Retrotransposon
[2] Through reverse transcription, retrotransposons amplify themselves quickly to become abundant in eukaryotic genomes such as maize (49–78%)[3] and humans (42%).
[4] They are only present in eukaryotes but share features with retroviruses such as HIV, for example, discontinuous reverse transcriptase-mediated extrachromosomal recombination.
LTR retrotransposons are characterized by their long terminal repeats (LTRs), which are present at both the 5' and 3' ends of their sequences.
On average, LTR retrotransposons span several thousand base pairs, with the largest known examples reaching up to 30 kilobases (kb).
LTRs are highly functional sequences, and for that reason LTR and non-LTR retrotransposons differ greatly in their reverse transcription and integration mechanisms.
In contrast, LTR retrotransposons undergo reverse transcription in the cytoplasm, utilizing two rounds of template switching, and a formation of a pre-integration complex (PIC) composed of double-stranded DNA and an integrase dimer bound to LTRs.
Additionally, some LTR retrotransposons have an ORF for an envelope (env) protein that is incorporated into the assembled capsid, facilitating attachment to cellular surfaces.
So many endogenous retroviruses have inserted themselves into eukaryotic genomes that they allow insight into biology between viral-host interactions and the role of retrotransposons in evolution and disease.
One endogenous retrovirus or LTR retrotransposon has the same function and genomic locations in different species, suggesting their role in evolution.
RNA-binding proteins bind the RNA-transposition intermediate and nucleases are enzymes that break phosphodiester bonds between nucleotides in nucleic acids.
While historically viewed as "junk DNA", research suggests in some cases, both LINEs and SINEs were incorporated into novel genes to form new functions.
Reverse transcriptase recognises these hydroxyl groups to synthesise LINE retrotransposon where the DNA is cut.
Most LINE copies have variable length at the start because reverse transcription usually stops before DNA synthesis is complete.
The second coding region has a purine/pyrimidine nuclease, reverse transcriptase and protein rich in amino acids cysteines and histidines.
SINEs do not encode a functional reverse transcriptase protein and rely on other mobile transposons, especially LINEs.
SVA are one of the youngest transposons in great apes genome and among the most active and polymorphic in the human population.
SVA was created by a fusion between an Alu element, a VNTR (variable number tandem repeat), and an LTR fragment.
[25] Retrotransposons ensure they are not lost by chance by occurring only in cell genetics that can be passed on from one generation to the next from parent gametes.
Due to their retrotransposition mechanism, retrotransposons amplify in number quickly, composing 40% of the human genome.
The LINE1 insertion rates have varied a lot over the past 35 million years, so they indicate points in genome evolution.
Notably a large number of 100 kilobases in the maize genome show variety due to the presence or absence of retrotransposons.
