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Genomic Characterization of the Zinc Transcriptional Regulatory Element Reveals Potential Functional Roles of ZNF658

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Abstract

The zinc transcriptional regulatory element (ZTRE) is a newly reported binding motif for human zinc finger protein ZNF658, which alters gene expression in response to cellular zinc. The ZTRE has two nucleotide components—the palindromic flanking pairs and the bridging “N” bases between these flanks that range in number from 0 to 100. There are 12 pairs of ZTRE flanks (designated A-L). Three thousand five hundred twenty-five genes contain one or more ZTREs − 1000 to + 200 bp from their transcriptional start site (TSS). ZTRE-E is observed at a greater frequency, and ZTRE containing 25 bridging bases are less frequent, within − 200 bp from the TSS. The genes with ZTREs in this range are enriched in processes that may compensate zinc deficiency, while other genes with ZTREs outside this range are enriched in transcriptional activation processes. The division of ZTREs into two groups may imply a dual role of ZNF658, similar to the homologous yeast protein Zap1, via binding to low or high affinity sequences dependent upon cellular zinc. The KLF/Sp1-family binding motif is prevalent within the ZTRE “N” bridging bases, suggesting ZNF658 may compete with Sp1-like transactivators to suppress transcription.

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Funding

This research was partially funded by the University of Georgia Experiment Station Hatch Funds (to AG), the National Institute of Health (R01 GM113242, R01 GM122080), and the National Science Foundation (DMS-1222718, DMS-1438957, DMS-1228288) (to PM).

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  1. Department of Foods and Nutrition, University of Georgia, Athens, GA, USA

    Michael Francis & Arthur Grider

  2. Department of Statistics, University of Georgia, Athens, GA, USA

    Huimin Cheng & Ping Ma

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Correspondence to Arthur Grider.

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Francis, M., Cheng, H., Ma, P. et al. Genomic Characterization of the Zinc Transcriptional Regulatory Element Reveals Potential Functional Roles of ZNF658. Biol Trace Elem Res 192, 83–90 (2019). https://doi.org/10.1007/s12011-019-1650-9

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