TMC 4- The Human Genome

Question 1

where is mammalian DNA methylated?

Answer 1

Mammalian DNA can be methylated at the carbon 5 of cytosine

in mammals, cytosine can be methylated at carbon 5 to generate 5-methylcytosine (5-mC) at CG sequences (also called CpG).

Question 2

how can Methylation patterns be altered

Answer 2

by DNA methyltransferases (DNMTs)
and by demethylation enzymes.

Question 3

when are DNA methylation patterns laid down

Answer 3

In the early embryo

Question 4

Demethylation event in zygotes

Answer 4

In mammals, a demethylation event demethylates the whole genome in zygote shortly after fertilisation and in
primordial germ cells.

New (de novo) methylation then
occurs generating a methylation pattern that persists throughout development and becomes modifed at genes that are expressed in a tissue specific manner.

Question 5

what does Deamination of cytosine generate in DNA

Answer 5

uracil

Question 6

what enzyme works in deamination of cytosine

Answer 6

UDG - uracil DNA glycoslase

** doesnt act on uracil in RNA

Question 7

What happens once uracil is removed as a part of the deamination process

Answer 7

Once the uracil is removed,
– DNA repair enzymes of the base excision repair pathway (BER) – repair the area and – reinserts cytosine.

Question 8

What does deamination of
5-methylcytosine (5-mC) in DNA generate

Answer 8

thymine

Question 9

what enzyme works in deamination of
5-methylcytosine (5-mC)

Answer 9

TDG - Thymine DNA Glycosylase

Question 10

deamination of 5-methylcytosine (5-mC)

Answer 10

• C is replaced w/ T
• repair by TDG and other DNA repair enzymes of BER replace T w/ cytosine
  – thus CG when replicated gives GC
• However TDG not as efficient as UDG
  – thus usually replication without repair
  – produces AC from TG instead of GC
  This is an example of an SNP

Question 11

What is the most common SNP in people

Answer 11

C to T changes at CG sequences

Question 12

BER?

Answer 12

Base Excision Repair pathway

Question 13

SNP

Answer 13

Single Nucleotide Polymorphism (SNP) – A single DNA base change found between humans or individuals of any species

Question 14

deamination of cytosine

Answer 14

• Cytosine is replaced with Uracil
• UDG recognises uracil - and removes it
• UDG along with other DNA repair enzymes of the Base Excision Repair pathway (BER) come in and replace Uracil with Cytosine
• If replication without repair – U is not replaced with C
  – Thus instead of G pairing with C – A is paired with a T (as U is replaced with a T in DNA)

Question 15

how do DNA changes occur

Answer 15

• mistakes in copying DNA
• through damage to bases in DNA that change their base pairing properties

Question 16

mutations vs polymorphisms

Answer 16

polymorphism - Harmless chnage in DNA
Mutation - chnage in DNA that causes a change in the phenotype of an organism

Question 17

How many new mutations are present in each newborn

Answer 17

about 200 new DNA changes in a new born

Question 18

why do mutations accumulate in humans and other organisms over successive generations?

Answer 18

• due to DNA replication errors and naturally occurring damage to the DNA over time – 200 new DNA changes found in a newborn
• These changes passed onto the offspring of the newborn along with 200 more new DNA chnages
• Thus more the generations - more the DNA chnages accumulating

Question 19

CpG islands and where they occur

Answer 19

Regions rich in CGs occur in ~ 60-70% of human / mammalian promoters.

Question 20

CpG and CpG island methylation

Answer 20

CpG islands in promoters in DNA – mostly not methylated
If CpG islands in promoters are methylated – silences the gene - thus silences/NO transcription
CpGs not in CpG islands – generally methylated

Question 21

Genome instability

Answer 21

Term used when increased frequency of alterations
of the genome are seen in a cell
Typical alterations:
- change in chromosome number
- change in chromosome structure

Question 22

What are the diff -omes

Answer 22

• genome
• transcriptome
• proteome
• methylome
• epigenome
  (Go To Pick ME)

Question 23

Genome

Answer 23

• DNA sequence of a species.
• same in all somatic cells
• doesnt change within the cell or when the cell divides into daughter cells

Question 24

Transcriptome

Answer 24

• It is the RNA transcribed from genes in a cell or tissue
• also known as RNA profile
• differs between cells of different tissues
• Transcriptome changes in cells depending on various factors - the environment, age, signals etc.

Question 25

Proteome

Answer 25

• Full complement of proteins expressed in a cell or tissue
• similar to transcriptome in that:
  – differs btwn cells of diff tissues
  – also changes in cells depending on various factors – envrmnt, signals, age etc.

Question 26

Methylome

Answer 26

• Pattern of methylation on the DNA in the genome
• Diff in cells from diff tissues
• Changes within a cell in response to various factors – envrmnt, signals, age …

Question 27

Epigenome

Answer 27

• DNA
• Nucleosome
• pattern of all Methylated cytosines
• Transcription factors bound to chromatin
• pattern of all Modifications to chromatin
• Remodelling complexes bound to chromatin

DRc MeMo TfN

Question 28

Are the different –omes the same in different tissues?

Answer 28

No - all different in cells of diff tissues except genome - same in all somatic cells (w/ exception of few mutations)

Question 29

What is the difference between the genome, the methylome, the epigenome, the transcriptome and the
proteome?

Answer 29

• genome – all DNA sequence - same in all somatic cells
• transcriptome – RNA transcribed from genes
• proteome – full complement of proteins in a cell/tissue
• methylome – pattern of methylation of DNA in genome

Question 30

Answer 30

:)