TE introduction

Transposable element

Transposable element (TE), also known as transposon or mobile element, is a diversity of DNA segments that can, in a process called transposition, move, or duplicate, from one location in the genome to another. The length of TEs ranges from less than 100-bp to more than 20-kb. After transposition, many types of TEs are flanked by short (~1–20 bp) direct repeats, target site duplications (TSDs), which are derived from the target sequence. However, some TE types, such as Helitron, several Harbinger families and CR1 retrotransposons, do not produce TSDs. The length of TSD is usually a characteristic of a group of TEs and its relatives, but may vary across different groups and superfamilies. TEs constitute the major part of repetitive sequences in most eukaryotic genomes. Other repetitive sequences include tandem repeats (satellite sequences or mini-satellite), sporadic genomic duplications and some multiple-copy host genes (such as rRNA, tRNA, histone genes, etc.). In fact, TEs can be viewed as intra-genomic parasitic elements. Similarly, inter-cellular virus can also be viewed as TEs since they can integrate into the host genome, such as the LTR-retrovirus. TEs have diverse evolutionary impact on host genome.

Machinery and classification of TEs

The transposition of TEs is largely depending on the diverse TE-encoded enzymatic machinery. Some identified enzymes or domains so far include reverse transcriptase, endonuclease, DD[E/D]-transposase (Tpase), Tyrosine-recombinase and Rep/Helicase1. Depending on whether reverse transcription is involved in transposition, TEs are classified into retrotransposon (Class I) and DNA transposon (Class II). In DNA transposons, the underlying enzymes could be either DD[E/D]-transposase (Tpase), or Rep/Helicase (for Helitron), or Tyrosine-recombinase (for Crypton). Depending on the sequence similarity of the key enzymes and additional DNA features, TEs are classified into superfamilies (see TE classification). Each superfamily includes numerous different families.

TE family

In the evolutionary history, a given TE, and its active copies, often maintain their activity in a relatively short period of time. Copies generated from them thus form a family. In older families, the TE members have undergone excessive degeneration, and barely represents the original active sequences. Therefore, family consensus sequences are often rebuilt from individual copies to represent the family. In genome sequences, TEs in most loci are only partial fragments, losing the transposition ability due to the lost of the functional element recognized by the transposition machinery. For example, most Non-LTR retrotransposons are 5’-truncated, due to the earlier termination of reverse transcription, and solo-LTR are likely the recombinant from two identical LTRs of LTR retrotransposons. Only a small percentage of TEs are complete in the sense of containing both termini and encode a full set of enzymes for its transposition. These TEs are termed as autonomous. Consequently, non-autonomous TE does not encode any enzyme involved in transposition, and are transposed in trans. Notably, except for these essential enzymes, TEs may occasionally capture some host genes or gene fragments in the long evolutionary history.

Weidong Bao, Ph. D.