A unified classification system for eukaryotic
transposable elements
Wicker et al
Sarah Mangum
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)
Class II mobilization (‘cut and paste’)
DNA Transposons
• Double strand break in donor DNA
Target
Donor
Transposon w/ ORF
Pol II transcription
Translation
Transposase
• Helitrons and Mavericks undergo ‘copy and paste’ mobilization however
have no RNA intermediate.
Target Site Duplications (TSDs)
Upon insertion, small direct repeats are created flanking the element.
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.
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 Copia differ in order of RT and INT
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
LTR transposition
Solo LTR – easy to lose internal region of LTR transposon
during replication.
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
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
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
Class II Elements
• Subclass I (cut and paste)
• DNA Transposons
• Subclass II (copy and paste)
• Helitrons
• Mavericks
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
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)
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
Autonomous vs NonAutonomous 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
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
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
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
Questions?
Emiliani G, Paffetti D, Giannini R. 2008. Identification and molecular characterization of LTR and LINE retrotransposable elements in Fagus sylvatica L.