Transposable elements

Transposable Elements (TE)

mobile elements/jumping genes, biological agent that cause mutations, can disrupt gene function depending where inserts

Transposable genetic elements

DNA sequences, move within genome, enzyme(transposase) driven process (Transposition), vary in length/ sequence/ composition/ copy number, movement occurs in 2 ways, cause change in DNA sequence (mutation)

Movement of transposable genetic element

Excision from original location and insertion in new location (cut + paste) or Duplication and insertion of copy in new location (copy + paste), move within same chromosome or between plasmid/phage chromosomes

Characteristics of Transposable elements

complexity varies, terminal inverted repeats at end, bracketed by flanking direct repeats

Characteristics of transposition events

staggered cuts made by transposase at new location (single strand overhangs), transposable element inserted at new location, DNA replicated at site of insertion - fill single strand gaps produce flanking direct repeats

Categories of transposable elements

DNA transposons (Class II), Retertransposons (Class I)

DNA transposons

Class II transposable elements, transpose as DNA sequence, replicative or non replicative

Retrotransposons

Class I transposable elements, composed of DNA, transpose through RNA intermediate, reverse transcriptase converts back to DNA

Replicative transposition

Copy + Paste, Leave copy of original while inserting new copy, element replicates, increase number of transposons

Replicative transposition mechanism

donor and recipient DNA fusion - Cointegrate, resolved by recombination, result 2 molecules each with a transposable element

Non replicative transposition

Cut + Paste, removes copy from one location and move to new, simple insertion, no replication, no increase in number of transposons

Bacterial transposable element

Insertion sequences (IS) - small, Composite transposons, Non-composite transposons

Insertion sequence (IS) element

simple, small(<2kb), terminal repeats surrounding gene (sometimes 2), encode transposase, need flanking inverted repeats (where binds), replicative or nonreplicative

Insertion sequence (IS) mechanism

small target site(5-9bp), transposase makes blunt cut at donor site (IS) and staggerred cut at target site, blunt element inserted at target, single stranded sites filled by DNA synthesis - create direct repeats (target site duplication)

Transposons

larger, code for transposase and other proteins, more complex than IS, composite and non composite

Composite Transposons

carry transposase gene, 2 flanking IS elements, additional genes that may confer a growth advantage, Ex: Tn10 (inverted) or Tn9 (direct)

Tn10

bacterial composite transposon, inverted IS element, produce target site duplication - flanking direct repeats

Non composite transposons

no IS elements, has transposase gene, additional genes but no insertion sequence, transpose same as composite, has IR sequence required for transposition, ex:Tn3

Tn3

bacterial non composite transposon, central region codes for transposaes, result in target site dupication

Mutagenic effect of transposition

Create mutation by insertions (Insertional inactivation) →non functional gene product

Transposable element in Eukaryotes

short sequence with inverted repeats (Ac/Ds in corns or P in flies), Retrotransposons (Alu/ Ty/ Copia)

Transposable element in plants

have inverted repeats resulting in target site replication, can insert into genes

transposable element in corn

Ac element and Ds element, dicovered by barbara McCkintock, chromosome breakage occuring at Ds gene only when Ac present, Ds transpose into C gene inactivating or out of C gene restoring

Autonomous elements

Can transpose self - independent movement, code for transposase, ex: Ac(activator)

Non autonomous elements

can’t transpose self - dependent movement, doesn’t code transposase - deletion or mutation, require presence of autonomous element, Ex: Ds (dissociation) - from Ac deletion

Transposase

enzyme, DNA binding protein, cut target site and transposable element site

Unstable mutant corn allele

autonomous element inserted, Ds element inserted but Ac can excise and restore WT

Stable mutant corn allele

insertion non autonomouse element, Ds cannot be excise in absence of Ac

Transposition of Ac and Ds elements

Replication associated - only during or right after replication, conservative/ non replicative, move already replicated region - the same # vs move unreplicated region - increase # elements

Ty elements - Yeast

~6kb, 2 long direct terminal repeats (LTR ~300bp), contain promoter, code for reverse transcriptase, Retrotreanpsosn - move via RNA intermediate

Retroviruses step

RNA pol makes RNA trasncript from dsDNA, Reverse transcriptase make dsDNA from RNA transcript, dsDNA integrated at new point

Discovery of retrovirus

Promoter added to increase transcription of Ty element, Ty element alter by inserting intron, final product inserted at new location has no intron, indicated Intron spliced pout during post transcriptional modification

Transpoable element in Drosophila

Copia and P elements, 15% of genome, hald of spontaneous mutation due to

Copia

Retrotransposons (RNA intermdiate), Pol codes RT, has LTR, abindant (5% of Drosophila genome), Ex; white-apricot eye mutation cause by instertional inactivation of copia into white eye locus

P element

DNA intermediate, IR and transposase (autonomous), only in reproductive tissue (tissue specific splicing), activation of causes Hybrid dysgenesis

P element tissue specific splicing

in somatic cells 3rd intron of transposase is not spliced out leading to non functional transposase

Hybrid dysgenesis

When sterility occurs in F1 progeny of certain crosses, occur when female M cytotype are mated with P strain males (get P element but not cytoplasmic transposition repressor - maternally inherited)

P genome

contain P element, encode for cytoplasmic transposition repressor (R) - prevent expression of transposase

What Hybrid dysgenesis causes

sterility, high mutation rate, chromosomal aberration, nondisjunctions

M genome

no P element and no cytoplasmic transposition repressor (R)

Transposable element in humans

45% of human genome, Lines and Sines, retrotransposons, repetitive sequence interspersed with unique sequence

Long Interspersed Nuclear Elements (LINES)

>5kb, code for reverse transcriptase (RT) and transposase, autonomous, 35kb apart, 20% of genome, no LTR, ex: L1 elements

Short Interspersed Nuclear Element (SINES)

100-400bp, depend on enzyme produced by LINES, Non-autonomous, 1-2kp apart, >10% of genome, ex: Alu element

L1 elements

LINES, cause Hemophilia by inserting into clotting factor gene (insertional inactivation), spontaneous (de novo) mutation

TE mechanism to prevent harm to host

‘dead’ TE - inactivated by mutation or epigenetic silencing (can be activated by stress), Insert into ‘safe havans’ (heterochromatin/ intragenic regions), Transcriptional + Translational regulation of transposase