Jumping Genes

In 1950, Barbara McClintock published ‘The Origin and Behavior of Mutable Loci in Maize’ based on her studies on the unusual phenotypic features in maize, thus introducing the idea of jumping genes or transposons. Her discovery was revolutionary and was met with criticism as it suggested that an organism’s genome is not stationary but part of the genome jumps around and rearranges. However, the role of transposons was eventually recognized and appreciated and McClintock was awarded the Nobel Prize in 1983 for this and her other contributions in the field of cytogenetics.

Jumping genes or transposons are segments of DNA with length varying from 100 to 20,000 base pairs. They move around to different positions in the genome of a single cell which may cause modifications in the genome length of the cell and its descendants. They are found in almost all organisms and typically in large amounts. For example, almost 50% of the human genome is made of transposons.

There are mainly two types of transposons:

Class I transposons or retrotransposons: They move by a ‘copy and paste’ mechanism via an RNA intermediate. They are first transcribed into RNA, then reverse-transcribed into DNA before being inserted into a new location in the genome.
Class II transposons or DNA transposons: These move by a ‘cut and paste’ mechanism without an RNA intermediate. They are excised from one location and inserted into another.

Impact of transposons on genome:

Mutations: Transposons can disrupt gene function if they insert within or near a gene, leading to mutations.
Genetic diversity: By creating genome modifications, they contribute to genetic diversity within populations, thus playing a significant role in the evolution of genomes.
Genome size: They can modify the size of the genome by copying or cutting and inserting into the genome.

Sequencing of transposons:

Whole genome sequencing (WGS): Next generation and third generation methods can be used to sequencing of the entire genome enabling the identification, assembling, and annotation of transposons.
Targeted sequencing: Techniques such as TE capture, where probes are designed to specifically bind and enrich the transposon sequences and PCR-based primers designed to amplify the specific transposons can help in subsequent sequencing.
Bioinformatics tools: Software such as RepeatMasker (https://www.repeatmasker.org/) , and databases such as Repbase (https://www.girinst.org/repbase/) can facilitate identification and classification of transposons. TEdenovo (https://urgi.versailles.inra.fr/Tools/REPET/TEdenovo-tuto) and TEannot (https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto) can help in identifying de novo transposons and annotate them to the genome.