High throughput screen identifies novel small molecules that derepress genes repressed by DNA methylation

Genes repressed by DNA methylation can be derepressed by various compounds targeting DNA methyltransferases, histone deacetylases, etc. Here, we report a high throughput screen against a 308,251-member chemical library aiming to identify novel small molecules that derepress an EGFP reporter gene silenced by DNA methylation. RNA-seq was used to measure mRNA abundance in control and compound-treated cells. Overall design: RNA-seq was used to measure mRNA abundance in DMSO-treated cell, 5aza-dC treated cells, RG108-treated cells and 7 top hits novel compunds treated cells. MeDIP-seq was also done in untreated control cells.