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

2. Reverse transcription and insertion
Two Classes: Class I (Retrotransposons) and Class II (DNA Transposons)
Class I mobilization (‘copy and paste’)
Reverse transcription and insertion
Pol III transcription
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 = kb; 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 Copia differ 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: Penelope-like (PLE) 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: 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 Lisch Nature 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:

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_AA
R = RNA (Class I)
L = LTR
C = Copia

20. Families Defined by: 80-80-80 rule: similarities in sequence in:
coding region (or internal domain)
Terminal repeats
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
Emiliani G, Paffetti D, Giannini R Identification and molecular characterization of LTR and LINE retrotransposable elements in Fagus sylvatica L.