Junk DNA (jDNA) is the part of DNA which have no genetic codes for proteins and RNAs. This part of the DNA was thought to be useless, but recent studies have shown that this non-coding DNA does not seems to be junk anymore. Therefore, modern genetics does not recommend the use of the term junk to illustrate this non-coding DNA segment. However, in recent years, researchers have used these terms to mention jDNA: extra DNA, selfish DNA, and non-coding DNA (The Lancet 2012; Dawkins 1989; Stein 2003; Lodish et al. 2008).
What is Junk DNA?
The inactive portion of DNA containing no genetic codes for functional proteins and RNAs is known as junk DNA or non-coding DNA.
In past, the geneticists have concentrated on just the small part of the DNA that codes for proteins. Proteins are synthesized through the process of transcription and translation by a small portion of the DNA and the rest of the DNA was declared to be junk. Moreover, researcher says that some part of the active DNA later became junk after losing their functionality through mutations happens in past. It is assumed that the major portion of non-coding DNA has been evolved through continuous evolutionary mutations (Doolittle 2013).
Salient Features of Junk DNA
Some key points concerning the non-coding or junk DNA are:
- Much of the DNA has no function
- Non-coding DNA sequences may be functional in the past but have become function-less over time
- Non-coding DNA may be an evidence for the past mutational abnormalities
- Coding DNA has less chance to be damaged by chemicals and mutations, than the non-coding DNA
- Non-coding DNA is the main source of evolution, because of its non-coding genetic codes
- Some of the non-coding regions may link enzymes with the coding regions
- Non-coding DNA performs specific functions to support the functioning of coding DNA
- Change in the non-coding DNA can cause a severe effect on the coding DNA by altering its functionality and leading to a deleterious effect on the genome
- Non-coding DNA sequences are also termed mobile elements, which do not have specific functions in the genome but arbitrarily hampers the functions of coding DNA leading to deleterious effects (Walkup 2000)
Types of Junk DNA
Some of the major types of non-coding DNA are:
- Introns: The genic internal segments, that are separated at the RNA-level (Chorev and Carmel 2012).
- Pseudo-genes: Genes disabled by an insertion or deletion (Tutar 2012).
- Non-coding functional RNA: The RNA sequences that are not decoded into protein (Bhat et al. 2016).
- Cis- and Trans-regulatory elements: The promoter sequences, enable the transcription of a specific gene (Shi et al. 2012).
- Transposable elements: The mobile repetitive elements that can change their site in the genome (Augé-Gouillou 2013).
- Viral sequences: The Retro-virus sequences arise through reverse transcription (Burrell et al. 2017).
- Telomeres: The repetitive DNA segments, lie at the end of the chromosome and avert the decline of the chromosome (Augé-Gouillou 2013).
- Satellite sequences: The cyclic arrangement of short repeats (Plohl 2010).
- Inter-spread repeats: The long repetitive sequences, derived from T-elements (Smit 1996; Walkup 2000).
Mysterious Role of Junk DNA
In human genetics, one of the major unsolved mystery is the proportion of functional and non-functional sequences in the genome. Recent studies about the genome exposed that the majority of the DNA is bio-chemically vigorous and functional, which were designated as biochemically functional. Therefore, scientists have focused on this evidence to debunk the concept of non-coding DNA repetitive elements and their effect on higher organisms. However, according to the concept of evolution, there is a great difference between biochemical activity and functionality.
It was thought that the excess DNA, is informationally junk and has no role in the past or current selection in organisms, and also has no role in the historical evolution (Pennisi 2012). The non-coding sequences are not an extra material that is attached to the coding sequences, which has no functional abilities. However, it acts as a major raw material for the mutations, which is an important aspect of evolution. Haldane’s work suggests that without the non-coding DNA, evolution cannot be explained mathematically how mutation works and how much time is required for a single mutation to occur.
Parasitic Replicating Nature
According to recent genetics, it is assumed that this DNA keeps replicating into generations due to its parasitic nature and also provided a space for new genetic codes (Walkup 2000). Moreover, modern studies have exposed some of the DNA sequences which have been thought to be junk, but now have a major role in gene regulation and gene function in different ways. This innovative information about the genome, that 80% of it is biochemically active increases the interest of scientists in it. Among these non-coding DNA sequences, some are those sequences that go for potential regulatory functions in the genome (Wong et al. 2000).
However, studies have revealed that the abundance of the single nucleotide polymorphism site in the active regions of the genome, which are associated with the diseases and other phenotypic characters, maybe functional but not a trustworthy proof of functionality (Niu and Jiang 2013). Only 2% of the human genome codes for the protein and the rest is all junk. That 2% have more than 20,000 protein-coding genes and the rest of 98% is of no use, therefore termed as “Junk DNA”. There are many genes found in the genome which synthesize RNAs but do not produce the final protein products (Ezkurdia et al. 2014; Jani 2015).
Since 3-6 million years ago, humans have diverged from the chimpanzee’s, which means there are millions of mutations that have happened by which the chimpanzee’s genome has changed into the human’s genome with great adaptabilities and variations (Boyd et al. 2015). The chimpanzee’s genome is 13% more than the human’s genome, but 95% of which is total junk. Some evolutionists thought that this 95% non-coding DNA provided the opportunity for mutations, which led to the evolution of humans as a more complex and adaptive species on earth.
It is believed that they had 1,00,000 to 3,00,000 generations to fix these worthy mutations. Each discovery of the non-coding DNA led the researcher to the new aspects of the evolution of life on earth (Walkup 2000). As we know that, many organisms have more DNA than humans e.g., Onion has 5 times more DNA than humans (Palazzo and Gregory 2014). As compare to onion, humans are more complex organisms and this does not justify that why onion has more DNA, but studies have shown that it is necessary (Freeling et al. 2015).
There are some misunderstandings about the non-coding DNA that it has a boundary between information and structure of the DNA, however, the loci which are not transcribed yet also encodes useful information. This shows that the gross structure of the chromosome encodes information related to gene functions. As we know that, the DNA itself serves as a template for the replication, which means the same information passes as of the template (Djebali et al. 2012; The Lancet 2012).
Moreover, the cellular complexity is also present between different organisms, as in the fruit flies which have more genes than humans, but the humans are more complex organisms than the fruit flies and the other organisms with a greater number of genes. The genes present in humans are thought to be more refined and expressive due to which the humans have better physical and structural development than the other organisms (Frazer 2012). There are several agricultural crops that also exhibit this complexity.