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ATAC-seq Reveals Global Changes in Transcription Factor Activity Upon Perturbation of Cellular Zinc

ABSTRACT: Zinc (Zn2+) is an essential metal required in approximately 10% of the human proteome. Of this, nearly half of these proteins are involved in transcription. Little is known on how these proteins get their Zn2+, but it is becoming increasingly clear in the literature that Zn2+ may function in some capability as an intracellular messenger. Here, we sought to profile the effect that Zn2+ has on global transcription. Using ATAC-seq, we observed broad changes in chromatin accessibility when Zn2+ was both increased and depleted. These changes in chromatin accessibility correlated with changes in the enrichment of hundreds of transcription factors, many of which are Zn2+ finger transcription factors. To validate whether these changes in motif enrichment correlate with changes in transcription factor occupancy, we selected p53 as a candidate to follow up on. Using previously published p53 ChIP-seq datasets and new nascent transcription datasets, we identified high-probability p53 binding sites to validate using ChIP-qPCR. We found that the global changes in p53 motif enrichment correlated with our ChIP-qPCR results but some targets yielded local accessibility differences, a reminder that genomics datasets require experimental follow-ups before generalizations can be made. We believe that the experimental and computational workflow presented here will allow researchers to use ATAC-seq in conjunction with publicly available datasets as a relative starting point for studying transcription factor occupancy in the future.

ORGANISM(S): Homo sapiens

PROVIDER: GSE212763 | GEO | 2023/09/01

REPOSITORIES: GEO

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Project description:Determining mechanism-based biomarkers that distinguish adaptive and adverse cellular processes is critical to understanding the health effects of environmental exposures. Shifting from in vivo, low-throughput toxicity studies to high-throughput screening (HTS) paradigms and risk assessment based on in vitro and in silico testing requires utilizing toxicity pathway information to distinguish adverse outcomes from recoverable adaptive events. Little work has focused on oxidative stresses in human airway for the purposes of predicting adverse responses. We hypothesize that early gene expression-mediated molecular changes could be used to delineate adaptive and adverse responses to environmentally-based perturbations. Here, we examined cellular responses of the tracheobronchial airway to zinc (Zn) exposure, a model oxidant. Airway derived BEAS-2B cells exposed to 2–10 µM Zn2+ elicited concentration- and time-dependent cytotoxicity. Normal, adaptive, and cytotoxic Zn2+ exposure conditions were determined with traditional apical endpoints, and differences in global gene expression around the tipping point of the responses were used to delineate underlying molecular mechanisms. Bioinformatic analyses of differentially expressed genes indicate early enrichment of stress signaling pathways, including those mediated by the transcription factors p53 and NRF2. After 4 h, 154 genes were differentially expressed (p <0.01) between the adaptive and cytotoxic Zn2+ concentrations. Nearly 40% of the biomarker genes were related to the p53 signaling pathway with 30 genes identified as likely direct targets using a database of p53 ChIP-seq studies. Despite similar p53 activation profiles, these data revealed widespread dampening of p53 and NRF2-related genes as early as 4 h after exposure at higher, unrecoverable Zn2+ exposures. Thus, in our model early increased activation of stress response pathways indicated a recoverable adaptive event. Overall, this study highlights the importance of characterizing molecular mechanisms around the tipping point of adverse responses to better inform HTS paradigms.

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ATAC-seq Reveals Global Changes in Transcription Factor Activity Upon Perturbation of Cellular Zinc

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