Lecture 16

Question 1

What is epigenetics?

Answer 1

• Changes in gene expression that do not involve a change in DNA sequence • Epigenetic modifications alter gene expression in a variety of ways without changing the DNA including: – DNA methylation – Histone acetylation – RNA interference – chromatin modification -if you methylate upstream of a gene- turns it off

Question 2

Give an example of epigenetics (fat fathers)

Answer 2

Daughters of obese fathers have a greater incidence of diabetes- like disease Epigenetic modification of the the father’s sperm might underlie this observation -daughters of obese fathers= influencing the phenotype of daughters- insulin issues -probably happening in sperm= influence on glucose metabolism

Question 3

How are genes methylated?

Answer 3

In tissue-specific genes or time-specific genes the enzyme DNA methyltransferase adds a methyl (CH3) group to the 5’ carbon of cytosine • When the CpG islands are methylated a gene is switched off -adding a methyl group to CpG islands (p=phosphase, C-cytosine, G-guanine) so you add CH3 group to 5’ of the cytosine= done by enzyme methyltransferase

Question 4

Is methylation reversible?

Answer 4

-yes

Question 5

What are the CpG islands?

Answer 5

-• CpG islands are approx 1000-2000bp in length and a series of these CG dinucleotides are found in the ‘island’ CpG = dinucleotide of G and C p = phosphodiester link between them • In housekeeping genes (switched on all the time) the CpG islands are unmethylated so the gene is continuously expressed -CpG islands, upstream from the gene in the promoter region

Question 6

What genes can be switched off?

Answer 6

-the ones that can be methylated

Question 7

How can chromatin be modified for expression?

Answer 7

Amino acids at the N terminal of the histone can be modified : -Methylation (Me) -Acetylation (Ac) -P phosphate groups (phosphorylation) -get the chromatin so compact that it can’t be expressed -histones have tails=that can be accetylated, phosphorylated or methylated

Question 8

When is DNA not available for expression?

Answer 8

-closed configuration -DNA is methylated at CpG islands and histones are deacetylated

Question 9

When is DNA available for expression?

Answer 9

-open configuration -DNA is unmethylated at CpG islands and histones are acetylated

Question 10

What are two examples of epigenetics?

Answer 10

X-inactivation and genomic imprinting

Question 11

What is genomic imprinting?

Answer 11

-sex of transmitting parent produces observable differences in the phenotype • specific genes are differentially marked during parental gametogenesis -depends from which parent you inherit a particular locus as to whether it will be expressed or not

Question 12

Why does genomic imprinting occur?

Answer 12

In diploid organisms, somatic cells possess two copies of the genome. Each autosomal gene is therefore represented by two copies, or alleles, with one copy inherited from each parent at fertilisation. For the vast majority of autosomal genes, expression occurs from both alleles simultaneously. In mammals, however, a small proportion (<1%) of genes are imprinted, meaning that gene expression occurs from only one allele.[4] The expressed allele is dependent upon its parental origin.

Question 13

How many genes are subject to genetic imprinting?

Answer 13

Approximately 80 human loci • Has to be reversible • Reverses in gametogenesis • Methylation of cytosines? • CpG islands - CH3 group added to cytosine silences a gene but can be reversed –about 80 genes affected by the sex of the parent transmitting them, not sex influenced or limited- it is if the gene will be active or not -gametes reversal- due to methylation again

Question 14

How is teratoma and hydatiform mole evidence for genomic imprinting?

Answer 14

-difference depending on whteher two sets of paternal or maternal l- they look different so epigenetic not just genes -taratoma= 2N mat+ 1N pat -hydatiform= 2N pat + 1N mat

Question 15

What are the two syndromes that are evidence for genomic imprinting?

Answer 15

Prader willi and Angelman syndromes -they are both on chromosome 15, Prader willi if dad’s erased and Angelman if mum is

Question 16

What causes Prader willi syndrome and how does it manifest?

Answer 16

chromosome no 15, q11-13, deletion in the long arm of the chromosome, if you delete it in the region coming from dad= prader willi syndrome = abnormal behaviour (temper), eat voraciously, obesity, sugar intolerance, dental problems, increased risk of cardiovascular disease

Question 17

What causes Angelman syndrome and how does it manifest?

Answer 17

chromosome no 15, q11-13 deletion in the long arm of the chromosome, if you delete it in the region coming from mum= Angelman angelmann syndrome -both males and females can get it -puppet syndrome- mentally retarded -they find thing that’d be sad they find it funny etc

Question 18

What is special about chromosome 15?

Answer 18

on chromosome 15 some genes that are only expressed from the chromosome that comes from father and vice versa= monoallelic expression plus the same region(q11-q13) but different outcomes

Question 19

What is monoallelic expression?

Answer 19

When only maternal or paternal allele is expressed

Question 20

What is uniparental disomy (UPD)?

Answer 20

both chromosomes of a pair come from the same parent -these cases had both copies coming from one parent= uniparental disomy when two pat- angelmann two maternal- prader willi

Question 21

What is heterodisomy?

Answer 21

When a pair of non-identical chromosomes is inherited from one parent= result of non-disjunction in meiosis I

Question 22

What is isodisomy?

Answer 22

When a single chromosome from one parent is duplicated= result of non disjunction at meiosis II

Question 23

What happens normally when a cell has 2 chromosomes already?

Answer 23

normally the cell rescues the trisomy, kicks out the paternal chromosome, when sperm coming in and the cell already has two chromosomes 15 it ejects the paternal one= then have two maternal ones

Question 24

How does imprinting occur?

Answer 24

• Due to methylation • If a male inherits a maternal imprint but passes to his
daughter the imprint changes (therefore not inherited)
• Wiped in primordial germ cells but reestablished according to the sex of the parent
• so new methylation pattern according to the sex of the parent (may be different from what parent had)

-imprinting is epigenetic, methylation and deacetylation plays a role! in the offspring it can be reversed

Question 25

How is variation mainatined in a population?

Answer 25

• mutation - the original source of all variation
• recombination at prophase I of meiosis
• segregation of alleles at anaphase 1 of meiosis
• independent assortment of chromosomes at anaphase I of meiosis
• fertilisation between genetically different gametes

Question 26

How can we measure variation?

Answer 26

• variety in • DNA structure • Epigenetic effects
• Variation can be at the phenotypic level through to the molecular level
• look for visible differences in the phenotype
• chromosome differences eg., length of long arm of Y
• immunological markers eg., blood groups
• protein gel electrophoresis eg., esterases in Drosophila
• SSLPs (Simple sequence length polymorphisms) or VNTR (variable number of tandem repeats)
• STR or (short tandem repeats)

• Single nucleotide polymorphisms (SNP)

Question 27

How can we measure variation by observing differences in the phenotype?

Answer 27

• discontinuous variation (eg. mid digital hair present or absent)
• continuous variation= measuring variation like 50% offspring brown hair etc

=look at the phenotype and score them

Question 28

How can we measure variation by observing chromosome differences?

Answer 28

eg. length of Y chromosome long arm

• Polymorphism (two or more clearly different phenotypes exist) for length of long arm of Y chromosome • Chromosome 9 polymorphism

eg.• Changes in chromosome numbers eg., polyploidy

there is lot of variability in the shape size etc in the same chromosomes in different individuals

chromosome 9- under centromere= heterochromatin so can compare that
or polyploid at the chromosome level and compare

Question 29

How do we observe variation through changes in chromosome structure?

Answer 29

• deletions • duplications - globin genes
2 x alpha globin genes
• translocations • inversions

Question 30

What is a translocation?

Answer 30

a chromosome abnormality caused by rearrangement of parts between nonhomologous chromosomes.

Question 31

What is an inversion?

Answer 31

a chromosome rearrangement in which a segment of a chromosome is reversed end to end. An inversion occurs when a single chromosome undergoes breakage and rearrangement within itself.

Question 32

What are the three types of DNA polymorphisms that we use to look at variation in species?

Answer 32

• SSLPs (Simple sequence length polymorphisms=repeated sequences in the DNA, differ how many times in an individual) or VNTR (variable number of tandem repeats)
• STR or (short tandem repeats)
• Single nucleotide polymorphisms (SNP)= just one base differences

all of these=on one chromosome may have 20 repeats and on another have 5- often occur in non coding regions

-accumulation without any disadvantage as they are not expressed

Question 33

What is a minisatellite?

Answer 33

15 -100b (eg., tandem repeat of 18 bases) total length from 1-5kb.

VNTR variable number of tandem repeats

Question 34

What is a microsatellite?

Answer 34

• short tandem repeats (STR) - 2 - 9 bases – can have several alleles according to how many repeats

Question 35

What is a single nucleotide polymorphism?

Answer 35

1 base – can only have two alleles at a locus

Question 36

What is a VNTR?

Answer 36

• Minisatellites
• In non coding regions of the genome
• Repeat sequence between 15bp -100bp long
• But number of repeats varies from person to person so VNTR can be from 1 - 20kbs in length

-used in forensics!

VNTR- between 15-100 bases
doeasn’t influence the phenotype=in a non coding non regulatory region
Eg., Core repeat is 16 bases long GACTGCCTGCTAAGAT

Question 37

How do you do a multilocus minisatellite probe?

Answer 37

• Multilocus probe – found in more than one location - minisatellites eg., tandem repeat of 18 bases
total length from 1-5kb.

Question 38

Where are a lot of the variable regions in DNA?

Answer 38

-in non-coding regions

Question 39

What are single locus probes used for?

Answer 39

• Single locus probe – minisatellites (as above) – microsatellite - short tandem repeats (STR) - 2 - 4 bases

Question 40

How can SNPs (single nucleotide polymorphisms) be detected?

Answer 40

DNA sequencing, restriction cutting sites- the change, loss or gain of a restriction enzyme recognition sequence

To be a SNP has to occur in 1% population
About 10 million SNPs exist in human populations, where the rarer SNP allele has a frequency of at least 1%.

assosciation with disease: About 10 million SNPs exist in human populations, where the rarer SNP allele has a frequency of at least 1%.

apolipoprotein E and Alzheimers Disease ApoE gene!alleles E2, E3, and E4. Each allele differs by DNA base, and the protein product of each gene differs by one amino acid. one E4 allele; person will have a greater chance of developing Alzheimer’s disease