Noncoding DNA :

Junk or untapped treasure?

A peculiar finding

Once the human genome was sequenced, scientists were in for a surprise as they found that only a tiny percentage-1.5%- of the genome coded for proteins or is transcribed. The bulk of eukaryotic genomes consists of DNA sequences that neither code for proteins nor are transcribed to produce RNAs. In the early decades, scientists considered these major portions of DNA as not having any biological function, Its existence did not contribute to the fitness of the organism.

An infographic showing the relative composition of the human genome. Protein coding genes only form about 2–3% of the total genome.

Junk?

However the comparison of the genomes of multiple eukaryotes have revealed the conserved nature of this DNA across species. For example, the genomes of mice, rat and humans contain almost 500 regions of identical non-coding DNA sequences. A level of conservation higher than is seen for protein-coding regions in these species. This in turn strongly suggests that “junk” DNA, might not be junk after all.

The curious case of jumping genes

In 1944, Barbara McClintock discovered transposable elements(TEs) while working on the maize plant. These TEs can move around different positions of the genome of the organism either by copy-paste mechanism or by the cut-paste mechanism. Hence these mobile segments of the DNA are popularly known as jumping genes. These segments are surprisingly prevalent making up to 44% of the entire human genome(which is 75% of the “junk” DNA).

First evidence of TEs was found by Barbara McClintock when studying the inheritance patterns of variegation in corn kernels.

Jumping genes can introduce foreign DNA into a genome. It is also able to produce various genetic alternations upon insertion in a genome that is it can inactivate or alter the expressions of the genes. It can also help in the reorganization of a genome. Not only this, but jumping genes are also responsible for the deletion of mutated genomic DNA, and therefore nowadays jumping genes are widely used in the biotechnology field.

Mechanism of transposon transmission , these TEs move with a “cut-and-paste” mechanism with the help of the enzyme transposase. Another type of TE, called a retrotransposon move with the help of an RNA intermediate and a “copy-and-paste” mechanism.

However, these jumping genes aren’t all good as many TEs are linked with multiple harmful mutations in the human genome ranging from haemophilia, SCID to a predisposition to cancer and Alzheimer’s disease.

Other “Junk”

Repetitive DNA not related to TEs probably arises from mistakes during DNA replication accounting for about 14% of the human genome. About 33% of this consists of duplications and repetitions of long stretches of DNA, with each unit ranging from 10,000 bp to 300,000 bp.

Tandem repetition

In contrast to these long sequences, the DNA also contains many copies of tandemly repeated short sequences known as simple sequence DNA. These Short tandem repeats or STRs are used for genetic analyses, these make up about 3% of the total genome. Much of this DNA is located at the telomeres and the centromere of the chromosome, suggesting a structural role for this DNA.

DNA as a structural molecule

Centromeric DNA might also help with the organisation of chromatin inside the nucleus. Telomeric DNA also binds proteins that protect the chromosomal ends from degradation and from joining with other chromosomes. These regions of simple sequence DNA, are surprisingly difficult to sequence and determine the extent of and account for much of the uncertainty of the estimates of genome sizes.

Conclusion

We have seen the fascinating journey of the noncoding DNA discovered till now. So be ready to know such interesting facts in the future also as technology is enhancing day by day.