Traditionally, epigenetic gene regulation is understood from the perspective of DNA-protein interaction at a molecular level. But recent studies have shown that RNA is an important player in the epigenetic regulation of gene activity. Numerous chromatin-binding proteins have been reported to interact with RNA. However, understanding the functional importance and molecular mechanism of such RNA interactions has been still challenging. In this talk, I will discuss how RNA is involved in epigenetic gene regulation focusing on the two contexts that we have recently investigated. First, I will talk about the role of RNA in the formation of a repressive mark (H3K27me3) of facultative heterochromatin that is essential in stem cell identities. Using human stem cell, CRISPR technologies, and genomic analyses, we showed that polycomb repressive complex 2 (PRC2), an enzyme of depositing H3K27me3 requires RNA binding for chromatin localization in human pluripotent stem cells and in turn for defining cellular state. Second, we looked into the RNA interaction of Sox2 protein, a transcription factor critical for the maintenance of pluripotency and neurogenesis. We determined that Sox2 directly binds RNA in mouse embryonic stem cells and found more than a thousand Sox2-RNA interactions in vivo. I will finish my talk with a discussion of how we can take advantage of our findings for understanding or intervening against diseases such as cancer.