Interplay between enhancer hierarchies and histone demethylase JMJD3

Abstract

Precise regulation of gene transcription is central to development and homeostasis. Distal regulatory elements known as enhancers play a crucial role in gene regulation. Thousands of these enhancers populate the mammalian genome, but only a fraction of them are functional in transcriptional regulation. Multiple enhancers that are present within a certain distance cut-off from the next enhancer are stitched together, and the cluster is referred to as super-enhancers (SE). SEs are believed to be functional and exert effects on a target gene in a sum-of-all manner. However, these predictions are based on computational and deep learning-based approaches that lack experimental evidence. My thesis work challenges these assumptions through the functional dissection of an SE cluster present in the 9p21 locus. I observed that not all enhancers within this enhancer cluster regulate the target promoter. Further, the important enhancers depend on other functional enhancers within the same cluster for promoter regulation.

Furthermore, the functional enhancers within the 9p21 locus require histone demethylase JMJD3 for their activity. JMJD3 induces transcription by removing methylation at histone H3K27. I will present my findings that JMJD3 binds to functional enhancers genome-wide and requires its intrinsically disordered region (IDR) and RNA for efficient targeting of enhancers. JMJD3 miss- localizes to promoters in the absence of IDR, suggesting that the presence of IDR and its ability to interact with RNA have enabled the enzyme to bind mainly to enhancers instead of promoters.

Overall, my work underscores the inadequacy of biochemical marking-based assignment of functionality as currently practiced and emphasizes that, even though laborious, a careful enhancer-by-enhancer dissection is the only way forward toward a comprehensive understanding of enhancer function and diversity.