Temporal clustering of gene expression links the metabolic transcription factor HNF4α to the ER stress-dependent gene regulatory network

Abstract

The unfolded protein response (UPR) responds to disruption of endoplasmic reticulum (ER) function by initiating signaling cascades that ultimately culminate in extensive transcriptional regulation. Classically, this regulation includes genes encoding ER chaperones, ER-associated degradation factors, and others involved in secretory protein folding and processing, and is carried out by the transcriptional activators that are produced as a consequence of UPR activation. However, up to half of the mRNAs regulated by ER stress are downregulated rather than upregulated, and the mechanisms linking ER stress and UPR activation to mRNA suppression are poorly understood. To begin to address this issue, we used a “bottom-up” approach to study the metabolic gene regulatory network controlled by the UPR in the liver, because ER stress in the liver leads to lipid accumulation, and fatty liver disease is the most common liver disease in the western world. qRT-PCR profiling of mouse liver mRNAs during ER stress revealed that suppression of the transcriptional regulators C/EBPα, PPARα, and PGC-1α preceded lipid accumulation, and was then followed by suppression of mRNAs encoding key enzymes involved in fatty acid oxidation and lipoprotein biogenesis and transport. Mice lacking the ER stress sensor ATF6α, which experience persistent ER stress and profound lipid accumulation during challenge, were then used as the basis for a functional genomics approach that allowed genes to be grouped into distinct expression profiles. This clustering predicted that ER stress would suppress the activity of the metabolic transcriptional regulator HNF4α—a finding subsequently confirmed by chromatin immunopreciptation at the Cebpa and Pgc1a promoters. Our results establish a framework for hepatic gene regulation during ER stress and suggest that HNF4α occupies the apex of that framework. They also provide a unique resource for the community to further explore the temporal regulation of gene expression during ER stress in vivo.

UPR, autophagy, and mitochondria crosstalk underlies the ER stress response

“…In turn, reciprocal activation is illustrated by the ability of Parkin to enhance select branches of the UPR signaling through the activation of the sXBP1 pathway [28]. ATF6 is also associated with the activation of PCG1α (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha), a master regulator of mitochondrial biogenesis, thereby linking the UPR with metabolic gene programs [29]. …”

Lipase Maturation Factor 1 (Lmf1) Is Induced by Endoplasmic Reticulum Stress Through Activating Transcription Factor 6α (Atf6α) Signaling

“…Although Atf6␣ is a transcription factor, multiple lines of evidence suggest that the involvement of Atf6␣ in the regulation of Lmf1 is indirect. First, the kinetics of TM-induced Lmf1 expression is significantly delayed compared with direct targets of Atf6␣ such as Dnajc3, Erdj3, and Erp72 (34). Moreover, whereas stress-induced activation of Atf6␣ is a posttranslational process, TM-induced Lmf1 expression depends on new protein synthesis, as demonstrated by the inhibitory effect of cycloheximide.…”

“…Using this model, we previously applied microarray analysis to document temporal changes in global gene expression patterns associated with ER stress in the liver of wild-type and Atf6␣ Ϫ/Ϫ mice (28,34). Analysis of these data sets revealed that TM treatment led to modest but detectable induction of Lmf1 8 h after drug injection and produced a more robust increase a day later (Fig.…”

Hepatocyte Nuclear Factor 4-α, Glucocorticoid Receptor and Heat Shock Protein 70 mRNA Expression during Embryonic Development in Chickens

“…In addition, HNF-4α has a critical role in the adult liver, where it controls a number of genes involved in stress response such as endoplasmic reticulum stress-dependent gene (Arensdorf et al, 2013) It has been implicated the function of HNF-4α in early endodermal development (Duncan, 2000). The absence of HNF-4α in mouse embryos resulted in embryonic death before completing gastrulation due to the dysfunction of visceral endoderm system (Chen et al, 1994).…”