Lecture 2 ‘Cross species conservation and variation’

Question 1

pseudogene insertion, expression

Answer 1

Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Most arise as copies of functional genes, either directly by DNA duplication or indirectly by reverse transcription of an mRNA transcript.
Pseudogenes are not expressed because they don’t have a promotor

Question 2

Ultraconserved elements (UCE)

Answer 2

are >200 bp sequences which have not changed in the last 100 million years. many UCEs are part of enhancers and not essential for normal development

Question 3

Human Accelerated Regions (HARs)

Answer 3

elements that have stayed conserved for a long time, which have rapidly changed between chimp and human. So only in the human they are rapidly evolving. Many HARs are part of enhancers / gene regulatory elements.
HAR2 is an example, this gene is coding for our thumb. Only in human we see that there are two fragments in stead of three.

Question 4

differences between single nucleotide substitutions and single nucleotide polymorphisms.

Answer 4

Between species it is called single nucleotide substitutions and between the human population it is called SNPs, single nucleotide polymorphisms.

Question 5

SNPs

Answer 5

Single nucleotide polymorphism. SNPs can occur in non- and coding sequences, in both situations it can have negative effects.
Non-Synonimous SNPs leads to a different amino acid, and a Synonimous SNPs leads to the same amino acid.

Question 6

INDELS

Answer 6

Small insertions or deletions in the genomic DNA. INDELS in coding DNA can disrupt protein-coding potential by causing frame shifts. INDELS in regulatory elements can cause dissociation of TFs. INDELS can create/delete exon splice sites.

Question 7

Sources of INDELS

Answer 7

• Repair of DNA damage
• DNA polymerase slippage
• Transposable element insertion
• Pseudogene insertion

Question 8

sources of healthy genomic variation

Answer 8

Chromosomal recombination / homologous crossover

Non-homologous crossover, can cause duplications/deletions in the genome

Question 9

Chromosomal recombination / homologous crossover

Answer 9

• Leads to recombination of chromosomes
• Shuffling of alleles
• Important and necessary source of genetic variation in off sping
• Multiple crossover events per cell during meiotic cell division

Question 10

Non-homologous crossover, can cause duplications/deletions in the genome

Answer 10

• Unequal crossover
• Can lead to duplications and deletions
• Often involved with regions displaying high levels of sequence similarity / repetitive DNA
• An important source of novel genetic material and new genes!