A unified classification system for eukaryotic transposable elements

1. A unified classification system for eukaryotic transposable elements Wicker et al Sarah Mangum

2. Pol III transcription Two Classes: Class I (Retrotransposons) and Class II (DNA Transposons) Class I mobilization (‘copy and paste’) Reverse transcription and insertion 1. Usually a single or a few ‘master’ copy(ies) 2. Transcription to an RNA intermediate (copy) 3. Placed back into another location in the genome (paste)

3. Class II mobilization (‘cut and paste’) DNA Transposons • Double strand break in donor DNA • Helitrons and Mavericks undergo ‘copy and paste’ mobilization however have no RNA intermediate. Target Donor Transposon w/ ORF Pol II transcription Translation Transposase

4. Target Site Duplications (TSDs) Upon insertion, small direct repeats are created flanking the element.

5. Classification Class -- divided by presence of RNA intermediate Subclass -- distinguish between ‘copy and paste’ and ‘cut and paste’ Order -- differences in insertion mechanisms and organization Superfamily -- differences in protein structure and non-coding domains and TSDs Family -- DNA sequence similarity Subfamily -- phylogenetic; autonomous and non-autonomous derivatives Insertion -- individual copy after insertion event *All classification names below order should be italicized.

6. Long Terminal Repeat (LTR) Retrotransposon • High presence in plants • LTRs flanking element = 300- 5kb; start with 5’-TG-3’ and end with 5’-CA-3’ • Produce 4-6 bp TSD • Usually code for GAG and POL • POL contains aspartic proteinase (AP), reverse transcriptase (RT), RNase H (RH), and DDE intergrase (INT) • Gypsy and Copiadiffer in order of RT and INT

7. Long Terminal Repeat (LTR) Retrotransposon • Also within the LTR order are retroviruses and endogenous retroviruses (ERVs) • Retroviruses may have evolved from LTRs or vice versa • Retroviruses contain an envelope protein (ENV) as well as other additional proteins different from the LTR • ERVs are retroviruses whose domains were either inactivated or deletion of domains necessary for extracellular mobility • ERVs also encode for capsid and matrix functions as well as ENV

8. LTR transposition Solo LTR – easy to lose internal region of LTR transposon during replication.

10. Class I (con’t) • DIRS-like element: • Contain tyrosine recombinase instead of INT thus, no TSDs • Termini contain split direct repeats (SDR) or inverted repeats • Penelope-like (PLE) element: • Detected in over 50 species but variable distribution among taxa • RT similar to telomerase • Some contain functional introns • LTR-like flanking sequences direct or inverse

11. Long Interspersed Elements (LINEs) • Can reach several kb in length • Autonomous • Encode RT and nuclease in pol • R2: nuclease = endonuclease in C-terminal of RT • L1, RTE, I, Jockey: nuclease = endonuclease in N-terminal of RT • Usually forms TSD upon insertion • Weak RT falls off leaving many truncated LINEs • 3’ end contains either a poly(A) tail, tandem repeat or A-rich region

12. Short Interspersed Elements (SINEs) • Non-autonomous • Use LINE machinery • Some have obligatory partners, other are generalists • Not autonomous derivative • Originate from accidental retrotransposition of polymerase III transcripts (tRNA, 7SL RNA, and 5S RNA) • 5’: RNA Polymerase III transcription start site; often derived from tRNA • 3’: usually LINE derivative; can contain poly(T) tail, A or AT rich, or 3-5 bp tandem repeat • 80 – 500 bp long TSD: 5-15 bp

13. Class II Elements • Subclass I (cut and paste) • DNA Transposons • Subclass II (copy and paste) • Helitrons • Mavericks

14. DNA Transposons (TIRs) • Distinguished by terminal inverted repeats (TIRs) and TSD size • Can increase numbers by transposing during chromosome replication • Use transposase for transposition • Tc1-Mariner: two TIRs and transposase ORF; usually TA TSD • hAT: TSDs of 8bp; TIRs of 5-27 bp; overall length of less than 4kb • Mutator: TIRs can reach several hundred bp; 9-11 bp TSDs • P element: 8 bp TSDs • piggyBac: 8 bp TSDs usually TTAA • PIF-Harbinger: TSD: TAA • CACTA: 3-bp TSDs

15. Helitron • Replication without double stranded (ds) cleavage • Replicate via rolling circle mechanism with no TSDs • Short hairpin structure defines the end 3’ end along with TC or CTRR motifs • Encode tyrosine recombinase Damon LischNature Reviews Genetics 14, 49-61 (January 2013)

16. Mavericks • Also called Polinton • Replication without ds cleavage • Large! • 10-20 kb • Long TIRs border • Encode DNA pol B and INT • No RT Kapitonov V V , and Jurka J PNAS 2006;103:4540-4545

17. Autonomous vs Non-Autonomous Classification • Autonomous: encode all domains necessary for transposition • Defective code is still classified autonomous • Non-Autonomous: containing no or not all of the domains necessary for transposition

18. Non-Autonomous Derived from LTRs: • Large retrotransposon derivatives (LARDs) • Large; greater than 4 kb; no coding region for transposition • Terminal repeat retrotransposons in miniature (TRIMs) • Small; less than 4 kb; no coding region for transposition • Miniature inverted repeat transposable elements (MITEs): • Flanked by TIRs; often found close to genes

19. Naming system • A three-letter code: • Letters denote class, order, and lastly superfamily • Family name, separated by an underscore • Sequence ID of element location RLC_Angela_AA123456-1 R = RNA (Class I) L = LTR C = Copia

20. Families • Defined by: • similarities in sequence in: • coding region (or internal domain) • Terminal repeats • 80-80-80 rule: • 80% sequence similarity over 80% of the sequence and over 80 base pairs long • Can apply to internal region or terminal repeat region or both

22. Questions?

24. Emiliani G, Paffetti D, Giannini R. 2008. Identification and molecular characterization of LTR and LINE retrotransposable elements in Fagus sylvatica L.