Microsatelites, Centromeres, & Telomeres Flashcards
What are Microsatelites?
Simple sequence repeats (SSRs)
- Repeat units of usually 1 –6 bp
- Usually 6-30 repeats long, but can be longer
Expansion and contraction by replication slippage steps
Initiation, dissociation, rehybridation and misalignment, new strand is a different length to the template
How do new microsatellites form?
- Arise from random sequences by mutation to form proto-m-sats, expand into m-sats
- Can arise from retrotransposons
Microsatellite mutation:
- Highly polymorphic
- Evolution is a balance between: Length mutations and Point mutations
What are length mutations?
Length mutations: repeats grow or contract; longer m-sats tend to contract
What do point mutations do?
Point mutations: break long repeat arrays into smaller units
Replication slippage expansion or contraction?
Expansion: New strand loops = increase in repeat length
Contraction: Template strand loops = decrease in repeat length
What protein-coding genes are composed of tandemly repeated segments?
Collagen gene’s corresponding protein structure is a repeat: (Gly-X-Y)n
- single strand
- triple coil
- central glycines
What is the use of microsatelites?
1) Genetic diversity studies
2) Parentage analysis in populations
3) Forensics cases: DNA fingerprinting
- High mutation rate enables analyzing individuals in population
- Very useful, highly variable, neutral genetic markers
What are the features of centromeres?
Densely packed heterochromatin, highly methylated especially histone methylation,
deacetylated
- Little recombination
What are Centromeric histones?
Modified histone H3: CenH3
What is the structure of the inner centromere?
cytologically constricted region
Composed of satellite sequences – repeated regions, larger than microsatellites
- Tandem repeats 100-200 bp
What is the structure of the outer centromere (pericentromere)?
- No satellite structure
- a few repeat sequences and pseudogenes
- occasional gene towards the outer parts
- Many transposons: some are centromere specific; ample non-coding DNA targets
Where on the chromosome is the peri-centromere, or outer region?
Sequence from last alpha satellite repeat outward to the first cytogenetic band on a chromosome arm
What is the length of centeomeric DNA?
Several megabases
Gene patterns in chromosomes
Gene density increases further away from the inner region
What is the sequence composition of the outer centromere?
Pseudogenes, retroelements, transposons, and the occasional gene
What is the sequence composition of the inner region?
Composed of higher order repeats (1-3kb) that make HOR satellite arrays (~Mb)
repeated regions, larger than microsatellites
- Tandem repeats 100-200 bp
Unit in HOR is ~171bp
Nucleosomes at the centromere?
CenH3
Why are centromeres difficult regions of chromosomes to sequence & assemble?
- due to many repeats, especially with short read sequences;
- frequently remain unassembled in genome sequencing projects
Centromere DNA evolution
Rapid rate of sequence evolution; little similarity between closely related species; rapid changes within a species
- Large scale changes typically do not disrupt
centromere function
How were transposable elements involved in centromere evolution?
Evolution of centromeric TEs
Evolution of centromeric and pericentric repeats
Evolution of centromeric TEs
TE amplified tandemly by
unequal crossing over
Evolution of centromeric and pericentric repeats
TE diverges in sequence, repeats form by unequal crossing over
