WHAT ARE TRANSPOSONS

Transposons, also known as "jumping genes," are segments of DNA that have the
ability to move from one location to another within a genome, they sometimes
creates or reverses mutations and alter the cell's genetic identity and genome size,
they can be found in the DNA of various organisms, including humans.
Transposons can cause genetic changes by inserting themselves into different
regions of the genome, which may impact gene expression and can potentially lead
to genetic mutations. They play a significant role in genome evolution and have
been found to contribute to genetic diversity within populations.

In the human genome, L1 and Alu elements are two examples. Barbara
McClintock's discovery of them earned her a Nobel Prize in 1983. Its importance
in personalized medicine is becoming increasingly relevant, as well as gaining
more attention in data analytics given the difficulty of analysis in very high
dimensional spaces.

Transposable elements make up a large fraction of the genome and are responsible
for much of the mass of DNA in a eukaryotic cell. Although TEs are selfish
genetic elements, many are important in genome function and evolution.
Transposons are also very useful to researchers as a means to alter DNA inside a
living organism.

There are at least two classes of TEs: Class I TEs or retrotransposons generally
function via reverse transcription, while Class II TEs or DNA transposons encode
the protein transposase, which they require for insertion and excision, and some of
these TEs also encode other proteins.

PROPERTIES OF TRANSPOSONS

1. Mobility: Transposons possess the ability to move within a genome. They can
"jump" from one location to another, either within the same chromosome or to
different chromosomes. This mobility is facilitated by specific enzymes encoded
by the transposon itself.

2. DNA Sequence: Transposons are composed of DNA sequences that contain

coding regions for enzymes required for their transposition. These coding regions
are flanked by inverted repeat sequences, which serve as recognition sites for the
transposase enzyme.

3. Classification: Transposons can be classified into two main types based on their
mechanism of transposition. Class I transposons, also known as retrotransposons,
transpose via an RNA intermediate, while Class II transposons, also called DNA
transposons, move directly as DNA.

4. Impact on Genome Evolution: Transposons play a significant role in genome

evolution by causing genetic rearrangements and mutations. Their movement can
disrupt genes, alter gene expression patterns, or lead to the creation of new genes
through insertional mutagenesis.

5. Copy Number Variation: Transposons can exist in multiple copies within a

genome, leading to copy number variation. This variation can contribute to
genomic diversity and influence the phenotypic variability observed within a
population.

6. Regulation: Transposon activity is tightly regulated to prevent excessive genome

disruption and maintain genome stability. Host mechanisms, such as DNA
methylation and small RNA-based silencing pathways, help control the activity of
transposons and prevent their uncontrolled movement.

7. Genetic Tools: Transposons have been harnessed as genetic tools in various

organisms. They can be used for gene tagging, gene knockout, and gene transfer
experiments. Transposon-based systems, such as the piggyBac system, have been
developed for efficient gene transfer and genetic manipulation in both plants and
animals.

Overall, transposons are dynamic elements that can influence genome structure,
gene regulation, and evolution. Their properties and behavior have significant
implications for understanding genetic diversity, genome stability, and the genetic
manipulation of organisms.
CLASSES OF TRANSPOSONS

Transposons can be broadly classified into two main classes based on their
mechanism of transposition:

1. Class I Transposons (Retrotransposons): These transposons transpose via an

RNA intermediate. They are typically found in eukaryotic genomes and have the
ability to reverse transcribe their RNA into DNA, which is then integrated into a
new genomic location. Retrotransposons are further divided into two subclasses:

a. Long Terminal Repeat (LTR) Retrotransposons: These retrotransposons have

long terminal repeat sequences at their ends. LTR retrotransposons resemble
retroviruses, which include human immunodeficiency virus (HIV). They encode
reverse transcriptase and integrase enzymes.

b. Non-LTR Retrotransposons: Non-LTR retrotransposons lack long terminal

repeats but still transpose via an RNA intermediate. They are further classified into
long interspersed nuclear elements (LINEs) and short interspersed nuclear
elements (SINEs).

2. Class II Transposons (DNA Transposons): These transposons move directly as

DNA. They are found in both prokaryotic and eukaryotic genomes. Class II
transposons are typically flanked by inverted repeat sequences, which serve as
recognition sites for the transposase enzyme. They are further categorized into two
subclasses:

a. Cut-and-Paste Transposons: These transposons excise themselves from their

original location and then reinsert into a new genomic site. The process involves
the activity of a transposase enzyme.
 b. Copy-and-Paste Transposons: Copy-and-paste transposons replicate
themselves and insert the copy into a new genomic location while retaining the
original transposon. This process is mediated by a transposase enzyme.

These classes of transposons exhibit distinct mechanisms of transposition and have

contributed significantly to genome evolution and diversity. Their movement
within genomes can lead to genetic rearrangements, gene disruptions, and the
creation of new genetic variations.

FUNCTIONS OF TRANSPOSONS

Transposons, also known as "jumping genes," are segments of DNA that can move
within a genome. While traditionally considered as "selfish" or "parasitic"
elements, transposons have been found to have several functional roles in genomes.
Here are some functions of transposons:

1. Genetic Variation: Transposons contribute to genetic diversity within a

population or species. Their movement and insertion into different genomic
locations can create new genetic combinations and variations, leading to
phenotypic diversity.

2. Gene Regulation: Transposons can influence gene expression and regulation.

When inserted near genes, they can act as regulatory elements, affecting the
expression levels of nearby genes. Transposons may contain regulatory sequences
that can activate or silence nearby genes.

3. Genome Rearrangement: Transposons can cause genomic rearrangements

through their movement within a genome. This can lead to the shuffling of genetic
material, including the relocation of genes, duplication or deletion of genomic
regions, and rearrangements of chromosomal structure.

4. Genetic Innovation: Transposons can contribute to the creation of new genes and
functional elements. When transposons insert into coding regions of genes, they
can disrupt the gene's function. However, in some cases, this disruption can lead to
the evolution of new genes or the acquisition of new functional domains.

5. DNA Repair and Recombination: Transposons can participate in DNA repair

and recombination processes. They can serve as substrates for DNA repair
enzymes and participate in homologous recombination events. This can have
implications for genome stability and the repair of DNA damage.

6. Evolutionary Drivers: Transposons can act as evolutionary drivers by promoting

genetic changes and adaptations. They can facilitate the rapid evolution of
genomes by introducing new genetic material, promoting gene duplication, and
contributing to genome plasticity.

Transposons have functional roles, their activity needs to be tightly regulated to

prevent excessive genome disruption and maintain genome stability. Host
mechanisms, such as DNA methylation and small RNA-based silencing pathways,
help control the activity of transposons and maintain their functional balance
within genomes.
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