Snapshot: What is RNA-seq?

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.

a densely densely back library shelf with an assortment of books
A library full of shelves of books, much like a human cell full of DNA. Photo by Alfons Morales on Unsplash.

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.

If you would like to learn more about RNA-seq, take a look at these resources by Thermo Fischer Scientific and Bite Size Bio.

Snapshot written by Sophia Leung and edited by Maxime Rousseaux.

Snapshot: What is RNA?

RNA is an important molecule that helps with regulating the function of cells. To fully understand how RNA fits in here, we must first look at the bigger picture: genetics. The central dogma of molecular biology, depicted below, states that DNA is copied (transcribed) into RNA, which is later decoded (translated) into proteins, which perform many vital functions in the cell. So, when the cell needs a specific protein, it locates the stretch of DNA that contains the code for this protein and starts to write a copy of that stretch of DNA. This copy is made using RNA, or ribonucleic acid, as a backbone. RNA is very similar to DNA, but contains one extra oxygen atom in the basic building block. Only one strand of the DNA is copied, so RNA ends up looking like half a DNA molecule. The RNA molecule can be seen as the messenger between the archive of your genes (DNA) and the protein production site. However, RNA is very versatile and is also involved in protein regulation, transport of molecules and as a structural component of large complexes in the cell.

The "central dogma" of molecular biology: DNA makes RNA, then RNA makes protein.
The “central dogma” of molecular biology: DNA makes RNA, then RNA makes protein. Adapted from Wikimedia.

The shifting stream of RNA

Apart from small random mutations during the course of a lifetime, the DNA contained in every cell remains the same from birth to death. However, since different cells need different proteins at different stages of growth, there needs to be a selection of which genes are copied and translated into proteins. This means that the process of making RNA has to be very flexible. This flexibility is achieved through a large network of signals that tell the cell which regions of DNA should be transcribed into RNA, and at what rate. To keep up with the demands of the cell, there are millions of RNAs being made at all times, to send out instructions to makes proteins.

How can RNA cause disease?

In some spinocerebellar ataxias, such as e.g. SCA8, the messenger RNA molecules contain long repetitive sequences that become sticky to other copies of the same RNA or to proteins, forming both small and large clumps in the cell. There is still controversy surrounding which steps in the process that ultimately causes cell death in large brain areas, but it seems that unsolicited binding of these sticky RNAs to proteins and other RNAs causes disruption to several functions in the cell simultaneously. Therefore, many researchers are hopeful that reducing the amount of these RNAs in the cell using Antisense Oligonucleotides or RNA interference can help treat spinocerebellar ataxias and other similar diseases.

If you would like to learn more about RNA, take a look at these resources by the Encyclopedia Britannica and Khan Academy.

Snapshot written by Frida Niss and edited by Dr. Hayley McLoughlin.