Genome stability-Mobile Genetic elements L1-3 Mark Szczelkun

Question 1

What are the 2 classes of jumping genes?

Answer 1

1) Conservative site-specific recombination

2) Transpositional recomnination

Question 2

You need a Ds and another gene to be present in order for a breakage to occur-what is the other enzyme?

Answer 2

Ac.
Ch. became broken frequently and at random locations due to DNA element (Ds-dissociator) and an in trans acting enzyme, called Ac (associator), part of the hAT family of transposases

Question 3

Mobile genetic elements

Answer 3

Many MGEs have evolved highly specific targeting mechanisms that direct their integration to genomic “SAFE HAVENS” thereby minimising their damage to the host

eg Yeast Ty elements preferentially integrate DNA genes into specific ch. loci close to RNApol III transcription start sites
Package RNA into virus like particles that cannot escape the cell (BENIGN system)
Different Ty elements are inserted yet they don’t disrupt the activity of RNAP III

Question 4

Are all MGEs benign?

Answer 4

Not necessarily?
Certain retroviruses, for example HIV1 which are descended from LTR retrotransposons , also exhibit preferential integration into gene rich regions-cause disease

In humans there are at least 65 documented cases of ideas resulting from de novo insertions

Cells have adapted strategies such as CpG methylation to block activity of these elements, turn off expression of genes that are required for that element to move

Question 5

Example of serine recombinase in flagella in Salmonella?

Answer 5

Hin recombinase
Hin sgene expresses the recombinase flanked by hix sites
Inverted rotation of MGE.
Promoter faces opposite direction.
Initially promoter encodes to the right FljB and FljA
FljB=H2 protein
FljA=H1 repressor
The expression of these flagellin genes are switched as the MGE is inverted. so it changes surface proteins in flagella which leads to the bacteria evading the immune response

Question 6

For a transposon what orientation is their recombination sites?

Answer 6

Inverted repeats

tail to tail

Question 7

Transposase active site consists of which residues?

Answer 7

DDE
enzyme has evolved a very flexible active site that can either use water to cut the DNA like a restriction enzyme and it can also use the DNA as a nucleophile to do the strand transfer reaction

Question 8

For antibodies what chromosomes are for light chain and heavy chains?

Answer 8

Light locus ch22 and ch2

heavy locus ch14

Question 9

How does VDJ recomb occur?

Answer 9

Recomb occurs specifically b/w the VDJ elements with SPECIFIC RECOMBINATION SIGNAL SEQUENCES (rss)
2 types:
1) 12bp spacer
2) 23bp spacer
From inverted repeats for DNA transposons and viral retrotransposons

Question 10

COPY AND PASTE DNA TRANSPOSONS

Answer 10

resolvase-serine recombinase removes cointegrate

Question 11

What enzyme is used in VDJ recombination with 23/12 break alignment rule?

Answer 11

RAG endonucleases
RAG1/RAG2
Use activated water molecule as nucleophile

Question 12

How is somatic mutation introduced?

Answer 12

By cytidine deaminase (AID) only acts on ss DNA

and uracil glycosylase (UNG)

Question 13

AID

UNG

Answer 13

AID (somatic mutation, class switching)
UNG (influences the pattern of somatic mutations) produces an abasic site so that it enters the base excision repair pathway