Genome-wide census of ATF4 binding sites and functional profiling of trait-associated genetic variants overlapping ATF4 binding motifs
Open Access
- 31 October 2023
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS Genetics
- Vol. 19 (10) , e1011014
Abstract
Activating Transcription Factor 4 (ATF4) is an important regulator of gene expression in stress responses and developmental processes in many cell types. Here, we catalogued ATF4 binding sites in the human genome and identified overlaps with trait-associated genetic variants. We probed these genetic variants for allelic regulatory activity using a massively parallel reporter assay (MPRA) in HepG2 hepatoma cells exposed to tunicamycin to induce endoplasmic reticulum stress and ATF4 upregulation. The results revealed that in the majority of cases, the MPRA allelic activity of these SNPs was in agreement with the nucleotide preference seen in the ATF4 binding motif from ChIP-Seq. Luciferase and electrophoretic mobility shift assays in additional cellular models further confirmed ATF4-dependent regulatory effects for the SNPs rs532446 (GADD45A intronic; linked to hematological parameters), rs7011846 (LPL upstream; myocardial infarction), rs2718215 (diastolic blood pressure), rs281758 (psychiatric disorders) and rs6491544 (educational attainment). CRISPR-Cas9 disruption and/or deletion of the regulatory elements harboring rs532446 and rs7011846 led to the downregulation of GADD45A and LPL, respectively. Thus, these SNPs could represent examples of GWAS genetic variants that affect gene expression by altering ATF4-mediated transcriptional activation.Keywords
Funding Information
- Eesti Teadusagentuur (PRG1475)
- Eesti Teadusagentuur (PUT269)
- Eesti Teadusagentuur (IUT34-4)
- European Molecular Biology Laboratory (VLTAT18559)
This publication has 100 references indexed in Scilit:
- ER-stress-induced transcriptional regulation increases protein synthesis leading to cell deathNature Cell Biology, 2013
- DISC1–ATF4 transcriptional repression complex: dual regulation of the cAMP-PDE4 cascade by DISC1Molecular Psychiatry, 2013
- An integrated encyclopedia of DNA elements in the human genomeNature, 2012
- The accessible chromatin landscape of the human genomeNature, 2012
- Brain-Specific Disruption of the eIF2α Kinase PERK Decreases ATF4 Expression and Impairs Behavioral FlexibilityCell Reports, 2012
- The eIF2 kinase PERK and the integrated stress response facilitate activation of ATF6 during endoplasmic reticulum stressMolecular Biology of the Cell, 2011
- The GCN2‐ATF4 pathway is critical for tumour cell survival and proliferation in response to nutrient deprivationThe EMBO Journal, 2010
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell IdentitiesMolecular Cell, 2010
- Elevated ATF4 Expression, in the Absence of Other Signals, Is Sufficient for Transcriptional Induction via CCAAT Enhancer-binding Protein-activating Transcription Factor Response ElementsJournal of Biological Chemistry, 2009
- An Integrated Stress Response Regulates Amino Acid Metabolism and Resistance to Oxidative StressMolecular Cell, 2003