Uncoupling Histone Modification Crosstalk by Engineering Lysine Demethylase LSD1 [RNA-seq]
Biochemical crosstalk between two or more histone modifications is often observed in epigenetic enzyme regulation but its functional significance in cells has been difficult to discern.  Prior enzymatic studies have revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine specific demethylase 1 (LSD1). Here we have engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation. Y391K LSD1 knockin cells show increased repression of a set of genes associated with cellular adhesion. Chromatin profiling revealed that the cis-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation than the baseline in unedited, parental cells. Y391K LSD1 knockin cells show diminished H3 mono-methyl Lys4 in the vicinity of these silenced genes, consistent with a role for enhanced LSD1 demethylase activity in these regions. These findings illuminate the functional consequences of disconnecting histone modification crosstalk for a key epigenetic enzyme in gene and chromatin regulation. Overall design: We performed RNA-Seq to investigate the transcriptomic changes induced by Y391K LSD1 in K562 cells. Y391K LSD1 is a gain-of-function mutant that can overcome H3K14ac-mediated impediment. Parental K562 cells are homozygously edited to express wtLSD1-GFP (C-terminal GFP-tag). Edited K562 cells 1 and 2 are heterozygously edited with Y391K-LSD1, in which two alleles contain Y391K-LSD1-GFP and one allele contain wtLSD1-GFP.