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Impact on genome


Transposition of transposable elements into or near a gene may cause deleterious effects by disrupting the protein coding sequence or altering the gene expression or regulation. Many genetic diseases and cancers caused by transposition of transposable elements have been reported. The presence of transposable elements may have a fundamentally negative effect on individual genomes, however, they cannot be neglected when considering the genome evolution.

Genome size

Beside the whole genome duplications, transposable elements also account for the genome size variation. Some studies on closely related species have indicated that such genome size difference can be explained by some recent massive multiplication of transposable elements.

Domestication and Exaptation

TEs can serve as sources of host genes. A significant number of human genes are partly originated from transposable elements. The most famous example is the recombination activating gene 1 (rag1), whose protein catalyzes V-D-J recombination of immunoglobulin gene, which is the main contributor to the variety of antibody. The gene rag1 is originated from a DNA transposon belonging to Transib superfamily. Another group of DNA transposons, Cryptons, contribute to at least 6 human genes, among which 4 are paralogous. Retrotransposons, as well as DNA transposons, have contributed to human gene repertoire. Syncytin 1 is derived from an envelope protein gene of endogenous retrovirus, and contributes to the formation of placenta. The gene peg10 was originated from a Gypsy superfamily of LTR retrotransposons, and the methylation status around this gene is silenced only on paternally inherited chromosome and controls the fetus development. These events are called “molecular domestication”, where the whole or a part of transposons is integrated with the system of their host organism. The term “exaptation” specifically indicates the events where a part of transposons is incorporated with their host system, but not as a part of protein-coding gene. TEs can act as promoter, enhancer, insulator, intron splice site, polyadenylation signal, or any other function in the cell. One example is an enhancer derived from an ancient SINE element, LF-SINE, which controls the expression of ISL1 in the limbs of tetrapods. Many other examples are reported that TEs are the main contributor of ultraconserved elements (UCEs), and are highly conserved in sequence along very long time scale. It is revealed that ancient transposable elements are going to be concentrated in UCEs.

Carrier subpopulation (CASP) hypothesis

GIRI’s team headed by the late Jerzy Jurka proposed a hypothesis called “Carrier subpopulation (CASP)”. It can explain the different repertoires of active transposon families in each species. During speciation, a large population is split into many small subpopulations. In each subpopulation, different active families of transposons multiplicate and are fixed at random due to genetic drift. In a small subpopulation, slightly disadvantageous mutations, such as transposition of transposable elements, can be fixed. It suggests that a new copy of transposable elements can be fixed without any immediate benefit. After the fixation, copies of transposable elements can be eliminated or domesticated/exapted.

Further readings

Kapitonov VV, Jurka J RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol, 2005 Jun;3(6):e181

Kojima KK, Jurka J Crypton transposons: identification of new diverse families and ancient domestication events. Mob DNA, 2011 Oct 19;2(1):12

Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Mi S, Lee X, Li X, Veldman GM, Finnerty H, Racie L, LaVallie E, Tang XY, Edouard P, Howes S, Keith JC Jr, McCoy JM. Nature. 2000 Feb 17;403(6771):785-9.

Deletion of Peg10, an imprinted gene acquired from a retrotransposon, causes early embryonic lethality. Ono R, Nakamura K, Inoue K, Naruse M, Usami T, Wakisaka-Saito N, Hino T, Suzuki-Migishima R, Ogonuki N, Miki H, Kohda T, Ogura A, Yokoyama M, Kaneko-Ishino T, Ishino F. Nat Genet. 2006 Jan;38(1):101-6.

A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. Nature. 2006 May 4;441(7089):87-90.

Jurka J, Bao W, Kojima KK, Kohany O, Yurka MG Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates. Biol Direct, 2012 Oct 25;7:36

Jurka J, Bao W, Kojima KK Families of transposable elements, population structure and the origin of species. Biol Direct, 2011 Sep 19;6:44

Jurka J, Bao W, Kojima KK, Kohany O, Yurka MG Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates. Biol Direct, 2012 Oct 25;7:36

Kenji K. Kojima, Ph. D.

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