G9a plays distinct roles in maintaining DNA methylation, retrotransposon silencing and chromatin looping

G9a is a lysine methyltransferase that regulates epigenetic modifications, transcription and genome organization. However, whether these properties are dependent on one another or represent distinct functions of G9a remains unclear. In this study, we observe widespread DNA methylation loss in G9a depleted and catalytic mutant embryonic stem cells. Furthermore, we define how G9a regulates chromatin accessibility, epigenetic modifications and transcriptional silencing in both catalytic dependent and independent manners. Reactivated retrotransposons provide alternative promoters and splice sites leading to upregulation of neighboring genes and production of chimeric transcripts. Moreover, while topologically associated domains and compartments A/B definitions are largely unaffected, the loss of G9a leads to altered chromatin states, aberrant CTCF and cohesin binding, and differential chromatin looping especially at retrotransposons. Taken together, our findings reveal how G9a regulates the epigenome, transcriptome and higher-order chromatin structures in distinct mechanisms.