The Tale of junk DNA

It was in 1972 that a geneticist named Susumu Ohno, was the first to coin the term “junk” DNA.He referred to it as defunct relatives of known genes and called them “generic fossils” due to evolutionary presuppositions. As it was assumed that this non coding, junk DNA was merely an accumulation over the course of evolution and was not needed now ,it would be under least selective pressure and be the easiest site of mutations. Unfortunately for many years this notion that non-coding DNA was not functional (“junk”) actually inhibited further studies on it.

It was then in 2010, The ENCODE Pilot Project was released. It studied the 1% of the human genome or approximately 30 million bases spread throughout the genome. The proteins are constituted using the coding and regulatory regions in the DNA.These proteins then express particular characteristics in an organism. The regulatory regions are responsible for exercising control over the production of amount ,activity of the protein. Looking at the complexity of regulation ,the regions of DNA identified as regulatory seem to be very less. Thus the junk DNA was considered to be functioning as regulatory sequences in the DNA.

Initially it was thought that the junk DNA is not transcribed into mRNA. However, the ENCODE Pilot Project discovered that almost all DNA is transcribed into RNA.The genome looks like it is far more of a network of RNA transcripts that are all collaborating together. It appears that many of the regulatory regions of proteins may be transcribed into RNA and serve their function as RNA particularly microRNA and siRNA.

ENCODE discovered some of the functions of the RNA transcripts including the regulation of transcription, replication of DNA, and the structure of chromosomes. This help account for the fact that even though we only have 20,000-25,000 genes in our DNA, we produce 100,000-300,000 proteins. Due to the complexity of the genome, it seemed a bit like trying to define the undefinable.
The ENCODE Project findings revealed that junk DNA is not junk and that most of it is functional in the form of RNA or protein. The genome scan thus be viewed as a  complex three-dimensional network of millions of interacting parts.The ENCODE not only studied the human genome but also studied and compared non-coding DNA across 23 different mammalian species such as mouse, dog, elephant, rabbit, cow, and chimp.

According to evolutionary beliefs, the most useful and functional DNA are conserved overtime and remain the same across a wide range of related organisms. Following this ,it was expected the non-coding DNA would be conserved (similar in sequence among species) because it is functional—just as many of the genes (protein-coding regions) are conserved.
Surprisingly, many functional elements [of the non-coding DNA] were found to be unconstrained [not conserved] across mammalian evolution.” This meant that a large portion of the non-coding DNA among the 23 different mammalian species studied was not conserved (or similar). About 50% of the non-coding DNA that was found to be functional was not conserved. On the other hand, 40% of the non-coding DNA that was conserved has no known function. This 40% will be further studied because of the belief that if it is conserved, it is important and does have a functioning-coding DNA.
The ENCODE Project Consortium stated that, “This suggests the possibility of a large pool of neutral elements that are biochemically active but provide no specific benefit to the organism.” The scientists admit that it has a function, but because of their evolutionary assumptions, they assume that if it’s not conserved it’s not important.

Consequently the concept of “neutral” DNA was proposed. One of the scientists  suggests that this pool may serve as a ‘warehouse’ for natural selection ,while another called it to be  biochemically functional but biologically inert [neutral] elements existing in the human genome and provide evolutionary potential from which new functions may arise .Basically the scientists are suggesting that over time and with the “help” of mutations, this “neutral” DNA could be altered to perform entirely new functions that would allow microbes to become monkeys.

Speaking of the finding of functional non-coding DNA that is not conserved among mammals, the ENCODE Project Consortium stated that, “This is perhaps the biggest surprise of the pilot phase of the ENCODE Pilot Project, and suggests that we take a more ‘neutral’ view of many of the functions conferred by the genome. Accordingly, “junk” DNA, whether conserved or not conserved among species, is important and should be studied.