Microsatelites, Centromeres, & Telomeres

Question 1

What are Microsatelites?

Answer 1

Simple sequence repeats (SSRs)

• Repeat units of usually 1 –6 bp
• Usually 6-30 repeats long, but can be longer

Question 2

Expansion and contraction by replication slippage steps

Answer 2

Initiation, dissociation, rehybridation and misalignment, new strand is a different length to the template

Question 3

How do new microsatellites form?

Answer 3

• Arise from random sequences by mutation to form proto-m-sats, expand into m-sats
• Can arise from retrotransposons

Question 4

Microsatellite mutation:

Answer 4

• Highly polymorphic

- Evolution is a balance between: Length mutations and Point mutations

Question 5

What are length mutations?

Answer 5

Length mutations: repeats grow or contract; longer m-sats tend to contract

Question 6

What do point mutations do?

Answer 6

Point mutations: break long repeat arrays into smaller units

Question 7

Replication slippage expansion or contraction?

Answer 7

Expansion: New strand loops = increase in repeat length
Contraction: Template strand loops = decrease in repeat length

Question 8

What protein-coding genes are composed of tandemly repeated segments?

Answer 8

Collagen gene’s corresponding protein structure is a repeat: (Gly-X-Y)n

• single strand
• triple coil
• central glycines

Question 9

What is the use of microsatelites?

Answer 9

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

Question 10

What are the features of centromeres?

Answer 10

Densely packed heterochromatin, highly methylated especially histone methylation,
deacetylated
- Little recombination

Question 11

What are Centromeric histones?

Answer 11

Modified histone H3: CenH3

Question 12

What is the structure of the inner centromere?

Answer 12

cytologically constricted region
Composed of satellite sequences – repeated regions, larger than microsatellites
- Tandem repeats 100-200 bp

Question 13

What is the structure of the outer centromere (pericentromere)?

Answer 13

• 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

Question 14

Where on the chromosome is the peri-centromere, or outer region?

Answer 14

Sequence from last alpha satellite repeat outward to the first cytogenetic band on a chromosome arm

Question 15

What is the length of centeomeric DNA?

Answer 15

Several megabases

Question 16

Gene patterns in chromosomes

Answer 16

Gene density increases further away from the inner region

Question 17

What is the sequence composition of the outer centromere?

Answer 17

Pseudogenes, retroelements, transposons, and the occasional gene

Question 18

What is the sequence composition of the inner region?

Answer 18

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

Question 19

Nucleosomes at the centromere?

Answer 19

CenH3

Question 20

Why are centromeres difficult regions of chromosomes to sequence & assemble?

Answer 20

• due to many repeats, especially with short read sequences;
• frequently remain unassembled in genome sequencing projects

Question 21

Centromere DNA evolution

Answer 21

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

Question 22

How were transposable elements involved in centromere evolution?

Answer 22

Evolution of centromeric TEs

Evolution of centromeric and pericentric repeats

Question 23

Evolution of centromeric TEs

Answer 23

TE amplified tandemly by

unequal crossing over

Question 24

Evolution of centromeric and pericentric repeats

Answer 24

TE diverges in sequence, repeats form by unequal crossing over

Question 25

How to detect Repositioning of centromeres along the chromosome?

Answer 25

Detected by comparing centromeres from closely related

species

Question 26

What are possible mechanisms to reposition centromeres along the chromosome?

Answer 26

Pericentric inversions,
acquisition from other chromosomes,
neocentromeres accumulating
heterochromatin

Question 27

Models for acquisition of centromere function

Answer 27

Centromere emergence
spreading
recruitment

Question 28

What are Sub-telomeric sequences composed of?

Answer 28

Composed of various types of repeats including
degenerate telomerase repeasts
- Occasional genes and pseudogenes

Question 29

What is the structure of telomeres?

Answer 29

Tandem arrays of telomeric repeats;

example: TTTAGGG
- Length typically 5-15 kb (depends on species)

Question 30

Telomeres in humans

Answer 30

• average repeat lengths vary substantially from
  individual to individual and have a heritable component
• Continuously shrinking by replication problems at ends of chromosomes, extended by telemerase

Question 31

Telermere extension mechanism

Answer 31

• Telomerase adds repeats to telomeres to keep them
  from shrinking, uses and RNA template
• Aberrant regulation of repeat tract lengths is
  associated with aging age-related diseases