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:91283
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:28 Nov 2018 19:18
Last Modified:28 Nov 2018 19:18

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