Chromosomal rearrangements

Question 1

How can Karyotyping be obtained ?

Answer 1

• “Karyotype” also refers to the actual collection of chromosomes being examined
• Can be obtained by staining of condensed chromosome with various agents that have different affinities of binding for DNA depending on sequence composition.

Question 2

What are some different types of chromosomes ?

Answer 2

• Classification based on position of centromere relative to arm length
  1. Metacentric
  2. Submetacentric
  3. Acrocentric
  4. Telocentric

Question 3

What are some different types of chromosomal rearrangements (deletion)?

Answer 3

• Duplication
• Inversion
• Translocation

Question 4

What are the effects of chromosomal deletions ?

Answer 4

Will cause looping in meiosis in heterozygotes, and a similar effect is observed for duplications

Question 5

When does Haploinsufficiency occur?

Answer 5

Haploinsufficiency can occur in hemizygosity

Question 6

What is Hemizygosity ?

Answer 6

Hemizygosity is when a diploid organism has a single copy of a gene, a situation that can of course occur when chromosome deletions are present

Question 7

What is Haploinsufficiency?

Answer 7

If the single copy of the remaining gene, even if normal, is insufficient to provide function

Question 8

What can incorrect DSB repair lead to ?

Answer 8

Various types of chromosomal abberation, including deletions

Question 9

What is Nonallelic homologous recombination?

Answer 9

The presence of homologous repeats can cause problems also if they are distantly spaced, with potential loss (or duplication) of the intervening sequence

Question 10

Unequal crossing over results in ?

Answer 10

A recombinant with a duplication for the region and a recombinant with a deletion. The deletion will give rise to William’s Syndrome

Question 11

What are some types of chromosomal duplications?

Answer 11

• Tandem duplication
• Displaced duplication
• Reverse duplication
• Displaced reverse duplication

Question 12

Intra-chromosomal recombination in tandem duplications can lead to?

Answer 12

The excision of the duplicated segment

Question 13

What are some types of chromosomal inversions?

Answer 13

• Paracentric inversion

- Pericentric inversion

Question 14

Explain chromosomal inversions ?

Answer 14

• Although no DNA is lost in inversions, phenotypic effects can be observed
• For example, the inversion points can disrupt (or fuse) genes at those loci
• Or the genes within the inversion can have their expression altered by position effects

Question 15

What are some types of chromosomal interactions?

Answer 15

• Reciprocal translocation
• Non-reciprocal translocation
• Robertsonian translocation

Question 16

If the damage involves both strands then a double-strand break (DSB) can occur and this is then often repaired by ?

Answer 16

The non-homologous end-joining pathway (NHEJ) which only relies on the two free ends bring brought together

Question 17

Alternatively, a more faithful homology-dependent pathway (HDR) which relies on? what does the require?

Answer 17

Recombination with intact DNA can be employed to repair DSBs. This requires the presence of a homologous chromosome, or of a sister chromatid

Question 18

DSBs are a major cause of chromosomal rearrangements. These are normally DSBs which are caused by ?

Answer 18

DNA damage, in itself induced by agents such as ionising radiation or by reactive oxygen species and DNA replication (SSBs turned into DSBs)

Question 19

When are Spo11-dependent DSBs generated and normally repaired by ?

Answer 19

Spo11-dependent DSBs are generated only during meiosis and are normally repaired correctly by HDR

Question 20

Explain some alterations of the genome that could occur?

Answer 20

• Small scale changes (point mutations, replication fork slippage, indels, etc)
• Chromosomal rearrangements (duplications, deletions, translocations, inversions)
• Chromosome number variations (aneuploidy)

Question 21

What is Chromothripsis?

Answer 21

Chromotripsis (the shattering of the chromosome followed by rejoining by NHEJ or replication-based mechanisms) can also occur in cancer cells

Question 22

Because of the 3 bp periodicity of the code, small indels that are not multiples of 3 bp will lead to?

Answer 22

Frameshift mutations that change the code of the entire sequence downstream of the mutation itself

Question 23

Because the code is redundant, and the third base often not discriminant, several point mutations are?

Answer 23

Synonymous (or silent) substitutions that do not lead to amino acid changes.

Question 24

Nonsynonymous (or missense) substitutions instead lead to ?

Answer 24

AA changes (nonsense substitutions create new stop codons)

Question 25

Nonsense and frameshift mutations lead to ?

Answer 25

Truncated proteins, or to degradation of the RNA by nonsense-mediated decay (NMD)

Question 26

What do nonsense and frameshift mutations cause?

Answer 26

Both these mutation frequently give rise to premature termination codons, which can be dangerous and act as dominant negative alleles

Question 27

What does the NMD pathway takes care of ?

Answer 27

Eliminating most of these transcripts

Question 28

Explain the Pathogenic splicing mutations ?

Answer 28

• Mutations in dinucleotides required for splicing can result in exon skipping or intron retention
• Mutations can also lead to creation of new splice (cryptic) place sites, producing truncated or extended exons

Question 29

Loss of function:
Amorph ?
Hypomorph ?

Answer 29

• Amorph (genetic null) = complete loss of gene function

- Hypomorph = reduced gene function

Question 30

Gain of function:
Hypermorph ?
Neomorph ?
Antimorph ?

Answer 30

• Hypermorph = increased gene function
• Neomorph - new gene function
• Antimorph (dominant negative): dominant allele inhibiting function of wild-type gene

Question 31

What has a stronger phenotype than null alleles (in heterozygote form) ?

Answer 31

Dominant negative alleles

Question 32

What does a null mutation often imply ?

Answer 32

A null mutation often implies complete loss of the gene, but not always, as null alleles can result from nonsense or splicing mutations that cause early termination or partial deletions. Missense mutations can also give rise to null alleles

Question 33

Explain a gain of function mutation ?

Answer 33

Gain of function mutations are rarer mutations. They typically do not produce radically new products but more often instead tend to make products that are expressed inappropriately (for example are constitutionally active, activated in the the wrong cell type, at the wrong time, or in response to the wrong signal)

Question 34

What is a classical example of a gain of function ?

Answer 34

The reciprocal translocation seen in chronic myeloid leukaemia between chromosomes 9 and 22

Question 35

Are nonsense and frameshift mutations easy to identify ?

Answer 35

Nonsense and frameshift mutations are relatively easy to identify as pathogenic. For missense mutations one can resort to conservation to evaluate the likelihood of the change being harmful

Question 36

Why are changes in noncoding RNAs much harder to evaluate ?

Answer 36

Changes in noncoding RNAs are much are harder to evaluate, also because of poor conservation and the role of secondary structure in RNA function. Often changes in these RNA affect complex diseases such as cancer (by affecting gene expression), rather than single-gene disorders