Module 9 - Part 2 Flashcards
Transposable Elements
fragment of DNA that can be excised and then moved elsewhere
Genetic elements that move are called: (5)
- controlling elements
- jumping genes
- mobile genes
- mobile genetic elements
- transposons
Barbara McClintock (1902-1992)
- discovered TEs in 1940/50s
- ignored for 20 years because…
1. it was too different
2. didn’t fit w the accepted understanding of the genome
3. other scientists didn’t understand
4. it was the 1950s and she was a women - her work eventually recognized w a Nobel prize in physiology in 1983
2 genetic factors that are required for chromosome breakage (in maize):
- dissociation factors (DS): always at site of breakage (cis factor)
- activator factor (Ac): at an unlinked locus, but was required to activate or cause breakage (trans factor)
Ac factor is considered
mobile (& resides in different location in different individual plants)
Abrupt changes associated with the activity of Ac and DS factors were given the name
controlling elements
Transposase
an enzyme that has a “cut and paste” mechanism that removes the DNA element from one locus and inserts it into another
Mechanism of transposition (3 steps)
- transpose makes a staggered cut in the host DNA molecule (creates overhang)
- transposon inserts between ends of cut
- host DNA repair machinery joins host DNA & transposon at each end using overhangs as templates
Ds is _______ in the absence of a func. Ac
stable
Ac is….
unstable
Ds is a _________ variant of Ac
deletion
Ac
autonomous element (encodes all info necessary for movement)
- transposase & IR = inverted repeats
Ds
non-autonomous element (requires a related autonomous element to move)
- no transposase
Class 1: retrotransposons
- related to retrovirus
- use an RNA intermediate
- they encode a reverse transcriptase that makes a DNA copy of the RNA that can be encoded into the genome
- found in eukaryotes only
Class 2: DNA transposons
- DNA element that moves directly from one position in genome to another (cut & paste)
or may be copied & moved as a DNA molecule - found in both eukaryotes and prokaryotes
Common characteristics of TEs
- have direct repeats - short repeated seq flanking the element (arise by transposition)
- carry a gene coding for an enzyme that catalyzes transposition
1. transposase: elements use DNA intermediate
2. reverse transcriptase: elements use RNA intermediate
Retrovirus
single-stranded virus, uses a double stranded DNA intermediate for replication
Retroviral genes
gag, pol, env
genes encoding proteins required for transposition
Gag
maturation of viral RNA genome
Pol
reverse transcriptase + integrase
Env
structural protein surrounding virus
LTR
long terminal repeat; recognition site for transposition
How do TEs cause mutations
- insert themselves in coding regions & disrupt protein func
- when DNA transposons move = cause a deletion or DSB
TEs can ______ gene expression by influencing….
increase, neighbouring promotor or replacing nascent promotor
______ can bind to TEs and can _______
insulators, block enhancer-promotor communication
- repress gene expression
TEs can turn gene expression ____ by blocking ________
on, inhibitory sequences (like repressive chromatin)
Maize
49-78% of genome is made up of retrotransposons
Wheat
90% of genome consists of repeated sequences
68% of TEs
Mammel
45-48% genome comprised of transposons or remnants of transposons
>45% genome made up of retrotransposons
DNA transposons accounts for 2-3%
SINEs
Short interspaced nuclear elements
- Alu - 300bp
LINEs
long interspaced nuclear elements (avg. length 6.5kb retrotransposons
Minisatellites
aka VNTRs
- regions 10-100bp long, repeated variably
Microsatellites
aka STRP
- regions 2-5bp repeated 10-30X
Alu elements
- found dispersed throughout the human genome
- > 11 mil elements in human genome (approx 11% of genome)
TEs impact on human genome
- increase metabolic burned on the cell (replication)
- leave a copy behind after transposition, therefore increase in number
- increase genome diversity
Where do TEs insert
mostly 5’ end of gene (regulatory region)
Are TEs mobile
most are not, maybe 0.05% can
Are TEs transcribed
yes
Do TEs impact chromosome structure
yes
Diseases caused by TEs (7)
- hemophilia A & B
- severe combined immunodeficiency
- porphyria
- predisposition to cancer
- Duchenne muscular dystrophy
- BRCA1
- neurofibromatosis
(deleterious insertions associated with Alu elements)
do SINEs (Alu seq) and LINEs causes mutations responsible for human genetic diseases
yes
HERV
human endogenous retrovirus
HERV-H
- subfamily most common
- expressed preferentially in embryonic SCs
- promote genome instability through non-allelic homologous recombination
“HERV susceptibility regions”
Case study HERV-H finding
deletion near 4 potential HERV-H loci on chromosome 3
