Long terminal repeats (LTRs) are identical sequences of DNA that repeat hundreds or thousands of times found at either end of retrotransposons or proviral DNA formed by reverse transcription of retroviral RNA The LTRs are partially transcribed into an RNA intermediate, followed by reverse transcription into complementary DNA (c DNA) and ultimately ds DNA (double-stranded DNA) with full LTRs. This method of dating is used by paleovirologists, though it fails to take into account confounding factors such as gene-conversion and homologous recombination.The LTRs then mediate integration of the retroviral DNA via an LTR specific integrase into another region of the host chromosome. in length and, like other retroviral LTRs, is segmented into the U3, R, and U5 regions.LTR retrotransposons have direct LTRs that range from ~100 bp to over 5 kb in size.LTR retrotransposons are further sub-classified into the Ty1-copia-like (Pseudoviridae), Ty3-gypsy-like (Metaviridae), and BEL-Pao-like groups based on both their degree of sequence similarity and the order of encoded gene products.Although retroviruses are often classified separately, they share many features with LTR retrotransposons.A major difference with Ty1-copia and Ty3-gypsy retrotransposons is that retroviruses have an envelope protein (ENV).
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The understanding of how retrotransposons and their hosts' genomes have co-evolved mechanisms to regulate transposition, insertion specificities, and mutational outcomes in order to optimize each other's survival is still in its infancy.
Because of accumulated mutations, most retrotransposons are no longer able to retrotranspose.
All of the required signals for gene expression are found in the LTRs: Enhancer, promoter (can have both transcriptional enhancers or regulatory elements), transcription initiation (such as capping), transcription terminator and polyadenylation signal.
The transcript begins, at the beginning of R, is capped, and proceeds through U5 and the rest of the provirus, usually terminating by the addition of a poly A tract just after the R sequence in the 3' LTR.