1. Chapter 11-b Transposon

2. Transposon Transposable Elements: An Overview
Transposable Elements in Bacteria
Cut-and-paste Transposonin Eukaryotes
Retroviruses and Retrotransposons
Transposable Elements in Humans

3. Transposons
A transposable element moves from one DNA address to another
Originally discovered in maize, transposons have been found in all kinds of organisms
Bacteria
Plants
Humans (40%)
Transposition

4. Categorization of transposon
Although each kind of transposable elements has its own special characteristics, most of them can be classified into one of three categories based on how they transpose.
Cut-and-paster transposon
Replicative transposon
Retrotransposons

5. Cut-and-paster transposons
Transposon is accomplished(熟练的) by excising an element from its position in a chromosome and inserting it into another position.
The excision and insertion events are catalyzed by an enzyme called the transposase(转座酶),which is encoded by the elements itself.
Geneticists refer to this mechanism as cut-and-paster transposons (切粘转座子) because the elements is physically cut out of one site in a chromosome and paster into a new site, which may even be on a different chromosome.

6. Cut-and-paster transposons

7. Replicative Transposons(复制转座子)
Transposition is accomplished through a process that involves replication of the transposable element’s DNA.
A transposase encoded by the element mediated an interaction between the element and a potential insertion site.
During this interaction, the element is replicated and one copy of it is inserted at the new site; one copy also remains at the original site

8. Retrotransposons (反转录转座子)
Transposition is accomplished through a process that involves the insertion of copies of an element that were synthesized from the element’s RNA.
An enzyme called reverse transcriptase uses the element’s RNA as a template to synthesize DNA molecules, which are then inserted into new chromosomal sites.
It flows from RNA to DNA

9. Key Points -1
A cut-and-paster transposonis excised from one genomic position and inserted into another by an enzyme, the transposase, which is usually encoded by the transposon itself.
A replicative transposon is copied during the process of transposition.
A retrotransposon produced RNA molecules that are reverse-transcribed into DNA molecules; these DNA molecules are subsequently inserted into new genomic position.

10. Key Points -2
The cut-and-paster transposonsare found in both prokaryotes and eukaryotes(切粘转座子真核和原核都有).
The replicative transposons are found only in prokaryotes(复制转座子仅存在于原核).
Retrotransposonare found only in eukaryotes (反转座子仅存在于真核).

11. Transposition Mechanisms
Transposons are sometimes called “jumping genes”, DNA doesn’t always leave one place for another
When it does, nonreplicative transposition
“Cut and paste”
Both strands of original DNA move together from 1 place to another without replicating
Transposition frequently involves DNA replication
1 copy remains at original site
New copy inserts at the new site
Replicative transposition
“Copy and paste”

12. Transposable Elements in Bacteria
Bacterial transposons move within and between the bacterial chromosome and various types of plasmids.
细菌转座子在细菌染色体内部或在细菌染色体和不同类型的质粒之间移动。

13. Main types of transposable elements
The insertion sequences(插入序列), or IS elements, are simplest, containing only genes that encode proteins involved in transposition.
The composite transposons(Tn) 复合转座子 and Tn3 elementsare more complex, containing some genes that encode products unrelated to the transposition process.

14. IS Elements (插入序列元件)
ISs are the simplest type of bacterial transposon.
They contain only the elements necessary for their own transpositon.
Short inverted repeats at their ends
At least 2 genes coding for an enzyme, transposase
They consist of fewer than 2500 bp. The smallest, IS1, is 768 bp long.
Because these terminal sequences are always in inverted orientation with respect to each other, they called inverted terminal repeats(反向末端重复).

15. IS Transposition

16. Structure of an inserted IS50 element showing its terminal inverted repeats and target site duplication.
The terminal inverted repeats are imperfect because the fourth nucleotide pair from each end is different.

17. Transposase
At least some IS elements encode a protein that is needed for transposition.
This protein, called transposase, seems to bind at or near the end of the element, where is cuts both strands of the DNA.
IS elements are therefore cut-and-paster transposons.

18. Production of target site duplications by the insertion of an IS element.

20. Composite Transposons
Composite transposons consists of two IS elements flanking a region that contains one or more genes for antibiotic resistance. 2.5 kb -20 kb
In effect, two IS elements “capture” a DNA sequence that is otherwise immobile and endow it with the ability to move (实际上是两个IS元件捕获了一个不能移动的DNA序列，并赋予了它移动的能力).

21. Composite Transposons -Tn5
Tn5 consists of two IS50 elements flanking genes for kanamycin(卡那霉素), bleomycin(博来霉素), and streptomycin resistance.
The flanking IS element is inverted

22. Composite Transposons - Tn9
Tn9 consists of two IS1 elements flanking a gene for chloramphenicol(氯霉素) resistance.
In Tn9, the flanking IS elements are in the same orientation with respect to each other

23. Composite Transposons - Tn10
Tn10 consists of two IS10 elements flanking a gene for tetracycline resistance.
The flanking IS element is inverted

24. Tn3 Elements
The elements in this group of transposons are larger than IS elements and usually contain genes that are not necessary for transposition—a feature that is also characteristic of composite transposons(与复合转座子的相同点).
However, unlike the composite transposons, the Tn3 elements do not have IS elements at each of their ends.
Instead, the Tn3 elements have simple inverted repeats 30 to 40bp long at their termini.
The Tn3 elements also produce target site duplication when they insert into DNA (与复合转座子的相同点).

25. Genetic organization of Tn3
There are three genes, TrpA, TrpB, and bla, encoding, respectively, a transposase, a resovase(解离酶)/repressor, and an enzyme called beta lactamase(内酰胺酶) . The beta lactamase confers resistance to the antibiotic ampicillin, and the other two proteins play important roles in transposition.

27. Cut-and-paster Transposons in Eukaryotes
Transposable elements were discovered by analyzing genetic instabilities in maize; genetic analyses have also revealed transposable elements in Drosophilia.
There are many different types of transposons in eukaryotes. These elements vary in size, structure and behavior. Some are abundant in the genome, others rare.

28. The feature of Transposon-based DNA recombination
Hotspots (热点)
Regional preference ( 在3kb区域内的随机插入)
d) 某些转座因子（Tn3）对同类转座因子的插入具有排他性
（免疫性）
不依赖供体序列与靶位点间序列的同源性 (非同源重组过程 ，不依赖 recA 酶)
Regional preference ( 在3kb区域内的随机插入) 有的转座元倾向于优先插入某些染色体上的某些大的区段，这些区段可长达3Kb左右
e) 靶序列在转座因子两侧会形成正向重复
f) 转座因子的切除与转座将产生复杂的遗传学效应

29. Types of transposons in eukaryotes
Ac and Ds Elements in Maize
P Elements and Hybrid Dysgenesis in Drosophila (P元件和果蝇的杂交不育)
Mariner, an Ancient and widespread Transposon (海员，古老而广泛的转座子)

30. Eukaryotic Transposons
Transposons have powerful selective forces on their side
Transposons carry genes that are an advantage to their hosts
Their host can multiply at the expense of completing organisms
Can multiply the transposons along with rest of their DNA
If transposons do not have host advantage, can replicate themselves within their hosts

31. Ds and Ac of Maize Ds (dissociator) cannot transpose on its own
Must have help from an autonomous transposon, Ac (for activator)
Ac supplies transposase
Ds is an Ac element with most of its middle removed
Ds needs
A pair of inverted terminal repeats
Adjacent short sequences that Ac transposase can recognize

32. Structures of Ac and Ds

33. P Elements
The P-M system of hybrid dysgenesis in Drosophila is caused by conjunction of 2 factors:
Transposable element (P) contributed by the male
M cytoplasm contributed by the female allows transposition of the P element
Hybrid offspring of P males and M females suffer multiple transpositions of P element

34. 23.4 Retrotransposons
Retrotransposons replicate through an RNA intermediate
Retrotransposons resemble retroviruses
Retroviruses can cause tumors in vertebrates
Some retroviruses cause diseases such as AIDS
Before studying retrotransposons, look at replication of the retroviruses
DNA
RNA
DNA

35. Retroviruses
Class of virus is named for its ability to make a DNA copy of its RNA genome
This reaction is the reverse of the transcription reaction – reverse transcription
Virus particles contain an enzyme that catalyzes reverse transcription reaction

36. Retrovirus Replication
Viral genome is RNA, with long terminal repeats at each end
Reverse transcriptase makes linear, ds-DNA copy of RNA
ds-DNA copy integrates back into host DNA = provirus
Host RNA polymerase II transcribes the provirus to genomic RNA
Viral RNA packaged into a virus particle

37. 图18.18：许多机制通过影响抑制Tn10转座，转座酶蛋白的功能或化合，单独转座子的转座被半甲基化限制发生，在复制后条件下，优先cis限制目标的选择，OUT/IN　ＲＮＡ对抑制转座酶化合。酵母 果蝇 哺乳
Several mechanisms restrain the frequency of Tn10 transposition, by affecting either the synthesis or function of transposase protein. Transposition of an individual transposon is restricted by methylation to occur only after replication. In multicopy situations, cis-preference restricts the choice of target, and OUT/IN RNA pairing inhibits synthesis of transposase.