Identification of the cholesterol-depletion-induced enhancers in HeLa cell using H3K27ac ChIP-seq

The transcription factor SREBP2, plays a specific and non-redundant role in cholesterol metabolism, autophagy of lipid droplets and apoptosis regulation. Under cholesterol-depletion condition, nuclear SREBP2 (nSREBP2) is released after proteolytic cleavage, enters nucleus and activates cholesterogenic genes expression. Here, we report that the nSREBP2 forms discrete nuclear condensates through its N-terminal intrinsically disordered region (IDR) and works together with transcription coactivators BRD4 and p300, partly on super-enhancers, for the transcriptional activation of SREBP2 target genes. The substitution of a critical and conserved phenylalanine (F) to alanine (A) within the IDR abolished the formation of nSREBP2 condensates. Conversely, the condensate formation and efficient transcription activation were rescued by fusion with a phase separation driving FUS-IDR. Knock-in of the F to A substitution in mice compromised the feeding-induced nSREBP2 activity and lowered the cholesterol levels. Furthermore, a SNP of SREBF2 in humans leading to single amino acid change, P183S, showed less nuclear condensate formation and lower transcriptional activity, underscoring the physiological relevance of nSREBP2 condensates. Together, this study reveals that nuclear condensates driven by the N terminal IDR of nSREBP2 facilitate the efficient activation of lipogenic genes and play an important role in cholesterol homeostasis. Overall design: As a cis-element sequence-specific TF, SREBP2 interacts with transcription coactivators and machineries for gene activation. The histone H3K27ac modification has been used as a marker to define the super-enhancer elements in multiple cells and studies. To investigate if SREBP2 correlates with or contributes to the enhancer or super-enhancer at chromatin level, we performed the H3K27ac ChIP-seq in HeLa cell upon cholesterol-depletion to identify the responsive enhancers and super-enhancers in response to cholesterol-depletion.