Regulation of pluripotency by RNA binding proteins

Abstract

Establishment, maintenance, and exit from pluripotency require precise coordination of a cell's molecular machinery. Substantial headway has been made in deciphering many aspects of this elaborate system, particularly with respect to epigenetics, transcription, and noncoding RNAs. Less attention has been paid to posttranscriptional regulatory processes such as alternative splicing, RNA processing and modification, nuclear export, regulation of transcript stability, and translation. Here, we introduce the RNA binding proteins that enable the posttranscriptional regulation of gene expression, summarizing current and ongoing research on their roles at different regulatory points and discussing how they help script the fate of pluripotent stem cells.

Figure 1. RBPs Involved in Pluripotency Act at Many Different Regulatory Steps

Summary of the RBPs and the events they regulate in the maintenance and exit from pluripotency as discussed in this Review. Starting in the nucleus, RBPs regulate splicing (FOX2, SON, SFRS2, MBNL1, and MBNL2) and alternative polyadenylation (FIP1) simultaneously with transcription. RBPs then regulate export of transcripts (THOC2 and THOC5). RBPs also can induce modifications to RNAs including nucleotide changes (ADAR, METTL3, and METTL14 in nucleus) and nucleotidyl transfer (LIN28A in association with the TUTases ZCCHC6 and ZCCHC11 in the cytoplasm), which in turn influence mRNA stability and translation. In the cytoplasm, the binding of RBPs to the 3′UTRs of transcripts directly regulates mRNA stability and translation (TRIM71, PUM1, and BRF1). Translation is also influenced by RBPs that bind the 5′UTR of transcripts (NAT1, RBM35A, and PTBP1). Blue circles indicate RBPs. RBP genes in red are positive regulators of pluripotency. RBP genes in green are negative regulators of pluripotency. Black circles indicate the protein products of the genes whose expression levels are affected by RBPs.

Figure 2. The Multifunctional RBP: The RNA Regulon Revisited

(A and B) Alternative models for RBP regulation of RNA metabolism. (A) In the classical view of the RNA regulon, an RBP (blue object) binds multiple transcripts to execute a single action on many RNAs (purple, blue, and green). This in turn can affect an array of cellular processes depending on the nature of the mRNAs targeted. (B) In an expanded version of the RNA regulon model, an RBP not only has multiple targets but also acts on those targets at multiple levels of intracellular RNA metabolism. An example RBP shown here regulates transcription, splicing, RNA stability, and mRNA translation of a common set of transcripts. While it is unlikely that such an RBP exists, we propose that many RBPs will have a subset of these functions on overlapping sets of targets.