Two papers published this month reveal elaborate regulatory mechanisms governing embryonic stem cells. As these cells differentiate, microRNAs (miRNAs) downregulate the expression of the pluripotency factors Nanog, Oct4 and Sox2. miRNAs are generally thought to work through the regions of gene transcripts that do not code for protein; however, new research from Isidore Rigoutsos of the IBM Thomas J. Watson Research Center in Yorktown Heights, New York, and Bing Lim of the Agency for Science Technology and Research in Singapore, identifies extensive miRNA binding sites that occur within the protein-coding regions of transcripts1.

Earlier computational work from the researchers had indicated that miRNAs likely bind in places other than the expected, untranslated regions. For this new work, published in Nature, the researchers identified miRNAs that met two criteria: they were enriched in differentiating mouse embryonic stem (ES) cells and were predicted computationally to bind the protein-coding regions of Nanog, Oct4 and Sox2. This process identified miRNA-296, miRNA-470 and miRNA-134, which interacted with several sites on their respective target genes. When mouse ES cells (as well as somatic cells into which these genes had been inserted) were exposed to these miRNAs, the target genes were downregulated as expected. These findings suggest more sophisticated miRNA activity than was previously understood. For example, a single miRNA can have several targets within a single protein-coding area of a transcript. What's more, two of the miRNA binding sites span sections of protein-coding transcripts that can be spliced together in various ways, suggesting that miRNAs can target different transcripts of the same gene.

In separate work, a research team also led by Lim showed that the same transcription factor regulates different sets of genes in different types of mouse stem cells.2 In ES cells, the transcription factor Sall4 is required for pluripotency and forms part of an autoregulatory network with the triumvirate of Nanog, Sox2 and Oct4. In stem cells derived from extra-embryonic endoderm, Sall4 is also necessary for stemness, but it regulates a different set of genes (Gata4, Gata6, Sox7 and Sox17). Though the mechanism is so far unclear, the work shows that stem cells can be defined by various sets of genes working together and that, unexpectedly, these different combinations of genes can be regulated by the same factor.