The CTCF-H3K27me3 axis supports melanoma cell migration by repressing cholesterol biosynthesis

Abstract

CCCTC-binding factor (CTCF) is a zinc finger protein that regulates correct three-dimensional chromatin folding in addition to activation and repression of transcription and splicing. CTCF was found to affect tumor cell migration, however the molecular mechanism is still obscure. To identify the molecular mechanism by which CTCF supports melanoma cell migration we used mouse melanoma cells with a partial loss of function (pLoF) of CTCF generated by the CRISPR-Cas9 system. Here we show that CTCF pLoF inhibited cell migration rate. Using RNA sequencing we identified an increase in the expression of multiple enzymes in the cholesterol biosynthesis pathway along with an increase in the cellular cholesterol levels. Inhibition of cholesterol synthesis in CTCF pLoF cells by Fatostatin restored the cellular migration rate, suggesting that CTCF supports cell migration by inhibition of cholesterol synthesis. Detailed analysis of the promoter of Hmgcs1, an upstream enzyme in the cholesterol synthesis pathway, revealed that CTCF pLoF led to reduced H3K27me3 levels in parallel to increased binding of the transcriptional activator SREBP2. Moreover, inhibition of H3K27 methylation in wildtype cells led to increased SREBP2 binding to this promoter. Taken together, our results suggest that CTCF represses transcription of Hmgc1 by promoting H3K27 methylation to suppress SREBP2 binding. By that, CTCF fine tune the cellular cholesterol levels to support cell migration.