Contact: Asmaa M. Abdel-Ghany
asmaa.elagamy@yahoo.com
1. INTRODUCTION. 2. Discovery of transposable elements. 3. The Classification of transposable elements. 4. Structure of Transposable elements. 5. The effects of transposable elements on gene and genome. 6. Effects of Transposition. 7. Function of transposable elements. 8. Uses of transposable elements. 9. Applications of Transposable Elements. 10. TEs as tools of evolutionary change. 11. Transposable elements as molecular tools .
• Transposable elements (TE) are segments of the genome that are capable of jumping around to different locations. • They are able to transport themselves to other location.
Transposable elements were first discovered In 1940s by Barbara McClintock in maize. She was awarded Noble prize for her discovery .
• Found genetic elements regularly jump to new location and affect gene expression • Maize kernels show variation in color. • Later in 1960s bacteria & bacteriophages were shown to posses TE.
Image courtesy of Lauren Solomon, Broad Communications
The reddish streaks on these corn grains are caused by transposons.
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We now know that only 1.1% to 1.4% of our DNA actually encodes proteins.
Snapshot of the human genome. The chart shows the proportions of our genome made up of various types of sequences.
Arabidopsis Drosophila Human Maize Lilium
14% 15% 50 % 60-80% 99%
Classified according to mechanism into two class
Class I Copy and paste Retrotransposons
Class II Cut and paste Transposones
Divided into two subclasses
Subclass I LTR Retrotransposons
SubclassII Non LTR Retrotransposons
Subclass II Non LTR Retrotransposable
Subclass I LTR Retrotransposable
Classified by Capy et al. (1997b).
Super family Ty1 -Copia Family: Ty1 Family: Copia
Superfamily: LINE (Long Interspersed Repetitive elements) 6-7 kb long 15% of human DNA
Super family Ty3-Gypsy Family: Ty3 Family: Gypsy
Super family LARD ( Larg Retrotransposone s Derivatives)
Suprrfamily: SINE (Short Interspersed Nuclear elements) 500 bp long 10% of human DNA
Super family TRIMs ( Terminal repeats Retrotransposones in miniature)
Segments of DNA that move from one genomic location to other. The simplest transposable elements is Insertion Sequences(IS).
IS is a short sequence of DNA carrying only the genes needed for transposition
and bounded at both ends by sequences of nucleotides in reverse orientation called Inverted repeats.
Retrotransposons transpose through reverse transcriptin of an mRNA intermediate, whereas DNA transposons cut and then paste a DNA copy of an element into a new location.
In contrast to DNA transposons, the replication mechanism of retro transposable elements can greatly amplify copy numbers, and thereby they rapidly increase host genome size. For example, the contribution of retrotransposons to genome content ranges from 3% in budding yeast to 50- 80% in maize
LTR: long terminal repeats contain the transcriptional promoter and terminator. The LTRs contain short inverted repeats at either end, shown as filled triangles. PBS: Primer binding site, Reverse transcription is primed at the PBS and PPT domains, respectively for the (−) and (+) strands of the cDNA. PPT: polypurin tract The internal region of the retrotransposon codes for the proteins necessary for the retrotransposon life cycle GAG: the capsid protein AP: aspartic proteinase, which cleaves the polyprotein IN: integrase, which inserts the cDNA copy into the genome RT: reverse transcriptase RH: RNaseH which together copy the transcript into cDNA. The internal region contains evolutionarily conserved domains (noted below the element as black boxes), necessary for function that can be used to isolate retrotransposons from previously unstudied plant species. The LTRs are generally well-conserved within families, and can serve for the design of primers to generate DNA footprints.
LTR retrotransposons
The abundance of retrotransposons is an important evolutionary factor in shaping genomes and driving processes such as mutation, recombination, sequence duplication and genome expansion.
• TEs cause different changes in the genome of their hosts • play important role in evolution . • they have the ability to rearrange genomic information in several ways : 1 – Modification of gene expression 2 – Alternation gene sequence 3 – Chromosomal structural changes • cut and pate mechanism often produce variation when they excise.
Effects of Transposition Transposable elements can:
• • • • •
Cause mutations in adjacent genes Cause chromosomal rearrangements Re-locate genes Change in gene structure and gene activity Source of new genetic variation for
stressed populations
Function of transposable elements • Mutation of genes by insertion. •Regulation of gene expression by insertion. •Transposable element-mediated rearrangements; deletion, duplication, and inversion.
•new change in genome new function during evolution
Use of transposable elements
Prokaryotes : conventional antibiotic-resistance marker. Eukaryotes: generation of insertion mutations, mapping, gene cloning and transgenic organism.
Retrotransposons can be used as markers because their integration creates new joints between genomic DNA and their conserved ends.
Applications of Transposable Elements Transposable elements may: • Create genetic diversity • Act as promoters • Carry antibiotic resistance genes on
bacterial cells • Increase the number of copies of an exon of a gene
TEs as tools of evolutionary change • TEs usually inactive. • “Stress” conditions may activate TEs. • Active TEs increase mutation frequency. • Most mutations caused by TEs neutral or harmful.
• A rare TE-induced mutation (or rearrangement) may be adaptive. Transposable elements can shake up otherwise conservative genomes and generate new genetic diversity.
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There are several techniques using retro- elements as molecular markers: 1- S-SAP
(Sequence-Specific Amplified Polymorphism)
2- IRAP
(inter retrotransposon amplified polymorphism)
3-REMAP (retrotransposon microsatellite amplification polymorphisms) 4- RBIP (Retrotransposons-based insertion Polymorphism) 5- iPBS
(Inter primer binding sites)
SSAP (Sequence Specific Amplified Polymorphism) measure the distance from the transposon to the restriction site. Amplification is carried out between primers matching an LTR and a restriction site adapter ligated to genomic DNA digested with a restriction enzyme.
Inter-Retrotransposons Amplified Polymorphisms (IRAPs). IRAP product measures the distance between retrotransposon and another.
REMAP (Retrotransposon-microsatellite amplified polymorphism). Amplification is carried out between primers matching an LTR and a microsatellite domain (SSRs).
Retrotransposon based insertion polymorphism (RBIP). This technique can detect the presence and absence of retrotransposon.
The inter PBS amplification (iPBS) scheme
LTR retrotransposon structure: LTR and PBS sequence Two nested LTR retrotransposons in inverted orientations amplified from single primer or two different primers from primer binding sites. PCR product contains both LTRs and PBS sequences as PCR primers in the termini. In figure schematically showing general structure for PBS and LTR sequences, between 5’LTR(5’-..CA) and PBS (5’-TGG..3’) is spacer with several nucleotides (0-5 bases).
Transposons are present in the genomes of all organisms, where they can constitute a huge fraction of the total DNA sequence. They are a major cause of mutations and genome rearrangement. The ability of transposable elements to insert and to generate deletions and inversions accounts for much of the macromolecular rearrangement.
As a result they are used in the genetic studies and as a molecular marker .