Transposable Elements Flashcards
Transposable elements
Segments of DNA capable of moving from one location in the chromosomes do another or even to a different chromosomes
also called jumping genes
Found in many organisms
Can constitute a significant portion of the genome
Can lead to chromosomal breakage and insert in new locations
becomes a major source of mutations
Why are transposon’s important in the generation of some human diseases?
Due to their ability to alter gene function
General characteristics of transposable elements
- Create staggered, breaks in target DNA.
- Attaches to single stranded ends of DNA.
- DNA is replicated at the gaps.
Flanking direct repeats
The transposase enzyme
Terminal inverted repeats
Flanking direct repeats
3-12 bp long
Generated in the process of transposition
Don’t belong to the transposable element
Created by dna replication of the staggered single stranded pieces of dna
Transposase enzyme
Often encoded by the transposable element
Makes the staggered break in the dna and catalyses the transposition
Terminal inverted repeats
9-40 bp long
Inverted and complimentary
- Found at the ends of (within) many transposable elements
- Recognized by the enzymes that catalyze transposition (like transposase)
Two classes of transposable elements
Based on DNA or RNA
Class I. - retrotransposons (RNA intermediate)
Class II. DNA transposing - catalyze by transposase
Includes:
- nonreplicative transposons and
- replicative transposons
Class I transposons
Aka retrotransposons (RNA intermediate)
- rna is transcribed from the transposable element (DNA)
- Dna copy of element made from rna by reverse transcription and then inserted into a new chromosomal site
Requires a reverse transcriptase - reverse flow of genetic information from rna to dna
(RNA dependent DNA polymerase)
Class II transposons
Dna transposons catalyze by transposase
Includes
Nonreplicative transposons
And
Replicative transposons
Non replicative transposons
Sub class of class II transposons
Element is physically cut out of one side in a chromosome or plasmid and pasted into a new site
Cut and paste
Number of transposable elements is preserved
Replicative transposons
Element is replicated with one copy and inserted at a new site and one remains at original site
Copy and paste
Number of transposable elements increases (new copy at new site, old copy remains)
Structure of class one transposable elements
Long terminal direct repeats,
short, flanking, direct repeats at target site
Structure of class two transposable elements
Short terminal, inverted repeats,
short, flanking, direct repeats at target site
Genes encoded by class I (retrotransposons)
Reverse transcriptase gene (and sometimes others)
What genes are encoded by class II transposons
Transposase gene (and sometimes others)
Which class of transposons are more common in eukaryotes
Eukaryotes contain both dna transposons and retrotransposons but retrotransposons are more common
What kind of transposons are present in bacteria
Just DNA transposons
What are the mechanisms in place to control or limit transposition
- DNA is methylated where transposon’s are common
- Methylating DNA suppresses transcription
- Prevents production of a transpose enzyme - Alterations in the chromatin structure (eg. heterochromatin) prevent transcription
- Control of the transposes translation by piwi interacting RNAs (piRNAs) Bind to piwi proteins in Arabic translation of transposase mRNA.
Why are transposable elements mutagenic
Due to their ability to insert themselves into DNA, they are mutagenic
Transposition is a spontaneous mutation
Transposition entails the exchange of dna sequences and recombination
Leads to dna rearrangements such as duplications, deletions, inversions and translocations
What is the cause of hemophilia
Insertion of the L1 transposable element into the blood clotting factor VIII gene causes hemophilia (frameshift/nonsense mutation)
Insertion can cause a loss of function mutation (disrupts the coding sequence of a gene)
How can insertion cause a gain of function mutation
By activating a nearby gene
Beneficial: ex activating a channel to pump out insecticide in insects
Detrimental: ex. Activating protooncogene (cancerous)
What causes black pigment in grapes
Lack of transposons
black pigment in the grapes is due to anthocyanins in the skin
What causes a green/white grapes?
Gret1 Transposon inserted near the VvmybA1 gene disrupts the gene and synthesis of the anthocyanins that encode the black pigment
Results in no anthocyanin production
What causes red grape colour?
Red grapes came about from a partial removal of retro transposon, allowing the summer, but not full production of anthocyanin
How does can transposons lead to deletion
Pairing of direct repeats can result in deletion
How can transposons lead to an inversion
Pairing of inverted repeats can lead to inversion
What are the affects of misalignment and e equal exchange between transposable elements located on sister chromatids
Leads to one chromosome with a deletion and another with a duplication
Corepressor
A small molecule that binds to a repressor, and it allows the repressor complex to bind to the operator which inhibits transcription used in negative repressible, operon
What does negative mean for negative regulation?
The regulator protein is an inhibitor or repressor
Positive control
Regulator protein is an activator activator, binds operator and induces transcription alternatively, an activator combined upstream of the operator to influence transcription
CAP
Catabolite activator protein
A positive activator of transcription
Binds just upstream of the promoter and enhances the binding of rna polymerase to the promoter
What does lac Y encode
Permeate
Transports lactose across the bacterial cell membrane
Lac Z
B-galactosidase
enzyme that catabolizes Break down into glucose and galactose
Can also convert lactose into allolactose
Lac A
Thiohalactoside transacetylase
Function is unclear
LacP
Common promoter of the lac Y, lac z and lac A
Lac operon in the absence of lactose
Very little of the operon is transcribed (but not none)
Repressor protein (lac I) binds to the operator (lacO) and inhibits transcription
Coordinate induction
The simultaneous synthesis of several proteins by a specific mlc called the inducer
Two major groups of transposable elements in bacteria
Simple and complex
Simple transposable elements
Major group of transposable elements in bacteria only carries information required for movement,
insertion sequence contains the transposes gene
contain terminal, inverted repeats,
and flanked by direct repeats at the target site
Complex transposable elements
Major group in bacteria
Includes composite and non composite
Composite transposons
Any sequence that is flanked by 2 simple transposable elements
Composite transposons is flanked by direct repeats
Ex. Tn 10
Non-composite transposable elements
Possess transposase gene and have terminal inverted repeats
Contain extra dna not related to transposition
Tn3 is an example
Carries ampicillin resistance gene
Barbara McClintock
Discovered chromosome breakage caused usually clear kernels to become mosaic
Genetic analysis of the mechanism of chromosome breakage led her to discover the cut and paste Ds and Ac elements that moved around in the genome
Ac gene
Activator gene
Contains terminal inverted repeats
Has transposase gene
Autonomous transposition
Stimulates chromosome breakage at site of Ds
Ds gene
Dissociation gene
Similar to Ac
Possesses inactivated transposase gene
Requires transposase from Ac to transpose
Nonautonomous transposition
P elements
In drosophila flies
Possess terminal inverted repeats
Contain both a transposase and a repressor of transposition
Creates phenomenon of
Hybrid Dysgenesis
Occurs when p elements are introduced into a cell that does not have them in its genome
Sudden appearance of numerous mutations burst
Chromosome aberrations
Sterility
Repressor protein is a cytoplasmic protein that inhibits transposition
Repressor protein is incorporated into the cytoplasm of the egg
SINES
Most common transposable element in human genome is Alu
Identified as mutagenic in more than 20 genetic diseases
I Roz from RNA intermediate, contain shorten, five prime end
Have a short flanking repeats (100-300bp) when sequences inserted into DNA
LINES
Have shortened sequences but longer than SINES (900-6000bp)
