Signal integration by the CYP1A1 promoter -- a quantitative study

Abstract

Genes involved in detoxification of foreign compounds exhibit complex spatiotemporal expression patterns in liver. Cytochrome P450 1A1 (CYP1A1), for example, is restricted to the pericentral region of liver lobules in response to the interplay between aryl hydrocarbon receptor (AhR) and Wnt/β-catenin signaling pathways. However, the mechanisms by which the two pathways orchestrate gene expression are still poorly understood. With the help of 29 mutant constructs of the human CYP1A1 promoter and a mathematical model that combines Wnt/β-catenin and AhR signaling with the statistical mechanics of the promoter, we systematically quantified the regulatory influence of different transcription factor binding sites on gene induction within the promoter. The model unveils how different binding sites cooperate and how they establish the promoter logic; it quantitatively predicts two-dimensional stimulus-response curves. Furthermore, it shows that crosstalk between Wnt/β-catenin and AhR signaling is crucial to understand the complex zonated expression patterns found in liver lobules. This study exemplifies how statistical mechanical modeling together with combinatorial reporter assays has the capacity to disentangle the promoter logic that establishes physiological gene expression patterns.

Regulation of Drug Metabolism by the Interplay of Inflammatory Signaling, Steatosis, and Xeno-Sensing Receptors in HepaRG Cells

“…Wild-type HepG2 cells are deficient in both previously mentioned receptors. For monitoring AHR activity, a pT81luc-based luciferase reporter system driven by an array of three AHR-binding dioxin response elements from the human CYP1A1 gene promoter was transfected (Schulthess et al, 2015). A plasmid encoding Renilla luciferase under the control of a constitutively active promoter was cotransfected for normalization purposes.…”

“…In particular, induction of cytochrome P450 (P450) enzymes by exogenous compounds via the aryl hydrocarbon receptor (AHR), constitutive androstane receptor (CAR), and pregnane X receptor (PXR) has been studied extensively (Honkakoski and Negishi, 2000). In addition to xenobiotic nuclear receptor ligands, endogenous signaling pathways also affect the regulation of hepatic drug metabolism via nuclear receptors [e.g., see Braeuning et al (2009), Braeuning and Schwarz (2010), or Schulthess et al (2015)].…”

Regulation of Human Cytochrome P4501A1 (hCYP1A1): A Plausible Target for Chemoprevention?

“…In mice, this was demonstrated by the specific loss of CTNNB1 that encodes β -catenin and leads to a decrease of mCyp1a1 induction by AHR agonists such as 3-methylcholanthrene (3-MC), β -naphthoflavone ( β -NF), and butylated hydroxyanisole. Additionally, it has been observed that maximum mCyp1a1 induction was obtained when β -catenin acted as coactivator of AHR, although this protein also binds to the transcription factor TCF, which has a binding site in mCyp1a1 promoter, suggesting a different mode of action [32–34]. Similarly, in rat hepatoma, it has been observed that the interaction between AHR and hypophosphorylated retinoblastoma protein (pRb) aids maximum induction of rat CYP1A1 by 2.3, 7.8 tetrachlorodibenzo-p-dioxin (TCDD); pRb plays an important role in cell cycle control and it has been proposed that it could also act as a coactivator of AHR [35, 36].…”

Exon definition facilitates reliable control of alternative splicing in the RON proto-oncogene

“…3C), and the same type of predictions are possible for combined RBP knockdowns and combination of RBP knockdown and sequence mutations. Conceptually, the modeling framework resembles thermodynamic models of transcriptional gene regulation (30)(31)(32). However, for the case of splicing, regulation is more complex compared to transcription, as both the regulators (RNAbinding proteins) and the effectors (spliceosomes) show combinatorial binding to multiple sequence elements.…”