Genome Editing 101: Central Dogma of the Cell

Foreword


For the first time in human history, we not only understand the language of life, but we can also manipulate it. In the past two decades, a lot of advancements have been made to contribute to the realm of genome editing. Genome editing is the combination of techniques that allow us to manipulate the DNA of bacteria, fungi, and even humans. Manipulating genetic codes have an enormous influence and can be used to increase crop yields, produce medicines in bacteria, and even cure genetic diseases.


The Genome Editing 101 series offers to explain the relevant biology of gene editing, the mechanisms by which such techniques work, and the ethical and political problems that arise from this new field of biology. It will be mainly divided into the following chapters:


1. Genome Editing 101: Central Dogma of the Cell


2. Genome Editing 101: Gene Editing Techniques


3. Genome Editing 101: Applications of Genome Editing


4. Genome Editing 101: Politics on Genome Editing


5. Genome Editing 101: Ethical Problems in Genome Editing


6. Genome Editing 101: Future of Genome Editing



Before understanding how genome editing works, it is important to know what DNA is, and what implications its manipulation has. Over 60 years ago, an expert in the field, Francis Crick, published the concept of the Central Dogma of the cell. Together with Watson, Crick resolved the structure of DNA in 1953, for which he won the Nobel Prize in 1962 (Watson & Crick, 1953). Crick defined the Central Dogma as the "transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein". Information therefore cannot be transferred from protein to protein, nor from protein to nucleic acid. (Crick, 1958). Crick’s publication revolutionised the view on molecular biology and on the Central Dogma. Nowadays, the Central Dogma is seen as the fact that a DNA sequence is translated into a protein (Liu et al., 2018).


Figure 1: The scientists behind the discovery of the DNA structure; Francis Crick (left) and James Watson (right) (Academy of Achievement, n.d.).

DNA, RNA, and Proteins


Genetic information in DNA is transferred to RNA in a process called transcription. This is followed by translation, where the information is passed on to form proteins. When a cell multiplies, it duplicates all of its DNA, i.e., its genome, through DNA replication. These three processes together form the basis of the Central Dogma and are responsible for the expression and maintenance of every piece of DNA that codes for a gene (Liu et al., 2018).


To further understand these processes, one should first learn about what DNA, RNA, and proteins are. DNA is a molecule that stores genetic code. It is built up of nucleotides composed of four different nitrogenous bases: adenine (A), thymine (T), cytosine (C), and guanine (G). A DNA molecule consists of two strands that are said to be complementary. This means that at any position at which a G appears, a C will be placed on the other strand. A will in turn exclusively pair with T (Alberts et al., 2017). The regulation of DNA is incredibly complicated, as it includes mechanisms that have evolved over billions of years. This is also the reason why, though similar in the core, the genome of a bacterium is very differently regulated from that of a human being (Struhl, 1999).


RNA, on the other hand, contains A, C, G, and uracil (U). Another difference between DNA and RNA is that the latter is single-stranded. Furthermore, proteins are composed of small molecules called amino acids that are chained together to form a sequence. The sequence of amino acids gives proteins their specific shapes. In molecular biology, shape dictates function (Seiber, 2014). In other words, the unique sequence of amino acids results in a unique protein (Alberts et al., 2017).


Figure 2: An overview of the structure of DNA and RNA (Mackenzie, 2020).

Proteins come in many structures and have a wide variety of functions. These macromolecules are responsible for almost any chemical reaction taking place in an organism (Alberts et al., 2017). This is why mutations in DNA can have significant impacts. If a certain gene encodes a wrong protein, the protein may become harmful and cause diseases. Sometimes, a mutation leads to the aggregation of an erroneously folded protein, which causes the cell to die (Guthertz et al., 2022).


Replication, Transcription, and Translation


DNA is safely stored within the cell nucleus. Inside, an enzyme, called DNA polymerase, replicates the genome whenever necessary. This takes place before a cell divides. Another enzyme, called RNA polymerase, facilitates transcription, i.e., the process of RNA synthesis with DNA as a template. Many different RNA transcripts are present inside the cell nucleus at any point in time. These transcripts in turn carry different genetic information. After transcription, RNA is processed into messenger RNA (mRNA) and can leave the nucleus. The mRNA is transported to ribosomes, which are the protein factories of the cell. These ribosomes read each triad of nucleotides, also referred to as codons, on the mRNA. Depending on the three bases, a certain amino acid is recruited which together forms a long sequence called a polypeptide. This sequence is the backbone of any protein. Based on chemical interactions between these amino acids, the protein folds in a certain way and subsequently acquires a specific function (Kaiser et al., 2011). Every mRNA transcript also encodes a stop codon signalling to the ribosome that the full mRNA transcript has been translated, and the protein is complete.


The above processes - replication, transcription, and translation - combine to form the Central Dogma of the cell. Interestingly, although genetic information generally flows from DNA to RNA to proteins, this is not the only direction. Retroviruses like HIV, for example, have an RNA-based genome. When these viruses infect a cell by the process of reverse transcription, their RNA becomes DNA, which is then integrated into the host cell’s genome (Telesnitsky & Goff, 1997).


Figure 3: An overview of the Central dogma. DNA is transcribed into mRNA, which is translated into proteins, or polypeptides. Additionally, DNA is replicated when a cell divides. These processes form the Central Dogma (Khanacademy, n.d.).

Mutations and DNA Repair


Radiation is mutagenic, meaning that it induces errors, or mutations, in the DNA (Evans & Demarini, 1999). Many molecules, including those found in food, share the same mutagenic ability which in itself is not necessarily harmful (Goldman & Shields, 2003). DNA is an unstable molecule, and RNA is even more so. Mutations occur constantly in any single cell of the human body, but this does not always lead to cancer or genetic diseases. This is because living organisms have evolved incredibly complex molecular pathways by which various proteins repair damage to the DNA. However, these repair pathways do not always pick up on every single mistake made along the entire genetic sequence. This is how mutations can at times have drastic consequences (Aguilera & Gómez-González, 2008).


A well-known example of such a consequence is cancer. A normal cell needs to be tightly regulated in the sense that different proteins are expressed at certain concentrations. When a small mutation is not detected and repaired, it can lead to a feature that is common in tumour cells. For example, a mutation may cause the cell to grow and divide uncontrollably. It then not only competes for space with other healthy cells, but also divides over time to give birth to more cells with the same mutation. This ultimately creates larger tumours that eventually may become cancerous (Tomasetti et al., 2017).


Double-stranded breaks, on the other hand, are a certain type of damage that occurs in DNA when both strands are severed (Mourad et al., 2018). When this damage is detected, the cell has no way of knowing whether it just has to stitch the broken strands together, or whether there are bases missing. To minimise the risk of errors, the cell can start looking for a template. If its genome has already been replicated, the cell uses the copy of the DNA as its template (Jalan et al., 2019). Once found, DNA polymerase only needs to read the missing sequence and fill the gap with nucleotides that are lacking. This process is often the target of gene editing tools. By feeding the cell a certain template and inducing double-stranded breaks, scientists can manipulate the genetic sequence at a specific region (Danner et al., 2017).


Figure 4: A double-stranded break in DNA (Begley, 2018).

Function Specialisation


Every person starts their life as a single cell. Once a sperm cell fertilises an egg, the cells merge and form a zygote (Burgess, 2010). The rest of the body stems from this cell through multiplication and specialisation. Some cells will grow and become neurons, while others may become skin or muscle cells. Over the course of nine months, an incredibly complex human body forms, consisting of trillions of functioning cells. Because all of these cells originate from the same zygote, they share the exact same genome. However, cells in different parts of the body need to serve specific functions. A brain cell simply cannot function in the intestine, nor the other way round. To achieve this specialisation, cells have a very complex system of turning genes on and off. (Guttery et al., 2015; Ruijtenberg & van den Heuvel, 2016). This is often done through recruitment of transcription factors. These factors bind to specific genes and either inhibit or increase their transcription, thereby effectively turning on and off the gene (Mitsis et al., 2020).


The Central Dogma and all processes surrounding DNA, RNA, and proteins are very complex. They are results of over 3.4 billion years of evolution (Cavalazzi et al., 2021). Proteins are the primary actors of the cell with great diversity in both structure and function. They are encoded by DNA and formed through processes of transcription and translation. Hence, by editing the DNA of an organism, both the genes and their expression can be altered, which allows for vast possibilities. Now that it is clear how DNA, RNA, and proteins function, the next article will dive into how genes can be altered, and what implications this yields.



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