The metabolome regulates the epigenetic landscape during naïve to primed human embryonic stem cell transition

We performed mRNA-seq and small RNA-seq on the newly derived ELF human naïve pluripotent stem cell line and compared with the existing H1 human primed line. Expression analysis revealed that mitochondria oxidative phosphorylation and fatty acid beta-oxidaton is up-regulated in naive state while fatty acid synthesis is up-regulated in primed state. Small RNA-seq revealed consistent expression changes in microRNAs that target key fatty acid beta-oxidation and synthesis genes. Integration with metabolomics data revealed consistent changes in the expression of NNMT (higher in naive state) and IDO1 (higher in primed state) and in the concentration of corresponding metabolic substrates and products. As a regulator of S-Adenosyl methionine (SAM) level, NNMT is proposed as a candidate regulator of epigenetic states. ChIP-seq analysis releaved that naive lines have lower H3K27me3 marks in developmental genes. Inhibition of STAT3, a known regulator of NNMT, reduces NNMT expression level and decreases overall H3K27me3 marks around transcriptional start sites. In particular, STAT3 inhibitor treatment increased H3K27me3 marks in 313 genes that also have higher H3K27me3 marks in primed state than naive state. These 313 genes are enriched with developmental functions, and include several WNT pathway genes. In summary, integrative analysis of RNA-seq, ChIP-seq and metabolomics data revealed key metabolic differences between naive and primed pluripotency and identified NNMT as a key regulator of epigeneitc state. 2 biological replicates for ELF RNA-seq; 2 biological replicates for ELF small RNA-seq; one sample for ELF H3K27me3 ChIP-seq and one sample as input; one sample for ELF treated with STAT3 inhibitor for 6 hours and one sample as input. UPDATE: We performed RNA-seq on two additional human naïve embronic stem cell lines (H1 4iLIF and Lis1), as well as mouse in vivo preimplantation inner cell mass and postimplantation epiblast. These RNA-seq samples are included in the naïve vs. primed comparisons in the study; 2 biological replicates of H1 4iLIF; 2 biological replicates of Lis1; 3 biological replicates of mouse preimplantation inner cell mass; 2 biological replicates of mouse postimplantation epiblast.