Functional Characterization of RNA Profiles in Processing Bodies of Embryonic Stem Cells and Mesodermal Cells

Processing bodies (P-bodies) are membraneless organelles that exist in eukaryotic cells, contributing to the post-transcriptional regulation of gene expression. Abnormalities in P-bodies lead to diseases and developmental disorders. Recent studies have demonstrated the involvement of P-bodies in stem cell fate regulation by associating the depletion of P-bodies with cell fate change. However, how the dynamics of RNA components in different cell types are related to corresponding cell fates remains poorly understood. Here, we systematically characterized the RNA profiles of P-bodies from HEK293T cells, human embryonic stem cells (hESCs), and hESC-derived mesodermal cells. By functional analysis of the P-body-enriched and P-body-depleted RNAs across different developmental stages, we discovered the cell type-specific enrichment of P-body RNAs. We also captured the non-coding RNAs, including long intergenic non-coding RNAs and transposable elements in P-bodies in a cell type-specific manner. Furthermore, we verified the functions of P-bodies in regulating the differentiation of hESCs toward mesodermal cell fate by over-expressing LSM14A, one of the key P-body protein components, and knocking down SPTAN1, one of the P-body-enriched mRNAs. In summary, we characterized the mRNAs and non-coding RNAs in P-bodies from HEK293T, hESCs and hESC-derived mesodermal cells, deciphering the potential developmental roles of P-bodies in the maintenance and differentiation of hESCs.