Genetics, Transposons

Development

There are transposons in a wide variety of organisms, from bacteria and yeasts to humans. Transposition can take place from one site to another of the same chromosome, or from one chromosome to another (in eukaryotic organisms whose genome is organized into several chromosomes), or even from a chromosome site to a plasmid site (in organisms containing plasmids, genetic elements independent of the chromosome and capable of autonomous replication), or finally from the chromosome of one cell to that of another.

As widely documented, transposons can influence the output of the host genome; this mechanism allows the development of totipotency, a key stage of development. Some structures prove to be important for the epigenetic action of transposons, such as the presence of human leucine tRNA primer (HERVL), endogenous retroviruses (ERVs), and long interspersed nuclear elements (LINE-1s); these are important elements for the movement and action of transposons.

During embryological development, we find different transposons depending on the stage of development (without forgetting the retrotransposons).

Cellular

Researchers have found transposons in the genomes of eukaryotes and prokaryotes. Genomes of eukaryotes contain multitudes of repetitive DNA sequences. Transposons make up much of this repetitive DNA. 45% of the human genome is transposable elements.[4] Because so much of the genome is transposable, the theory is that they are participants in speciation and evolution, although the triggers are not understood.[5] Transposons have a similar structure to non-transposable DNA and contain the same nucleic acids and nucleotides (cytosine, adenine, guanine, and thymine).

Molecular Level

Bacterial transposons belong to two classes: compound transposons (class I) and complex transposons (class II). A class I transposon contains a copy of an insertion sequence (IS) at each end. At its ends, a class II transposon has two equal sequences of 30/40 pairs of nucleotides each, arranged in the opposite orientation.

The transposition can be replicative or non-replicative. In non-replicative transposition, there is a cut of the double helix to the original site before the transposon moves. In other cases, the transfer takes place without cutting the double helix to the site of origin (conservative transposition). In the replicative transposition, as a consequence of the replication, there will be a copy of the transposon at the insertion site and another at the origin site, without any cut of the double helix. This process will lead to the formation of an intermediate called co-integrated.

Function

Transposons are a mechanism to increase genomic diversity. Transposons can inactivate or alter gene expression by inserting themselves within introns, exons, and other regions. They can move non-transposon DNA. They can remove genes by internal deletions.[6] There are many mechanisms of transposition that minimize the deletions to promote the survival of the host.[6]

Mechanism

Transposons can be divided based on the mechanism of transposition and integration. Class I elements, retrotransposons, use an RNA intermediate that is reverse-transcribed into a cDNA copy that reintegrates into a new genomic home.  Class II elements are DNA transposons mobilized by a DNA intermediate or by replication involving a circular DNA intermediate. Each of these classes can further sub-categorize based on common genetic or monophyletic origins.

Class I elements are also called retrotransposons. They begin as DNA and become transcribed into RNA via the normal mechanism. Then reverse transcriptase and an endonuclease, which are generally coded for within their transposable element, are used to reverse transcribe the RNA back into DNA. This DNA is then inserted back into the chromosome at its new location. Their life cycle and structure are very similar to retroviruses.[7]

Class II elements, called DNA transposons, are the classic “cut-and-paste” transposons whose mechanism begins which excision from the genome. They are not replicated like Class I elements but often include a transposase gene. Transposase is an enzyme that facilitates transposon movement. TIRs (terminal inverted repeats) flank transposase, which transposase uses to excise the transposon. When the transposon is inserted into a new location, the DNA at the target site duplicates producing TSDs, or target site duplications. TIRs and TSDs are unique to transposons and are used to classify transposons into different families.[6]

Testing

Currently, tests can be used to detect pathogenic mutations from transposons, such as large deletions or large insertions/duplications.

Pathophysiology

Transposon insertions can be pathogenic, being able to alter gene expression; transposon inserts represent about 5% of the molecular pathology. Among the alterations in the function of the transposons, we find the: Kindler syndrome (in the FERMT1 gene or fermitin family member 1); hemophilia A (in the factor VIII gene or anti-hemophiliac factor or AHF).

Transposon inserts may play a role in determining susceptibility to multifactorial diseases such as tumors. Transposons, and real disease mutations, seem to be able to create hypomorphic alleles: they are not actual pathogenic alleles but alleles with reduced functionality that can worsen the phenotype when they are in association with a mutation- real disease. These hypomorphic alleles may have some weight in generating traits of susceptibility to multifactorial diseases.

Clinical Significance

Transposons can serve as genetic tools to introduce foreign DNA into the genome of another organism.  For example, the insertion of mouse DNA into zebrafish.[8] Since transposons are useable for insertional mutagenesis, they are important for better understanding genomes. Transgenics allows for a fast in vivo analysis of the genome and proteome. Transposons also play roles in the pathogenesis of some identified conditions, such as hemophilia A.

Transgenics has helped to identify genes related to diseases and pathologies. For example, transposons have been a tool to study novel culprits of cell transformation in cancer pathogenesis. Before insertional mutagenesis, studying genes involved in cancer pathogenesis was difficult.[9] Insertional mutagenesis has also helped to determine the pathogenesis of pathogens like Cryptococcus neoformans. It is an infectious fungus that is being analyzed through insertional mutagenesis to determine what genes were involved in fungal virulence.[10]

Worldwide mortality rates are increasing due to bacterial infectious disease, and bacterial transposons have implications in the development of bacterial antibiotic resistance.[11] All bacteria are capable of adapting to the evolutionary stressor of antibiotic usage. Resistance determinants that already exist in bacterial DNA become mobilized by transposition. Through this process, horizontal genetic exchange is possible and allows bacteria to attain resistance.[12]

Some diseases may have arisen from transposition within the human genome. Studies have found that some epithelial tumors arise from spontaneous retrotransposon integration. The research of these retrotransposons may be highly impactful in understanding tumorigenesis.[13] Hemophilia A, an X-linked recessive disorder that results in low amounts of clotting factor VIII, results in bleeding episodes. A study has demonstrated that insertional mutagenesis of a repetitive sequence, some L1 sequences, can be spread through transposition and cause disease.[14]

Gene therapy, using genetic tools to edit the human genome, has a high potential for benefitting patients with genetic pathology, but it is also high risk. The administration of retroviruses in gene therapy trials has correlated with adverse outcomes. In the treatment of 9 patients with SCID, 4 developed acute leukemia within ten years of being treated with gene therapy. One of the four who developed leukemia died. However, the eight remaining had sustained reversal of the immunodeficiency.[15] The Sleeping beauty (SB) transposon is the most researched transposon used in non-viral insertional mutagenesis gene therapy. Using transposons instead of viral vectors has two advantages in gene therapy: easier manufacturing and transposons like SB have less preference for integration sites.[16] The use of gene therapy to remove a deleterious mutation has successfully treated a mouse model of hemophilia. They were able to restore hemostasis in the mice treated.[17] Duchenne muscular dystrophy, another X-linked recessive disorder, results in a mutation in the dystrophin gene, which leads to muscle fiber degeneration, weakness, and death. A study utilizing the PiggyBac transposon demonstrated that muscles treated with an autologous cell-based therapy had become more resistant to fatigue.[18]