Lecture 10 'Tandem repeats & repeat expansion disorders'

Question 1

What are Tandem repeats

Answer 1

Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other.
Tandem repeats are highly polymorphic between individuals. they are able to form secondary structures, these structures can interfere with DNA replication and repair processes and cause expantion of repeats. Tandem repeats are highly variable in the number of repeat copies. They vary between individuals but can also vary within an individual, for example in different cell types or tissues. Tandem repeats can be used for DNA fingerprints.
Tandem repeats are defined in three categories based on size: (Macro)satellite DNA, minisatellites and microsatellites

Question 2

Models for STR repeat expansion

Answer 2

replication slippage model, double strand break repair model and transcription mediated model

Question 3

How to study STRs?

Answer 3

With long read sequencing, like Nanopore.
By using PCR it is difficult to map all the small fragments back

Question 4

The variation of tandem repeats has been linked to?

Answer 4

Rapid variation in microbial cell surface, tuning of internal molecular clocks in files, and dynamic morphological plasticity in mammals

Question 5

Potential mechanisms for gene expression regulation by TRs

Answer 5

Overlap with regulatory protein binding sites
Chromatin structure
Z-DNA formation
Spacing of promotor elements
RNA structure

Question 6

Corrolation between tandem repeats polymorphism and gene expression variation

Answer 6

There is a high density of microsatellites around the TSS of human genes. So there is a correlation between tandem repeat polymorphism and gene expression variation, this correlation can also be seen for DNA methylation

Question 7

STRs Small Tandem Repeats

Answer 7

Due to their highly variable nature and vicinity to genes it has been suggested that STRs offer a rapid and dynamic mechanism to alter gene expression in the face of environmental change
There is an enrichment of STRs in regulatory regions and around genes
Various proposed mechanisms through which STRs modulate gene expression

Question 8

Repeat expansion disorders (REDs)

Answer 8

REDs occur when a simple repeat expands a certain threshold.

Question 9

There are different pathogenic mechanism which can cause REDs

Answer 9

• Gene silencing –> significant reduction in the expression of nearby gene
• RNA binding protein sequestration –> proteins which are binding to the RNA will block the translation
• Toxic gain of function
• Repeat associated Non-AUG translation –> Making a protein but not from the start codon, ALS –> ran translation

Question 10

FXS

Answer 10

Fragile X syndrome (FXS) is caused by a repeat expansion in the FMR1 5’UTR. There are different phenotypes dependent on how much FMRP there is still produced, and production of FMRP is dependent on the length of the alleles, how large the expansion is and the methylation.

Another disease caused by expansion is neural intranuclear inclusion disease (NIID), also here the phenotypes are linked to the size and purity of the repeat

Question 11

Repeat expansions can cause diseases through a number of different mechanisms

Answer 11

• Expansion of the CGG repeat in the FMR1 5’UTR causes a number of different diseases
• The size of the expansion dictates the disease mechanism in humans
• It is unknown what triggers methylation once the repeat passes the 200x threshold
• Carriers of an unmethylated expansion could offer clues into the mechanism behind the CGG repeat methylation