Lecture 5: Transposition mechanisms, CSSR

Question 1

Nonretrovrial retrotransposase structure

Answer 1

Poly A at 3’ end of RNA transcript; 5’ end is often truncated

Question 2

If DNA sites are in same orientation for CSSR:

Answer 2

DNA can be integrated or excised

Question 3

Difference of CSSR and transposition

Answer 3

CSSR need special sites on EACH DNA that serve as recognition sites for recombinase
Form transient high energy covalent bonds and use it to complete DNA rearrangement

Question 4

Step 1/2 of non retroviral retransposition

Answer 4

L1 RNA synthesis

Synthesis of reverse transcriptase/endonuclease

Question 5

Step 1 of retroviral like transposon

Answer 5

Entire transposon transcribed by host

RNA transcript transcribed contains reverse transcriptase enzyme

Question 6

Non retroviral transposon characteristics

Answer 6

Comprise 40% of human genome
Most are immobile
Require endonuclease and reverse transcriptase to move, which they must use from other transposons

Question 7

Retroviral-like retrotransposon method of movement

Answer 7

Moves via an RNA intermediate whose production is driven by promotor in the LTR

Question 8

Retroviral-like transposon enzymes for movement

Answer 8

Reverse transcriptase

Integrase

Question 9

DNA-only transposon moves how

Answer 9

Moves as DNA, either by cut-and-paste or replicative pathways

Question 10

How does central intermediate attack target

Answer 10

Creates staggered break (breaking two phosphodiester bonds)

Breaks are repaired and result in duplication of target DNAs insertion site

Question 11

Nonretroviral retrotransposon enzymes required

Answer 11

Reverse transcriptase

Endonuclease

Question 12

Nonretroviral retrotransposon method of movement

Answer 12

Moves via RNA intermediate that is often synthesized from a neighboring promotor

Question 13

Transpososome

Answer 13

DNA only transposon

Two transposase molecules come together forming a loop juxtaposing two ends of element

Question 14

If DNA sites are in opposite orientation for CSSR:

Answer 14

DNA sequence is inverted instead of excised

Question 15

Transposase is what, acts on what, allows what

Answer 15

Enzyme encoded by transposon itself (DNA-only transposon)
Acts on specific DNA sequence on each end of transposon
Allows insertion into target DNA site

Question 16

Conservative site specific recombination does what

Answer 16

Mediates rearrangements of other types of mobile DNA elements

Question 17

DNA only transposon structure

Answer 17

Short inverted repeats at each end

Question 18

Step 4 of non retroviral retransposition

Answer 18

Endonuclease nicks the target DNA, revealing 3’ OH to serve as primer in reverse transcription step

Question 19

Transposons can provide and produce what

Answer 19

Provide benefits to the cell (abx resistance in bacteria)

Produce genetic variation

Question 20

“Hole” in donor chromosome on transposon is repaired by which three mechanisms and what is the result of each

Answer 20

DS break repair (transposon restored)
Homologous recombination (not restored)
Non homologous end joining (creates mutation at break site)

Question 21

Retroviral-like retrotransposon structure

Answer 21

Directly repeated long terminal repeats (LTRs) at each end

Question 22

Difference in outcome of CSSR depends on

Answer 22

The relative orientation of DNA sites

Question 23

Step 2 of retroviral like transposon

Answer 23

Reverse transcriptase makes DS DNA copy of RNA molecule via DNA/RNA intermediate

Question 24

Central intermediate

Answer 24

DNA-only transposon
Formed after transposase cuts the loop formed by two transposase monomers which recognized end sequences and brought them together

Question 25

Transposons are

Answer 25

Mobile genetic elements “jumping genes”.

Can move from one position in genome to another

Question 26

Integrase function

Answer 26

Cuts one strand at each end of viral sequence, exposing 3’ ends which attack phosphodiester bonds on target DNA

Question 27

Step 3 of retroviral like transposon

Answer 27

DS DNA integrates into site on chromosome using integrase

Question 28

Step 3 of non retroviral retransposition

Answer 28

Endonuclease and reverse transcriptase bind L1 RNA

Question 29

Step 6 of non retroviral retransposition

Answer 29

Double stranded L1 copy inserted into target DNA

Question 30

Step 5 of non retroviral retransposition

Answer 30

Single stranded DNA copy of L1 directly linked, DNA primed reverse transcription creates double stranded L!

Question 31

Different results of CSSR

Answer 31

DNA integration
DNA excision
Inversion

Question 32

DNA-only transposon- what is required for movement

Answer 32

Transposase

Sequences recognized by transposase necessary for movement