RNA-seq is a technology that has been used more and more in recent years to study both basic biology and disease. It’s a powerful tool has enabled scientific discovery at an unprecedented rate. But what exactly is RNA-seq? And, more importantly, what can it tell us?
RNA-seq is short for “RNA sequencing.” In essence, it’s quite similar to a technique you may have heard of before: whole genome sequencing. Our genome (i.e., our genetic code) is made up of DNA, which consists of 4 building blocks – chemicals abbreviated as A, T, C, and G – that are strung together in a code. Just like how different sequences of letters in the alphabet make up different words and sentences, different sequences of DNA building blocks make up the many different genes in our genome.
In whole genome sequencing, researchers determine the DNA code for every gene in an organism’s body. RNA sequencing, on the other hand, provides the sequence of a related chemical code: RNA.
What is RNA?
Picture a library full of shelves upon shelves of books. Together, the books contain all the instructions to make every piece of our bodies – everything from the smallest molecule in a cell to a whole organ. In this example, the books are our genes, and every cell in our body contains the whole library.
Say a cell needs to make protein X . Instead of checking out the book, a copy of the book is made. That copy is called RNA, which will then be used to make protein X. This copy-making process, known as “transcription,” gives the cell more flexibility when it comes to how much of protein X to produce: in general, the more protein X the cell needs, the more copies of RNA are made. The total amount of protein X that is made from its gene is called “gene expression.”
What can we learn from RNA?
Because each of our cells has a specific role, they do not express every one of our genes; like us, they only read the books that are relevant to the topic at hand. If a gene is not expressed, even when we have it on the shelf, it is not functional. So, if we could have a readout of what genes are being expressed in a certain tissue, we could better understand what the cells in that tissue are doing. The easiest way to do that is by sequencing RNA.
How can we use RNA-seq for research?
One of the great things about RNA-seq is that it provides information about not only which genes are being expressed, but how much each gene is being expressed. For instance, as we age, the amount of growth factor produced by our body drops. If you perform RNA-seq on tissue samples from both a child and an adult, you can expect increased gene expression of growth factors in the child (indicated by an increased amount of growth factor RNA in the child’s tissue sample).
Gene expression is affected by a number of other factors, as well. In the case of illness – even when the disease is caused by a mutation in a single gene – a number of genes are likely to be differentially expressed as the result of your body’s attempt to compensate. If we compare an ataxic patient to a healthy individual, for example, we can expect to find hundreds of differentially expressed genes.
By comparing healthy individuals and patients using RNA-seq, we can learn what gene expression patterns are altered in disease. Tapping into this information helps scientists determine what went wrong in a specific disorder, which then informs them about what to do next. Whether this leads them to identify biomarkers, honing diagnostic strategies, or developing new treatments, RNA-seq acts as an important preliminary step in their research.
To learn more about the process of gene expression, check out this animation.
Snapshot written by Sophia Leung and edited by Maxime Rousseaux.