A temporal hierarchy underpins the transcription factor–DNA interactome of the maize UPR

Ko, Dae Kwan; Brandizzi, Federica

doi:10.1111/tpj.15044

Title: A temporal hierarchy underpins the transcription factor–DNA interactome of the maize UPR

Journal Article · Sat Oct 24 00:00:00 EDT 2020 · The Plant Journal

DOI:https://doi.org/10.1111/tpj.15044· OSTI ID:1764725

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Michigan State Univ., East Lansing, MI (United States)

Summary Adverse environmental conditions reduce crop productivity and often increase the load of unfolded or misfolded proteins in the endoplasmic reticulum (ER). This potentially lethal condition, known as ER stress, is buffered by the unfolded protein response (UPR), a set of signaling pathways designed to either recover ER functionality or ignite programmed cell death. Despite the biological significance of the UPR to the life of the organism, the regulatory transcriptional landscape underpinning ER stress management is largely unmapped, especially in crops. To fill this significant knowledge gap, we performed a large‐scale systems‐level analysis of the protein–DNA interaction (PDI) network in maize ( Zea mays ). Using 23 promoter fragments of six UPR marker genes in a high‐throughput enhanced yeast one‐hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR. We established a temporal hierarchy of TF binding to gene promoters within the same family as well as across different families of TFs. Cistrome analysis revealed the dynamic activities of a variety of cis ‐regulatory elements (CREs) in ER stress‐responsive gene promoters. By integrating the cistrome results into a TF network analysis, we mapped a subnetwork of TFs associated with a CRE that may contribute to UPR management. Finally, we validated the role of a predicted network hub gene using the Arabidopsis system. The PDIs, TF networks, and CREs identified in our work are foundational resources for understanding transcription‐regulatory mechanisms in the stress responses and crop improvement.

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Research Organization:: Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States); Michigan State Univ., East Lansing, MI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); Michigan State Univ.; National Science Foundation Plant Genome Research Program; USDOE Office of Science (SC), Biological and Environmental Research (BER); National Inst. of Health

Grant/Contract Number:: SC0018409; FG02-91ER20021; MICL02598; IOS 1444339; R35GM136637

OSTI ID:: 1764725

Alternate ID(s):: OSTI ID: 1787366

Journal Information:: The Plant Journal, Vol. 105, Issue 1; ISSN 0960-7412

Publisher:: Society for Experimental BiologyCopyright Statement

Country of Publication:: United States

Language:: English

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