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

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)

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

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: 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

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 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

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: 80-80-80 rule: 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 Emiliani G, Paffetti D, Giannini R. 2008. Identification and molecular characterization of LTR and LINE retrotransposable elements in Fagus sylvatica L.