1. Transposition and transposable elements
Fahareen Binta Mosharraf
MNS

2. Transposable elements
“Mobile genetic elements”
Comprise 45% of human chromosomal DNA “middle repetitive DNA”
Ranging from hundreds to a few thousand base pairs in length,
Contribute to spontaneous mutation, genetic rearrangements, horizontal transfer of genetic material
In germ cells, the transposed sequences at their new sites can be passed on to succeeding generations
Within a somatic cell; transposed sequence is transmitted only to the daughter cells derived from that cell

3. transposable element
A transposable element (TE) is a DNA sequence that can change its relative position (self-transpose) within the genome of a single cell.
The process by which these sequences are copied/cut and inserted into a new site in the genome is called transposition

4. Discovery of transposons
Barbara McClintock 1950’s Ac Ds system in maize influencing kernel color
Rediscovery of bacterial insertion sequences

5. Types of transposible elements
Transposons Those that transpose directly as DNA. Mobile elements that transpose through a DNA intermediate are generally referred to as DNA transposons and
Retrotransposon Those that transpose via an RNA intermediate transcribed from the mobile element by an RNA polymerase and then converted back into double-stranded DNA by a reverse transcriptase. They are called retrotransposons because their movement is analogous to the infectious process of retroviruses .

7. Transposon

8. Transposon Encode an enzyme called Transposase.
Rather than converting RNA to DNA, this enzyme:
– directly removes the DNA sequence and
– inserts it in another location.
Transposons usually have inverted repeats (IR) on either side upstream and downstream.

9. Structure of transposon

10. Mechanism of movement:
Encode proteins that (1) move DNA directly to a new position i.e. non replicative or (2) replicate DNA and integrate replicated DNA elsewhere in the genome (prokaryotes and eukaryotes).
The mechanism of transposition can be either
“Copy and paste“ for replicative examples: Tn3, bacteriophage Mu or
“Cut and paste from host non replicative examples: Tn5, Tn10, P elements

11. Non replicative transposons
cut-and-paste mechanism
cut themselves out of original site, producing double strand break
cut target site and ligate to element ends, thereby inserting at new site
original site break repaired usually with sister chromosome

12. move DNA directly to a new position

13. Replicative transposons
orignal cut of transposon is only nick and only one strand is initially ligated
element replicates through itself
produces as intermediate a “co-integrate” structure
co-integrate is resolved by resolvase (as TnpR of Tn3) and at specific site (as res of Tn3)

15. Process of replicative transposition

16. Transposable elements in prokaryotes :
Two examples:
Insertion sequence (IS) elements
Transposons (Tn)

17. Insertion sequence (IS) elements:
Simplest type of transposable element found in bacterial chromosomes and plasmids.
Encode gene (transposase) for mobilization and insertion.
Range in size from 768 bp to 5 kb.
Ends of all known IS elements show inverted terminal repeats (ITRs).

18. Impact of insertion sequence (IS) elements in host :
Integration of an IS element may:
Disrupt coding sequences or regulatory regions.
Alter expression of nearby genes.
Cause deletions and inversions in adjacent DNA.
Result in crossing-over.

20. Integration of IS element in chromosomal DNA.

21. Transposons (Tn):
Similar to IS elements but are more complex structurally and carry additional genes
2 types of transposons:
Composite transposons
Noncomposite transposons

22. Composite transposons (Tn):
Carry genes (example might be a gene for antibiotic resistance) flanked on both sides by IS elements.
Eg: Tn10 is 9.3 kb and includes 6.5 kb of central DNA (includes a gene for tetracycline resistance) and 1.4 kb inverted IS elements.
IS elements supply transposase

23. Noncomposite transposons (Tn):
Carry genes (example might be a gene for antibiotic resistance) but do not terminate with IS elements.
Ends are non-IS element repeated sequences.
Tn3 is 5 kb with 38-bp ITRs and includes 3 genes; bla (-lactamase), tnpA (transposase), and tnpB (resolvase, which functions in recombination).

24. Fig. 7.22, Recombination, crossing-over, and duplication of a transposable element.

25. Retrotransposons

26. Retrotransposon
The DNA sequence in a retroposon codes for a reverse transcriptase,which catalyzes the formation of DNA from an RNA template.
Mechanism of movement:
Retrotransposons encode reverse transcriptase and make DNA copies of RNA transcripts; new DNA copies integrate at different sites (eukaryotes only).

28. Classification of retroelements
Have obligate RNA intermediate, use reverse transcriptase (RT, RNA-dependent DNA polymerase)
LTR-retroelements: long terminal repeats Ty1/copia, Ty3/gypsy, retroviruses
Non-LTR-retroelements “retroposons” LINES (Long INterspersed Elements), SINES
(Short INterspersed Elements)

29. LTR-retroelements Ty elements in yeast:
Similar to bacterial transposons; terminal repeated sequences
Ty elements share properties with retroviruses, retrotransposon
Synthesize RNA copy and make DNA using reverse transcriptase.

30. Non-LTR-retroelements “retroposons” LINES
Human retrotransposons
6.5 kb element, repeated (~5% of genome).
Contain ORFs with homology to reverse transcriptases; lacks LTRs.
2 ORFs, orf1, orf2

31. General properties of plant transposons:
Possess ITR sequences and generate short repeats at target sites.
May activate or repress target genes, cause chromosome mutations, and disrupt genes.
Two types:
Autonomous elements/Ac
Nonautonomous elements /Dc
McClintock demonstrated purple spots in otherwise white corn (Zea mays) kernels are results of transposable elements.

32. Examples of DNA Transposons:
Ac (Activator) Transposable Elements-
Ac transposons are self-sufficient in that they code for their own transposase enzyme and, therefore, can transpose independently.
Ds (Dissociator) Transposable Elements-
Ds transposons are non-autonomous, as they are unable to transpose independently. Ds transposons do not code for their own transposase enzyme so they must depend on excess transposase produced by nearby Ac transposons. Therefore, Ds transposons remain immobile without the assistance of Ac transposons.

33. McClintock’s discovery of transposons in corn:
c/c = white kernels and C/- = purple kernels
Kernal color alleles/traits are “unstable”.
If reversion of c to C occurs in a cell, cell will produce purple pigment
McClintock concluded “c” allele results from a non-autonomous transposon called “Ds” inserted into the “C” gene (Ds = dissassociation).
Autonomous transposon “Ac” controls “Ds” transposon (Ac = activator).