Human LSD2/KDM1b/AOF1 Regulates Gene Transcription by Modulating Intragenic H3K4me2 Methylation

Abstract

SUMMARY Dynamic histone H3K4 methylation is an important epigenetic component of transcriptional regulation. However, most of our current understanding of this histone mark is confined to regulation of transcriptional initiation. We now show that human LSD2/KDM1b/AOF1, the human homolog of LSD1, is an H3K4me1/2 demethylase that specifically regulates histone H3K4 methylation within intragenic regions of its target genes. Genome-wide mapping reveals that LSD2 associates predominantly with the gene bodies of actively transcribed genes, but is markedly absent from promoters. Depletion of endogenous LSD2 results in an increase of H3K4me2 as well as a decrease of H3K9me2 at LSD2 binding sites, and a consequent dysregulation of target gene transcription. Furthermore, characterization of LSD2 complex revealed that LSD2 forms active complexes with euchromatic histone methyltransferases EHMT1/2 and NSD3 as well as cellular factors involved in active transcription elongation. These data provide a possible molecular mechanism linking LSD2 to transcriptional regulation post initiation.

Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b

“…As the only other histone demethylase identified in the LSD1 amine oxidase family of proteins, LSD2 is emerging as an important epigenetic regulator [13][14][15]18]. Here, we present the high resolution crystal structures of LSD2 in its apo form and in complex with a mimic peptide of H3K4me2, together with a comprehensive structural and functional analysis of human LSD2.…”

“…The sequence alignment indicates that six of these basic residues are conserved in the LSD2 homologs among different species (Supplementary information, Figure S4). This positively charged surface may potentially interact with phosphorylated RNA polymerase II [14] and/or DNA and contribute to H3K4 demethylation by LSD2. We tested the function of these positively charged residues by generating LSD2 mutants with reduced positive charge.…”

“…Although LSD1 has been extensively studied [8, 12], the enzymatic activity and biological function of LSD2 have just begun to emerge. Several studies [13][14][15] have demonstrated that LSD2 specifically demethylates mono-and di-methylated H3K4 (H3K4me1/2). In one study [16], LSD2 was also shown to demethylate dimethylated H3K9 (H3K9me2).…”

“…Notably, demethylation of H3K4 by LSD2 requires the presence of a long stretch of H3 tail sequence and is strongly influenced by other modifications of H3 tails [13]. Biochemical studies indicate that LSD2 associates with transcriptional elongation factors and phosphorylated RNA polymerase II [14,17]. LSD2 is consistently enriched in the coding regions of actively transcribed genes, and may play a role in maintaining a repressive chromatin environment within gene bodies through its H3K4me1/2 demethylase activity [14].…”

“…Biochemical studies indicate that LSD2 associates with transcriptional elongation factors and phosphorylated RNA polymerase II [14,17]. LSD2 is consistently enriched in the coding regions of actively transcribed genes, and may play a role in maintaining a repressive chromatin environment within gene bodies through its H3K4me1/2 demethylase activity [14]. Notably, a genetic study has linked H3K4 demethylation by LSD2 to the establishment of maternal imprinting in mouse oocytes [18].…”