Global analysis reveals differential regulation of mRNA decay in human induced pluripotent stem cells
Date
2013
Authors
Neff, Ashley T., author
Wilusz, Jeffrey, advisor
Wilusz, Carol J., advisor
Thamm, Douglas H., committee member
Weil, Michael, committee member
Journal Title
Journal ISSN
Volume Title
Abstract
Induced Pluripotent Stem (iPS) cells are able to proliferate indefinitely while maintaining the capacity for unlimited differentiation and these properties are reflected by global changes in gene expression required for reprogramming of differentiated cells. Although the rate of transcription is an important regulator of steady-state mRNA levels, mRNA decay also plays a significant role in modulating the expression of cell-specific genes. The contribution of regulated mRNA decay towards establishing and maintaining pluripotency is largely unknown. To address this, we sought to determine global mRNA decay rates in iPS cells and the genetically-matched fibroblasts (HFFs) they were derived from. Using a microarray based approach, we determined half-lives for 5,481 mRNAs in both cell lines and identified three classes of mRNAs whose decay is differentially regulated in iPS cells compared to HFFs. We found that replication-dependent histone mRNAs are more abundant and more stable in iPS cells, resulting in increased histone protein abundances. This up-regulation of histone expression may facilitate the unique chromatin dynamics of pluripotent cells. A large set of C2H2 ZNF mRNAs are also stabilized in iPS cells compared to HFFs, possibly through reduced expression of miRNAs that target their coding regions. As many of these mRNAs encode transcriptional repressors, stabilization of these transcripts may support the overall increased expression of C2H2 ZNF transcription factors in early embryogenesis. Finally, we found that mRNAs containing C-rich elements in their 3'UTR are destabilized in iPS cells compared to HFFs and many of these mRNAs encode factors important for development. Interestingly, we also identified the Poly(C)-Binding Protein (PCBP) family as differentially regulated in iPS cells and investigated their possible involvement in regulation of the mRNAs in our dataset identified as destabilized in iPS cells and having C-rich 3'UTR elements. Thus, we identified several interesting classes of mRNAs whose decay is differentially regulated in iPS cells compared to HFFs and our results highlight the importance of post-transcriptional control in stem cell gene expression. Coordinated control of mRNA decay is evident in pluripotency and characterization of the mechanisms involved would further contribute to our limited understanding of pluripotent gene expression and possibly identify additional targets for reprogramming.