Post-Transcriptional RNA Regulons in Stem Cells

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 DESCRIPTION (provided by applicant): Induced pluripotent stem cells (iPSCs) could be a panacea for a wide range of human diseases. Both the generation of iPSCs and their differentiation into various lineages require massive and coordinated changes in gene expression. When cells are pushed from the adult state into pluripotency a large scale induction of pluripotency genes is required, but also a large scale down-regulation of genes expressed in the differentiated parent cells. Similarly, the more natural process of differentiation requires down-regulation of pluripotency factors with concomitant increased expression of tissue-specific genes. These changes occur at the transcriptional level, but also post-transcriptionally, particularly at the level of mRNA decay. Importantly, the contributions of post-transcriptional events to the achievement and maintenance of pluripotency are poorly characterized. We propose to study three post- transcriptional RNA regulons that likely contribute to the achievement and/or maintenance of pluripotency. First, we determined that a large number of Zinc Finger Protein (ZNF) mRNAs are stabilized in iPSCs. As these ZNF transcription factors have vital roles in development, and perhaps in controlling retrotransposition, understanding their regulation is essential. We will examine a potential mechanism by which miRNAs target repeated domains in the ORF of ZNF mRNAs to induce decay. We will also investigate why these ZNF mRNAs have unusually short poly(A) tails and uncover how this contributes to their expression. Second, we found that methylation of mRNAs, and particularly ZNF mRNAs, is correlated with increased stability in iPSCs. We will uncover the mechanisms by which this modification influences gene expression in pluripotent cells. Finally, we have shown that many mRNAs encoding transcription factors important for embryonic development contain C-rich elements and are significantly destabilized in iPSCs. We will identify the factors responsible for this regulation and decipher their mechanism of action. Overall, these experiments will give much needed insights into post- transcriptional control in stem cells that may lead to improved reprogramming and a better understanding of the differences between pluripotent cells and their fully differentiated relatives.