Ribonucleic acids (RNAs), the molecules intimately involved in the expression and regulation of genes, comprise a biological landscape with huge amounts of territory unexplored and unknown. On the frontier has been a community of tens of thousands of RNA molecules known as long non-coding RNAs, or lincRNAs. These RNA molecules don’t code for proteins but are nevertheless thought to play important roles in how genes are expressed.
Now, a team of researchers at Sanford-Burnham has created the first genome-scale RNA interference (RNAi) library targeting lincRNAs in the mouse – and in the process discovered a key RNA molecule vital for the differentiation of stem cells into neural cells. RNAi is a highly potent approach to study the function of genes in eukaryotes.
The team, led by Tariq M. Rana, Ph.D., professor in Sanford-Burnham’s Children’s Health Research Center, named the lincRNA molecule “TUNA” – short for Tcl1 Upstream Neuron-Associated lincRNA. Rana’s team found that TUNA is required for the ability of stem cells to differentiate into nearly any cell in the body – a characteristic known as pluripotency. The researchers also discovered that stem cells in which TUNA was knocked out could not differentiate into the many neural cells of the brain.
“This is the first time that someone has created such a library to probe for functions of every non-coding gene in the genome,” Rana said. “There is a huge number of non-coding RNAs found in humans that will not code for a peptide or a protein. These kinds of studies show what makes us such a complex species. It’s not just about the coding genes; there’s a lot of non-coding world out there that we need to explore and understand.”
The paper “An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment” was published online in the journal Molecular Cell. “This study gives the tools, the proof of concept, and the means to show that in addition to the coding world, non-coding RNA also plays a role in the differentiation of cells in the central nervous system,” Rana added.
The research team found that TUNA is strikingly conserved in vertebrates. Through collaboration with Duc Dong, Ph.D., assistant professor at Sanford Children’s Health Research Center, knocking out the molecule in zebra fish impaired the animal’s ability to swim, the researchers found. They also discovered that lamprey eels, an extremely ancient lineage of vertebrates in which the spine first started to form, also have the TUNA molecule.
“I jumped out of my chair in the lab and realized, ‘this has something to do with the spinal cord,’” Rana said of the moment he saw that lampreys had the molecule.
To explore the importance of TUNA further, the researchers analyzed published data on RNA and gene expression in human patients suffering from Huntington’s disease, a neurodegenerative genetic disorder that affects muscle coordination and also leads to cognitive decline. The data profiled gene expression levels at different stages of the disease. As the disease progressed TUNA expression declined in a region of the brain called the caudate nucleus. Expression had not declined among other genes in the caudate nucleus.
A further understanding of TUNA and other lincRNA molecules may potentially lead to new therapeutic approaches to restoring neuronal functions where it’s been compromised – in Huntington’s disease and other neurological diseases for example, Rana said.
The discovery also could have wider implications. A natural decline in adult neurogenesis – the ability of the adult brain to make new cells – has been associated with age-related memory loss. Identifying a key player in the differentiation of stem cells into new cells of the adult brain could be an important step toward understanding this relationship, Rana said.
Nianwei Lin, Ph.D., is a postdoctoral fellow in Rana’s lab and was first author on the paper.
The publication can be found at: http://www.cell.com/molecular-cell/abstract/S1097-2765(14)00082-3