Regulation of mammalian transcriptional enhancers by H3K4 methyltransferases and H3K4 demethylases

It is well known among the scientific community that mammalian promoters are enriched for histone H3 lysine 4 methylation (H3K4) specifically trimethylation of the lysine (H3K4me3). Such a definition for transcriptional enhancers, regulatory elements in the genome that positively contribute to the transcriptional activity of a particular promoter, has only been discovered recently. Earlier studies from our lab which were further corroborated by studies from other groups show that transcriptional enhancers in mammalian cells show the presence of H3K4me1,another modification of the same lysine (H3K4), but generally lack H3K4me3. It has also been well known that MLL family of lysine methyltransferases (KMTs) which are specific for H3K4 are the enzymes responsible for this H3K4me3. Although, earlier studies have shown that MLL family of KMTs are also capable of methylating H3K4 to H3K4me1 and H3K4me2, their presence at enhancers or their roles in regulation of transcriptional enhancers has not been elucidated completely. Other families of proteins, H3K4 specific demethylases, have recently been discovered to reverse this methylation of H3K4, which for a long time was considered an irreversible reaction. In our quest to identify the proteins that might have an important role in regulation of enhancers, specifically H3K4 monomethylation at enhancers, I started with the identification of the lysine methyltransferases and related proteins that bind to enhancers (Chapter 1). We found that MLLs, JARID1C and LSD1 are recruited to transcriptional enhancers in human cells. In Chapter 2, we do knock-down experiments on LSD1 and JARID1C to see the effect of their loss on gene expression. We find LSD1 acts as a repressor whose loss results in upregulation of a significant number of genes whereas JARID1C's loss results in upregulation and downregulation of similar number of genes. We also conduct GWLA of LSD1 in knock-down cells to show LSD1's loss result in a genome-wide increase in H3K27 acetylation and H3K4me3 at both promoters and enhancers. In Chapter 3, we study the role of LSD1 in DNA methylation and control of transcription from repetitive DNA elements in the mouse genome. Chapter 4 represents an unrelated study where we studied binding patterns of several transcription factors and histone modifications to identify cis-regulatory modules in the human genom