The White Rabbit put on his spectacles. "Where shall I begin, please your Majesty?" he asked.
“Begin at the beginning," the King said, very gravely, "and go on till you come to the end: then stop.” -Lewis Carroll, Alice in Wonderland
I’ve always loved this quote from Lewis Carroll. When you read the quote, it sounds so obvious. But when you try to form a story, sometimes it is unclear where the beginning is, and where the end is. I have a story about going to the store to buy eggs. Does the story start with me at home? With me realizing we are out of eggs? Or realizing I wanted an omelet for dinner? It depends. The beginnings and ends of a story, like a gene are not always clear. For instance, the simplist gene I can think of has 2 beginings and 4 ends. Can I tell you the story of a simple gene?
The first step in creating a useful product out of a gene is called transcription. Transcription is performed by RNA polymerase. RNA polymerase binds to the '5 end of the gene, also known as the transcription start site. Transcription continues until the RNA polymerase comes the transcriptional end of the gene. The product made by transcription is known as a pre-mRNA. The pre-mRNA has a start, known as the transcriptional start, and the end, known as the transcription end. We know very little about the transcriptional end of the gene, and because we know so little, this 3' end is one of my favorite research areas.
The pre-mRNA is processed co-transcriptionally (that means at the same time as the transcription is happening). There are two major processing steps; splicing and cleavage. Splicing removes pieces of the mRNA known as introns that are not needed to make a protein. Cleavage cuts the pre-mRNA into 2 pieces, the mRNA and the RNA 3' to the cleavage site. The RNA 3' to the cleavage site doesn't have a name, but I like to call it the endRNA. The mRNA then gets a polyA tail added. A polyA tail is exactly what it sounds like ~100-250 Adenosines added on to the end of the mRNA.
At this point, we can see that there is at least 1 start to the gene and 3 ends; the transcriptional stop, the mRNA stop and the mRNA polyA end. However, the story continues. Both the endRNA and the introns are very unstable. In fact, they are so unstable it's almost impossible to detected them via typical RNA assays. For that reason, the endRNA is rarely mentioned in textbooks, and has very little research associated. Personally, I find the endRNA extremely interesting.
After the mRNA is formed via transcription and processing, the mRNA is translated via the Ribosome. This translation creates the protein product which likely has an important function. Therefore the gene also has a translation start and a translation end. We are up to 2 start sites and 4 ends to the same gene! And this is the simplist gene we can describe. We are completely ignoring something called alternative isoforms, which is when a gene can be created in several different ways.
So this brings me back to my story and the quote above. When Lewis Carroll said Beginning at the beginning, which beginning did he mean? When he said end at the end, which end did he mean?
Last night I went home late because I was teaching. I had leftovers in the fridge, but they all sounded gross. Have you been in that situation? What I wanted was and omelet. But I had no eggs. Therefore I went to the store. I quickly found the eggs, and a few other tempting treats (mushrooms and brownies) and headed home. As I cooked my omelet I thought about the beginning and end of a gene, and how just like this story, I could begin in many places. So which beginning do I use? That depends strongly on what I want to study. If I want to study the protein, I probably talk about the translation start and translation end. If I want to study the mRNA, I probably tell you about the transcription start and the mRNA end, or the mRNA poly A end. Finally, if I study transcription, I tell you about the Transcription start and the Transcription end. And now, where do I end my story about the eggs? I got an omelet, it was delicious, and I came up with a great way to describe the 2 beginnings and the 4 ends found in the most simple description of a gene.
By the way, if I study the tiny worm C. elegans, there is a third place to begin a gene, but that's a story for another time.