Exploring the Mysteries of 'Junk' in DNA:

Introduction:

Fresh discoveries in the unexplored section of the genome; in the words of Sir Roger Vernon Scruton, a conservative philosopher and writer from England, is nothing more beneficial than things that may seem worthless or lacking in practicality. Researchers at the University of Sheffield's Neuroscience Institute and Healthy Lifespan Institute have made a significant discovery regarding the potential of junk DNA, which was previously understood to serve no purpose in protein-coding. This groundbreaking research emphasizes the relevance of junk DNA in understanding and potentially treating neurological disorders, including motor neuron disease (MND) and Alzheimer's disease. Recent research has discovered the process of how oxidative damages are created and fixed within the so-called useless DNA; previously believed by researchers and scientists, was classified as non-coding or non-functional because it does not contain information for protein-coding genes, a sequence that has no significant purpose. Many organisms possess non-functional DNA in their genetic material such as pseudogenes, fragments of transposons, and proviruses. However, there is a chance that certain organisms may carry a greater quantity of this non-functional DNA. Usually, all parts of a gene that code for proteins are considered to be functional components of a genome. In addition, non-coding regions of the genome, such as genes for ribosomal RNA, transfer RNA, regulatory sequences that control gene expression, elements involved in replication, centromeres, telomeres, and scaffold attachment regions, are also considered to be functional components of the genome. Determining the presence of functional elements in DNA is better done by considering coding or non-coding regions. Moreover, there is disagreement over the criteria that should be employed to identify function.

Scientists have an evolutionary perspective on the genome and they lean towards using criteria that rely on determining if DNA sequences have been conserved through natural selection. Although the antagonists have varying explanations for the data.

The term "junk DNA" was coined in the 1960s, with Susumu Ohno being credited as its originator. Duplication can help overcome the limitations imposed by natural selection on alterations in critical gene areas by permitting one duplicate to preserve the original function while the other undergoes mutation. Occasionally, these mutations may result in advantageous outcomes, leading to the emergence of a novel gene. Most often, a single copy is enough to support that. This causes the loss of its capacity to produce a functional protein and transforms it into a pseudogene. Initially, Ohno called these sequences "junk," but later discovered that they had significance.

Recently, scientists have started to recognize the importance and potential of what was previously referred to as junk DNA, despite it being overlooked in the past. The term junk DNA was not coined due to a lack of understanding of genomes, but rather to describe certain characteristics such as the variability in genome size, gene duplication mechanisms, degradation due to mutations, and theories in population genetics. All of these observations and theoretical considerations remain accurate and applicable.

David Comings listed four justifications for proposing the existence of junk DNA in a comprehensive paper published in 1972:

• Certain organisms possess a surplus of DNA that appears to exceed their actual needs.
• The current estimates of gene count fall significantly below the potential capacity for genes.
• The burden of mutations would be overwhelming if every part of the DNA had a function.
• Some non-functional DNA is clearly present.

The significance of non-coding DNA in the process of aging and cancer:

The recent increase in value for junk DNA within the scientific community is partly due to a broader shift in attention towards DNA sequences that go beyond solely aiding in protein synthesis. Junk DNA frequently contains RNA sequences that do not code for proteins but still have important functions in cellular activities. According to Pennisi's study in 2012, it was found that over 80% of human DNA has a biochemical role, implying that a significant portion of previously considered "junk" DNA must have a specific function. The variable number tandem repeat sequences have recently been examined closely as part of the ongoing study of junk DNA.

As cells grow older, they cease to divide and replicate. Telomeres are caps located at the ends of DNA strands that become shorter with each reproduction. When the telomere reaches a critically short length, it becomes incapable of duplicating, causing the cell to go through the aging process and ultimately die. This is the typical way in which the majority of mature cells in the body operate. Introducing telomerase reverse transcriptase; this enzyme aids in maintaining a consistent length of telomeres during cell division, resulting in telomere length homeostasis. The hTERT gene is responsible for producing an enzyme called telomerase reverse transcriptase, which is more active in tissues that have a plentiful supply of stem cells and in cancer cells. In their research, Xu and colleagues (2021) discovered that the VNTR2-1 sequence functions as an enhancer, which promotes the activation of hTERT transcription. Interestingly, they also observed that deleting the VNTR2-1 sequence from cancer cells disrupts this activation process, leading to a decrease in telomere length during cell division and a cessation of tumor growth. This information gives important understanding about the factors that affect cancer, going beyond oncogenes and tumor suppressor genes, which presently do not completely clarify the risk of cancer for patients.

It is worth noting that the quantity of DNA repetitions within the VNTR2-1 sequence differs among individuals. In 2021 researchers examined population groups that possessed VNTR2-1 sequences ranging from 53 to 160 repeats. The study discovered that individuals with longer sequences of repeats exhibited a greater level of hTERT gene activity. The research discovered differences in the length of VNTR2-1 among different demographic groups. It observed that African American individuals had the shortest VNTR2-1 sequences. Having a brief VNTR2-1 sequence is both advantageous and disadvantageous as it could imply a lower likelihood of developing cancer, but it may also suggest accelerated cellular aging.

The activity of telomerase will undoubtedly remain a key area of interest for scientists as they strive to combat cancer and address the effects of aging on the body. A recent research conducted on mice lacking telomerase has demonstrated that restoring telomerase can result in the revival of cell growth, a decrease in DNA harm, and the elongation of telomeres. Moreover, the reactivation of telomerase resulted in the elimination of degenerative characteristics in organs and showed potential in reversing neurodegeneration, as observed in the study conducted by Jaskelioff et al(2011). A clear understanding of how telomerase works and is controlled is crucial for the medical field. I hope that future research will be able to utilize the newfound knowledge about VNTR2-1 from the research community to create innovative treatments for cancer and anti-aging purposes.

The role of ‘junk’ in genetics:

There is ongoing discussion because researchers from different fields, such as genetics, evolutionary biology, and molecular biology, have varying perspectives and definitions when it comes to determining a "functional" element in the genome.

This lack of clarity in the scientific literature has resulted in different opinions and approaches being taken.

However, the notion of widespread transcription and splicing in the human genome has been considered as an additional sign of genetic function, alongside the conservation of the genome. This is important because poorly conserved functional sequences may not be identified through genomic conservation alone.

Additionally, a significant portion of the seemingly useless DNA is actually involved in regulating epigenetics and plays a crucial role in the development of complex organisms.

Certain critics have contended that it is necessary to evaluate functionality based on a suitable null hypothesis. In this scenario, the null hypothesis suggests that these specific regions of the genome serve no purpose and exhibit characteristics, either through conservation or biochemical activity, that align with what is typically observed in non- functional regions according to our existing knowledge of molecular evolution and biochemistry. These critics argue that a region should only be considered functional if it has been proven to have more characteristics than what would be expected based on the null hypothesis.

Until then, it should be temporarily classified as non-functional.

The makeup of the genome:

Another crucial factor to take into account is the structure of eukaryotic genome. Contrary to popular belief that it consists of enigmatic "dark matter," we have a good understanding of the features of the sequences that make up around 98% of the human genome, which do not code for proteins.

Transposable elements:

It refers to genetic sequences that have the ability to move or jump between different locations within a genome.

The most common form of non-coding DNA is made up of transposable elements (TEs), which include different types of retroelements like "Short and Long Interspersed Nuclear Elements" (SINEs and LINEs), endogenous retroviruses, and cut- and -paste DNA transposons. Transposable elements have often been associated with terms like "parasitic" or "selfish" due to their ability to multiply. Nevertheless, most of these components do not have any effect on humans because a significant portion of them have been severely damaged by genetic mutations. Because of this decline in quality, calculations of the portion of the human genome that is occupied by TEs has varied significantly, ranging from half to two-thirds. Bigger genomes, such as those found in salamanders and lungfishes, most likely possess an even greater amount of transposable element DNA. Numerous instances have been discovered in which TEs have assumed regulatory or other functional tasks within the genome. Kidwell and Lisch suggested a broader perspective on the relationship between transposable elements and their hosts, acknowledging the intricate dynamics involved. They proposed categorizing each transposable element on a continuum ranging from parasitism to mutualism. However, only a small fraction of TE sequences have shown evidence of function at the organism level.

Therefore, it is not clear that functional explanations can be extended from a limited number of specific examples to all TEs present in the genome.

DNA that is highly repetitive:

Another significant portion of the genome is made up of DNA that is repeated many times. These areas can vary greatly even among individuals from the same group (which is why they are called "DNA fingerprints") and can change in size due to processes like unequal crossing over or replication slippage. There are several repetitions that are believed to come from shortened TEs, while others are made up of consecutive arrays of two or three nucleotides. Just like transposable elements, certain repetitive sequences also have a function in controlling gene activity. Some repeats, like telomeric- and centromeric-associated ones, have important functions in preserving the integrity of chromosomes. However, at present, there is no proof indicating that most highly repetitive elements serve a purpose.

Introns:

They are sections of DNA that do not contain genetic instructions for protein synthesis. Based on Gencode v17, about 40% of the human genome consists of intronic areas. Nonetheless, this percentage might not be entirely accurate since it encompasses all annotated occurrences. It is worth mentioning that a significant portion of TEs and repetitive elements can be located within introns. While introns can contribute to a wider range of protein variations by influencing alternative splicing, it is evident that most of the intronic sequence evolves freely, accumulating mutations at a similar rate as neutral regions.

Despite the average intron size being approximately 1.5 kb in humans, research indicates that the majority of the restricted genetic material is found within the initial and final 150 nucleotides.

Pseudogenes:

They are non-functional genes that have lost their ability to produce proteins. Pseudogenes are also abundant in the human genome. The total number is estimated to be between 12,600 and 19,700. These consist of both traditional pseudogenes (which are exact duplicates, as described by Ohno) and processed pseudogenes, which are created by reverse transcription of mRNA. Once again, even though a few pseudo-genes have been repurposed to serve a function at the organism level, the majority of them are continuously changing without any constraints on their sequences and probably do not have any purpose.

Genetic load:

For a while now, it has been recognized that organisms can only handle a certain amount of harmful mutations in each generation. Usually, the existence of these genetic mutations is not detrimental since organisms with two complete sets of chromosomes typically only need one working copy of a particular gene. On the other hand, if the rate of generating these mutations exceeds the rate at which natural selection can eliminate them, the overall genetic makeup of the species will deteriorate over time due to the increasing number of harmful gene variations in each new generation. This ratio is approximately one harmful mutation occurring in each new generation. In this particular situation, it is evident that the rate at which mutations occur has a direct impact on the maximum amount of functional DNA that can exist. At present, it is believed that the frequency of genetic changes in humans ranges from 70 to 150 mutations per generation. Based on this argument, we can conclude that, at maximum, only 1% of the nucleotides in the genome are necessary for survival in a precise order. However, recent computational models have shown that genomes have the ability to tolerate multiple slightly harmful mutations in each generation. By utilizing statistical techniques, researchers have approximated that in each generation, humans experience an average of 2.1 to 10 harmful genetic changes. This information implies that only a maximum of 10% of the human genome shows observable functions at the organism level. On the other hand, it also suggests that a minimum of 90% of the genome is made up of useless or non-functional DNA. These statistics align with the findings on genome conservation and contradict the notion that 80% of the genome serves a functional purpose as suggested by ENCODE. It is still possible that significant quantities of noncoding DNA have functions unrelated to their nucleotide sequence, but it is not clear how this would fit with the "onion test."

Conclusion:

For many years, researchers have been curious about the potential impact of the majority of the DNA found in eukaryotic genomes on the development and functioning of organisms. The ENCODE data is just the latest addition to an ongoing research effort aimed at tackling this problem. Nevertheless, there has been existing evidence that raises doubts about the functional significance of the majority of the human genome for quite some time. This does not mean that the non-protein-coding parts of the genome have no function. It has been known for over fifty years that there are functional noncoding sequences, and even those who initially believed in the concept of "junk DNA" and "selfish DNA" anticipated the discovery of more functional noncoding sequences. However, they also emphasized that evolutionary factors, understanding of the variety of genome sizes, and our understanding of the origins and characteristics of genomic components do not validate the idea that every DNA has a purpose just because it exists. No recent research or commentary on the topic has disputed or questioned these observations.

Written and researched by: Hari priya T

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