Fig. 1

Transposable element structures. a)LTR retrotransposons: gag encodes a polyprotein with a capsid and a nucleocapsid domain. The Pol gene produces three proteins: a protease (PR), a reverse-transcriptase endowed with an RT (reverse-transcriptase) and an RNAse H domain, and an integrase (INT). The gag and pol genes are expressed either as a fusion into a single open reading frame (ORF) that is then cleaved, or by the introduction of a frameshift between the two ORFs. Sometimes an envelope gene (ENV) is found. LTRs are divided into 3 regions: U3 may contain regulatory motifs and a promoter region, R contains both the start and termination sites for transcription, and U5 is the remaining part. The PBS operates as tRNA primer-binding to prime the first strand DNA synthesis, the minus-strand. The PPT is a short purine-rich sequence that primes the second strand DNA synthesis, the plus-strand. TSD: Target Site Duplication is a short direct repeat that is generated on both flanks of a TE upon insertion. Gypsy and Copia superfamilies differ according to the position of the integrase in the polyprotein pol.b)LINE: Encodes two open reading frame: ORF1 and ORF2. ORF1 encodes a non-sequence-specific RNA binding protein that functions as chaperone. ORF2 encodes an endonuclease (EN), which makes a single-stranded nick in the genomic DNA and a reverse transcriptase (RT), which uses the nicked DNA to prime reverse transcription. They are terminated by a polyA or A/T-rich tail. SINE: SINE sequences contain the box A and B conserved motifs that serve as an internal promotor. c)TIR: TIR transposons encode a transposase protein necessary for mobility, and are bordered by Terminal Inverted Repeats (TIRs). Helitrons: generally contain a Y2-type tyrosine recombinase (YR) along with Replication protein A (RPA) and other proteins to catalyze their mobility, a hairpin structure, 5′ TC and 3′ CTRR termini (R = A or G). Insertion occurs into the target dinucleotide AT (shown in lowercase)