Histone demethylase complexes KDM3A and KDM3B cooperate with OCT4/SOX2 to construct pluripotency gene regulatory network

Abstract

The pluripotency gene regulatory network of porcine-induced pluripotent stem cells (piPSCs), especially in epigenetics, remains elusive. To determine this biological function of epigenetics, we cultured piPSCs in different culture conditions. We found that activation of pluripotent gene- and pluripotency-related pathways requires the erasure of H3K9 methylation modification which was further influenced by mouse embryonic fibroblast (MEF) served feeder. By dissecting the dynamic change of H3K9 methylation during loss of pluripotency, we demonstrated that the H3K9 demethylases KDM3A and KDM3B regulated global H3K9me2/me3 level and that their co-depletion led to the collapse of the pluripotency gene regulatory network. Immunoprecipitation-mass spectrometry (IP-MS) provided evidence that KDM3A and KDM3B formed a complex to perform H3K9 demethylation. The genome-wide regulation analysis revealed that OCT4 (O) and SOX2 (S), the core pluripotency transcriptional activators, maintained the pluripotent state of piPSCs depending on the H3K9 hypomethylation. Further investigation revealed that O/S cooperating with histone demethylase complex containing KDM3A and KDM3B promoted pluripotency genes expression to maintain the pluripotent state of piPSCs. Together, these data offer a unique insight into the epigenetic pluripotency network of piPSCs.SummaryErasure of H3K9 methylation in porcine pluripotent stem cells depends on the complex of transcription factors OCT4/SOX2 and histone demethylase KDM3A/KDM3B.

Super enhancers—Functional cores under the 3D genome

“…Indeed, H3K9 methylation can be recognized by heterochromatin protein 1 (HP1α), a common chromatin silence marker, which may cause the formation of heterochromatin. [45][46][47][48] Other histone modifications may also affect SEs. HDAC7 can regulate genes in breast cancer stem cells through SEs.…”

“…If chromatin is modified by inert epigenetic modification, such as H3K9 methylation, SEs will be destroyed. Indeed, H3K9 methylation can be recognized by heterochromatin protein 1 (HP1α), a common chromatin silence marker, which may cause the formation of heterochromatin 45‐48 . Other histone modifications may also affect SEs.…”