Our knowledge of the structure and composition of genomes is rapidly progressing in pace with their sequencing. The emerging data show that a significant portion of eukaryotic genomes is composed of transposable elements (TEs). Given the abundance and diversity of TEs and the speed at which large quantities of sequence data are emerging, identification and annotation of TEs presents a significant challenge. Here we propose the first unified hierarchical classification system, designed on the basis of the transposition mechanism, sequence similarities and structural relationships, that can be easily applied by non-experts. The system and nomenclature is kept up to date at the WikiPoson web site.

A unified classification system for eukaryotic transposable elements

http://web.mit.edu/manoli/www/publications/Brennecke_Cell_07_piwiRNAs.pdf

Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila

To study the evolutionary relationship of reverse transcriptase (RT) containing genetic elements, a phylogenetic tree of 82 retroelements from animals, plants, protozoans and bacteria was constructed. The tree was based on seven amino acid domains totalling 178 residues identified in all RTs. We have also identified these seven domains in the RNA-directed RNA polymerases from various plus-strand RNA viruses. The sequence similarity of these RNA polymerases to RT suggests that these two enzymes evolved from a common ancestor, and thus RNA polymerase can be used as an outgroup to root the RT tree. A comparison of the genetic organization of the various RT containing elements and their position on the tree allows several inferences concerning the origin and evolution of these elements. The most probable ancestor of current retroelements was a retrotransposable element with both gag-like and pol-like genes. On one major branch of the tree, organelle and bacterial sequences (e.g. group II introns and bacterial msDNA) appear to have captured the RT sequences from retrotransposons which lack long terminal repeats (LTRs). On the other major branch, acquisition of LTRs gave rise to two distinct groups of LTR retrotransposons and three groups of viruses: retroviruses, hepadnaviruses and caulimoviruses.

Origin and evolution of retroelements based upon their reverse transcriptase sequences.

Four consensus sequences are conserved with the same linear arrangement in RNA-dependent DNA polymerases encoded by retroid elements and in RNA-dependent RNA polymerases encoded by plus-, minus- and double-strand RNA viruses. One of these motifs corresponds to the YGDD span previously described by Kamer and Argos (1984). These consensus sequences altogether lead to 4 strictly and 18 conservatively maintained amino acids embedded in a large domain of 120 to 210 amino acids. As judged from secondary structure predictions, each of the 4 motifs, which may cooperate to form a well-ordered domain, places one invariant amino acid in or proximal to turn structures that may be crucial for their correct positioning in a catalytic process. We suggest that this domain may constitute a prerequisite 'polymerase module' implicated in template seating and polymerase activity. At the evolutionary level, the sequence similarities, gap distribution and distances between each motif strongly suggest that the ancestral polymerase module was encoded by an individual genetic element which was most closely related to the plus-strand RNA viruses and the non-viral retroposons. This polymerase module gene may have subsequently propagated in the viral kingdom by distinct gene set recombination events leading to the wide viral variety observed today.

Identification of four conserved motifs among the RNA-dependent polymerase encoding elements.

Epigenetics is the study of heritable changes in gene expression that occur without a change in DNA sequence. Epigenetic phenomena have major economic and medical relevance, and several, such as imprinting and paramutation, violate Mendelian principles. Recent discoveries link the recognition of nucleic acid sequence homology to the targeting of DNA methylation, chromosome remodeling, and RNA turnover. Although epigenetic mechanisms help to protect cells from parasitic elements, this defense can complicate the genetic manipulation of plants and animals. Essential for normal development, epigenetic controls become misdirected in cancer cells and other human disease syndromes.

https://science.sciencemag.org/content/sci/286/5439/481.full.pdf

Epigenetics: Regulation Through Repression

Eukaryotic transposable elements and genome evolution

The molecular basis of I-R hybrid Dysgenesis in drosophila melanogaster: Identification, cloning, and properties of the I factor

https://www.cell.com/cell/pdf/0092-8674(86)90815-9.pdf

Transposable elements controlling I-R hybrid dysgenesis in D. melanogaster are similar to mammalian LINEs

The ability of the Drosophila transposable element mariner to transpose in the chicken was tested using a plasmid carrying an active mariner element injected into chick zygotes. Surviving embryos and chicks were analyzed for presence of mariner. Analysis of embryos that survived for at least 12 days of development indicated that mariner had transposed at high frequency into the chicken genome. Germline transmission of mariner from one of three surviving birds confirmed transposition. Analysis of the first-generation (G1) chicks showed that they each contained between one and three copies of mariner. Six different transposition events were represented in the G1 birds, and the transposition was catalyzed by expression of the mariner element's transposase gene. Transmission from G1 to G2 occurred at a 1:1 ratio. Mariner therefore has potential for development as a vector for transgenesis in avian species.

David J. Finnegan

Papers

Eukaryotic transposable elements and genome evolution

The molecular basis of I-R hybrid Dysgenesis in drosophila melanogaster: Identification, cloning, and properties of the I factor

Transposable elements controlling I-R hybrid dysgenesis in D. melanogaster are similar to mammalian LINEs

Transposition of the Drosophila element mariner into the chicken germ line.

Genome evolution: Sex and the transposable element