MicroRNAs (miRNA) are short pieces of RNA that do not encode for a specific protein.  Instead, miRNAs play an important role in the regulation of gene expression.  They are essential for many aspects of development, and miRNA dysfunction has implications in diseases such as cancer, cardiovascular diseases and viral infections.  However, the role of a specific miRNA in a given cell is very difficult to elucidate.

A recent paper by Hanina, et al demonstrated one way to determine what genes a given miRNA was regulating.  The researchers were particularly interested in finding out what genes a given group of miRNAs that are expressed in mouse embryonic stem cells regulate.   To accomplish this, the team developed a cell line that is incapable of producing mature microRNAs and then added a specific mature miRNA that is expressed in mouse embryonic stem cells.

They used the SOLiD™ System to sequence the messenger RNA that was contained in a complex made up of RNA-degrading proteins and the mature miRNA.  The sequence data identified several genes involved in maintaining a cell’s pluripotency. 

This novel technique allows fine dissection of how miRNAs regulate the transcription of genes.  Its power lies in the ability of next-generation sequencing on the SOLiD System to identify DNA sequences independent of a known target sequence.