Genetics

Newly Discovered Functions of Pseudogenes – Elijah’s Blog

Posted on Updated on

This was a paper I wrote during the 2013 semester in my undergrad. I was particularly interested in the trends in genetics that pointed towards a more holistic understanding of the genome; a perspective that was evolving based on new information. Genes that were previously thought to have been left-over evolutionary relics were (and still are) the focus of much research and fascination. Given that it is 2016, these discoveries are still relatively new, but there certainly much newer discoveries.
Enjoy 🙂


Abstract

photo-1458040937381-49c067dfd49aResearchers have noted that there are portions of the DNA that look similar to functional genes, but contain lesions or premature stop codons. These genes have been assumed to be largely non-functional, but recent research suggests that many of these ‘pseudogenes’ are actually functional.  This paper is an overview of some of the research done in the area of  pseudogene functionality. I address several recent advances in the  area of genetic research regarding pseudogene functionality  chronologically, starting from one of the first discoveries of a  functional pseudogene and ending with a paper from this year (2013). Broadly speaking, it would seem that the assumption of non-functionality has been overturned regarding many pseudogenes, and the evidence suggests that many more pseudogenes may have a function that has yet to be discovered.


Pseudogenes have been typically understood as portions of DNA  that have lost their function and remain in the DNA as a relic that  signifies past functionality. The prefix ‘pseudo-‘ indicates that  something is fake or false, and a pseudogene is a portion of DNA  that looks like a functioning gene, but is not actually functional. Pseudogenes have been placed in the ‘junk DNA’ category, ‘dead’, non-functional by-products of evolution. If a pseudogene is transcribed at all, it is often considered to be largely a neutral process that hasn’t been weeded out by selection. However, recent evidence has shown that many pseudogenes have very important functions in the genome of nearly every organism, humans included. There are very good reasons to revise the definition of ‘pseudogene’ to include a wide variety of biological functions, from gene expression and cellular function to gene regulation and tumor suppression. The newly discovered functions are making the term ‘pseudogene’ notoriously ambiguous. This review will analyze a small handful of functions discovered for pseudogenes that were previously assumed to be non-functional byproducts of genome evolution. It is not intended to be an exhaustive treatment of newly discovered pseudogene functionality. Functions are being ascribed to pseudogenes on a fairly regular basis in contemporary genetics literature, and some of the literature is reviewed in chronological order. Read the rest of this entry »

Cancer. What the Heck is it? – Elijah’s Blog

Posted on Updated on

Many of you have likely encountered a kind of hype that is based almost entirely on the ignorance of the readers. People get a small glimpse into something they [rightfully] see as important, but because they don’t really understand it… they end up drawing erroneous conclusions.

Lets face it: many people don’t really understand cancer. And that’s why one of the topics I chose to research during my undergraduate studies was cancer; and this post is an adaptation from that study.
Cancer is a difficult disease to understand, and people will often assume that there is some easy cure ‘out there’ and it is being concealed/ignored because cancer research facilities are just in it for the money (or some other equally implausible conspiracy theory).

The first step in correcting this misconception is to understand what cancer is. With a proper understanding of the complexities of cancer, we can (hopefully) communicate this with people who do not understand it.

Cancer – What the Heck is it?

screen-shot-2016-10-25-at-1-55-14-amCancer is the name given to a large group of diseases  that behave in a variety of different ways, depending on the type of cell from which they originate. Broadly speaking, cancer is associated with at least two  primary symptoms: uncontrolled cell division and metastasis. In normal cells, the cell cycle is a tightly regulated system that is highly controlled and  managed by proteins, enzymes and the corresponding  genes on the DNA molecule. In some cells, however, the regulations of normal cell processes are interrupted/altered by mutations. These mutations cause many genes to be expressed inappropriately, and this can lead to cancer.

In a normally operating cell, the cell cycle typically goes through several phases of growth and reproduction, and if everything goes “according to plan”, it will live its life until it undergoes a “programmed cell death”, known as apoptosis. However, when a normal cell becomes cancerous, it is because there is an accumulation of mutations in critical portions of the DNA that are vital for normal cell functioning. There are many parts of the DNA molecule that are vital for normal cell functioning, including proto-oncogenes and tumor suppressor genes. These two genes play a particularly important role when diagnosing cancer.

Proto-oncogenes are genes that code for transcription factors, which stimulate the expression of other genes that control different aspects of the cell cycle. The proto-oncogenes are turned on and off, depending on the cell’s needs. In cancerous cells, proto-oncogenes are mutated into oncogenes (cancer-causing genes), resulting in constant expression of the gene that was previously only turned on when needed. This signals to the cell to constantly divide by giving it a constant “green light”, resulting in uncontrollable division.

Tumor suppressor genes are genes that “keep an eye on” the cell cycle, and initiate the process of apoptosis when needed. In a normal cell, proteins coded for by the tumor suppressor genes will inspect the cell cycle at certain checkpoints, making sure everything is in working order. If the cell needs to die, a properly functioning tumor suppressor gene will initiate the process. However, when the cell becomes cancerous, the tumor suppressor gene is turned off, and apoptosis is not induced at the appropriate times during the cell cycle. There is uncontrolled cell growth in the cancerous cells and, as the name suggests, tumors are no longer suppressed.

Generally speaking, cancer is caused by an accumulation  of genetic mutations in certain portions of the DNA (as  discussed above). However, there are a variety of ways that  an individual could accumulate these cancerous mutations:  genetic predispositions, sun (UV light) exposure and  carcinogens. If someone has a genetic predisposition to  cancer, this does not mean that they will definitely get cancer, because ultimately the mutations are random. However, this does mean that there is a higher likelihood that that individual will get cancer. The reason they are more likely to get cancer is because they may already have a mutated copy of a vital gene (allele), given to them by one of their parents. People without a genetic predisposition do not have an allele of the cancerous gene, and are therefore less likely to get cancer. However, both people are susceptible to cancer.

Over exposure to UV radiation is another way that someone may get cancer. The UV radiation has the ability to penetrate the cell in a way that other forms of light cannot, causing mutations in the DNA. In some instances, the UV radiation causes two nucleotides (thymines) to connect with each other (instead of the corresponding adenines), creating a “thymine-dimer”, which is one of the primary causes of skin cancer.

Carcinogens are another hazardous way that someone may get cancer. Like the UV light, carcinogens directly cause mutations in the DNA by interacting with it on the molecular level. Relatively common carcinogens include cigarette smoke, asbestos, engine exhaust, and viruses such as human papilloma virus.

In general, cancer is a relatively un-curable disease. It is treatable at the moment, but because cancer is a fundamental change at the DNA level, cancer only ever goes into remission. There may be some advancement in cancer research in the future, but for the time being, all we can do is understand what causes cancer and how we can prevent exposure to these things.