Genome Structure

Question 1

How big (roughly) is the human genome?

Answer 1

3 gbps

Question 2

Roughly how many genes does the human genome contain?

Answer 2

20000 genes

Question 3

Which histones form the nucleosome?

Answer 3

2 each of H2A, H2B, H3 and H4

Question 4

What does histone 1 do?

Answer 4

Binds linker DNA between nucleosomes

Question 5

What is a metacentric chromosome?

Answer 5

Where short and long arms are of equal length

Question 6

What is a submetacentric chromosome?

Answer 6

Long long arm and short short arm

Question 7

What is an Acrocentric chromosome?

Answer 7

When a chromosome doesnt have a short arm

Question 8

What is the arm length of a chromosome defined by?

Answer 8

The position of the centromere

Question 9

What are the different definitions of an exome?

Answer 9

all of the coding sequence or the whole gene sequence

Question 10

What is a gene?

Answer 10

All the DNA that is transcribed into RNA + all the local control regions that are required to ensure quantitatively appropriate tissue-specific expression of the final protein

Question 11

How much of the genome is intergenic?

Answer 11

98%

Question 12

What does the intergenic region contain?

Answer 12

Sequences of no known function

Question 13

What do gene clusters allow for?

Answer 13

Coordinated gene regulation but may just reflect the evolutionary history

Question 14

If you have ‘n’ exons, how many introns do you have?

Answer 14

N-1

Question 15

Can you have a gene with no introns?

Answer 15

Yes

Question 16

Where are TATA boxes found and what do they do?

Answer 16

Promoter region

Recruit general transcription factors and RNA polymerase

Question 17

Where are regulatory elements found and what do they do?

Answer 17

Promoter regions

Regulate recruitment of RNA polymerase

Question 18

What direction can RNA polymerase move in?

Answer 18

5’ to 3’

Question 19

What are the three types of regulatory regions?

Answer 19

Enhancers, silencers and insulators

Question 20

What do enhancers do in regulatory regions?

Answer 20

Upregulate gene expression

Question 21

What does position independant mean?

Answer 21

They can take affect from anywhere (ie in the gene or many kilo bases away)

Question 22

What type of transcription factors are the enhancers targets for?

Answer 22

Activators

Question 23

What type of transcription factors are the silencers targets for?

Answer 23

Repressors

Question 24

What do silencers do in regulatory regions?

Answer 24

Downregulate gene expression

Question 25

What are insulators in regulatory regions?

Answer 25

Short sequences that act to prevent enhancers/ silencers influencing other genes

Question 26

How has the organisation of somatic nuclear DNA been identified?

Answer 26

Hi-C and high throughput microscopy

Question 27

What does Hi-C detect?

Answer 27

Genomic DNA sequences in close proximity

Question 28

What does the organisation of somatic nuclear DNA involve?

Answer 28

CTCF protein and cohesin protein complex, as well as transcription machinery

Question 29

What are the names of the two compartments that the genome is split into?

Answer 29

Compartment A and B

Question 30

What do the genes in compartment A do?

Answer 30

Transcriptionally active with active histone modifications

Question 31

What do the genes in compartment B do?

Answer 31

Transcriptionally repressed with repressive histone modifications

Question 32

When are the compartments made apparent?

Answer 32

In the 3D genome structure

Question 33

What are the compartments made up of?

Answer 33

Non-interacting topologically associated domains (TADs)

Question 34

What are topologically associated domains (TADs) seperated by?

Answer 34

The transcriptional repressor CTCF protein

Question 35

How do the CTCF proteins control transcription?

Answer 35

The cohesin complex starts loading and extruding a length of DNA until it hits the CTCF proteins, which block any further extrusion taking place and forming a loop