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

Abstract

The pluripotency gene regulatory network of porcine induced pluripotent stem cells(piPSCs), especially in epigenetics, remains elusive. To determine the 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 2 of 18 | ZHU et al.

AXIN2 Reduces the Survival of Porcine Induced Pluripotent Stem Cells (piPSCs)

“…The endogenous OCT4 , which is the central factor of pluripotency [ 20 ], was not activated in piPSCs. Plenty of studies tried to boost the expression of OCT4 .…”

“…As CTNNB1 accumulated when AXIN2 was knocked-down, we also examined the effect of on the OCT4 promoter activity by dual-luciferase reporter assay; however, the negative outcome disappointed us. Until now, the inactivity of OCT4 was still a mystery of piPSCs [ 20 ].…”

“…Pigs are more similar to humans than rodents in organ size, physiology, and anatomy, and thus, autologous and/or homologous transplantation using pig iPS cell derivatives represents a superior model for regenerative medicine [ 18 , 19 ]. Moreover, the maintenance of the pluripotent state for many reported piPSCs was dependent on the regulation of the Wnt/β-catenin pathway [ 20 ]. However, as the key component of WNT signaling, the role of AXIN in piPSCs was unclear.…”

ESRRB Facilitates the Conversion of Trophoblast-Like Stem Cells From Induced Pluripotent Stem Cells by Directly Regulating CDX2

“…The signal intensity for each sample was calculated, which was defined as ±2 kb around the transcription start site (TSS). The OCT4 chromatin immunoprecipitation (ChIP)-seq data were based on the study of Zhu et al (2021b). Annotation and visualization of ChIP peak coverage over the chromosomes were conducted using the ChIPseeker package in R (version 1.18.0) (Yu et al, 2015).…”

“…Peptide confidence was set at high, and peptide ion score was set > 20. The OCT4 IP-mass spectrometry data were based on the study of Zhu et al (2021b), and the ESRRB IP-mass spectrometry data were uploaded in PRIDE datasets (PXD027539).…”