Control of Gene expression

Question 1

Constitutively expressed genes

Answer 1

Reads obtained from different cells are similar indicating that this gene is expressed at a similar level in different cell types

Question 1

How can we visualise which genes are expressed in a cell?

Answer 1

Through RNA sequencing: number of reads is proportional to the expression level of a gene

Question 2

Why is there a higher number of reads for exons than introns?

Answer 2

Because introns are usually degraded by nucleases when transcribed

Question 3

When is a homogenous signal seen between exons and introns?

Answer 3

in non-mature RNA

Question 4

Tissue-specific genes

Answer 4

genes expressed only in a specific cell type

Question 5

Enhancer

Answer 5

Control the transcription output of the gene

Question 6

Location of the promoter

Answer 6

Upstream of the transcription unit: localised in proximity of the transcription start site

Question 7

Transcription unit

Answer 7

exons+ introns

Question 8

Transcription start site

Answer 8

where RNA polymerase binds to transcribe the gene

Question 9

Types of cis-regulatory sequences

Answer 9

1. Enhancers
2. Silencers

Question 10

Cis-regulatory sequences

Answer 10

Regulate the expression of a gene located on the same DNA

Question 11

Trans-regulatory sequences

Answer 11

Regulate the expression of genes located on another chromosome

Question 12

Composition of Transcription regulators

Answer 12

DNA-binding domains
Effector domains

Question 13

DNA-binding domains

Answer 13

recognise specific DNA sequences and sites

Question 14

Effector domains

Answer 14

involved in the regulation of genes: tell a protein where to bind and what to do

Question 15

What can effector domains do?

Answer 15

modify chromatin by depositing acetylations, methylations

Question 16

What can transcription regulators recognise?

Answer 16

The outside of the DNA double helix which the edge of each bp presents a distinctive aptter of hydrogen-bond donors and acceptors and hydrophobic patches

Question 17

How can we monitor interaction between TF and DNA?

Answer 17

Using antibodies: Chromatin Immunoprecipitation sequencing ChIP-Seq

Question 18

What is the interaction between TF and DNA?

Answer 18

Highly specific

Question 19

Which is the most difficult attachment for DNA-binding proteins?

Answer 19

distinguishing between C-G and G-C in minor grooves

Question 20

Which are the main signals that control transcription factors?

Answer 20

1. Protein synthesis
2. Ligand binding
3. Covalent modifications [methylation, acetylation]
4. Addition of an additional subunit
5. Association with an inhibitor
6. Stimulation of nuclear entry
7. Release from membrane

Question 21

Ligand bind

Answer 21

Activates TF when a ligand binds to a TF such as glucocorticoid

Question 22

Association with an inhibitor

Answer 22

TF is bound to an inhibitor which when phosphorylated is removed in order to activate the TF

Question 23

How do right enhancers express a gene at the right time?

Answer 23

Because of the presence of DNA loops

Question 24

DNA loops

Answer 24

Takes the enhancers near the gene when needed, making the gene express certain features

Question 25

What helps make DNA loops?

Answer 25

Cohesin

Question 26

Insulator elements

Answer 26

Separate one transcription unit form the next

Question 27

Where do a significant proportion of mutations take place?

Answer 27

In enhancers

Question 28

What do insulator elements prevent?

Answer 28

Prevent transcription regulators from influencing distant gene and they compartmentalise a given regulatory domain by forming loops

Question 29

Superenhancers

Answer 29

A complex of several enhancers: carry out the work of multiple enhancers; has many more binding sites for TR

Question 30

What are superenhancers found to be associated with?

Answer 30

Cancer genes; they make a cell more susceptible to the presence of drugs