Gene Expression

Question 1

What is differential gene expression?

Answer 1

Multicellular organisms have the same genes in all cells, but cells at different areas of the body express genes differently (specialised genes are expressed at their specific tissues). This happens due to a series of signalling events and regulation of gene regulatory proteins (transcriptional control).

Question 2

Sites on DNA for protein binding:

Answer 2

• enhancer seq
• silencer seq
• promoter seq

Question 3

Promoter seq on DNA includes binding sites such as:

Answer 3

• regulatory protein binding site
• transcriptional factor binding site
• RNA polymerase II binding site

Question 4

How do transcriptional factors interact with DNA?

Answer 4

Transcriptional factors bind to TATA-binding protein that in turns bind to TATA box on DNA.

Question 5

Examples of DNA-binding proteins and site of binding:

Answer 5

• activator (binds to enhancer seq)
• repressor (binds to silencer seq)
• TATA-binding protein (binds to TATA box)
• RNA polymerase II (binds to rna poly binding site)

Question 6

What is modular domain?

Answer 6

Modular domain is the subunit on the transcriptional protein that regulates the interaction of that protein with other proteins (determines the binding partner for that protein)

Question 7

What are motifs?

Answer 7

Motifs are the structure of the DNA-binding domain within a DNA-binding protein

Question 8

Which are the 4 of the motifs?

Answer 8

1. Leucine zipper (common)
2. Helix-turn-helix (embryonic development)
3. Helix-loop-helix (on activators, for binding to enhancer seq)
4. Zinc finger

Question 9

Function of non-DNA binding proteins:

Answer 9

They recognise the distinct surface created by DNA-binding protein and recruit other gene expression regulatory proteins such as activators/repressors.

Question 10

7 types of gene regulatory protein regulation:

Answer 10

1. Protein syn.
2. Ligand binding
3. Protein phosphorylation
4. Addition of 2nd subunit
5. Unmasking
6. Stimulation of nuclear entry
7. Release from membrane

Question 11

RNAs involved in gene expression regulation:

Answer 11

• miRNA
• siRNA
• piRNA

Question 12

How do the regulatory proteins gain access to the tightly coiled DNA?

Answer 12

There are mechanisms that alter the structure of the chromatin.

Question 13

What is the function of barrier sequence?

Answer 13

To stop the spread of gene activation

Question 14

How does a barrier protein work? (3 ways)

Answer 14

• tethering regions of chromosomes to fixed sites
• binding of proteins to groups of nucleosomes
• recruiting histone modifying enzymes (erase marks required for gene activation)

Question 15

Why are DNA and histones tightly coiled together?

Answer 15

DNA is neg charged whereas histones are positively charged.

Question 16

Function of acetylation:

Answer 16

A step in chromatin remodelling that disaggregates the tightly coiled nucleosomes/DNA.

When there’s acetylation (hyperacetylation), histones loosen up and chromatin is ACTIVATED.

When there’s de-acetylation (hypoacetylation), histones aggregates and chromatin is INACTIVATED.

Question 17

Enzymes involved in acetylation/deactylation:

Answer 17

Acetylation: histone acetyltransferase

De-acetylation: histone de-acetylase

Question 18

Function of DNA methylation:

Answer 18

• control of gene expression
• programs of gene expression (differentiation and development)
• preservation of chromosomal integrity
• X-chromosome inactivation
• alteration in genomic patterns

Question 19

Difference between acetylation and methylation in terms of activation of genes?

Answer 19

Acetylation ACTIVATES the genes (chromatin deaggregates)

Whereas

Methylation DEACTIVATES the genes (chromatin aggregates)

Question 20

Briefly define the characteristics of DNA methylation:

Answer 20

• occurs at 5’ position of CYTOSINE
• regulated by methyltransferase
• imprinted/inherited during DNA replication
• DOES NOT CHANGE base sequence of DNA (‘EPIGENETIC’)

Question 21

Mechanism of DNA methylation in histone aggregation:

Answer 21

• methyl cytosine binding protein binds to methylated cytosine
• histone de-acetylase binds to MCPs
• de-acetylation of histones occurs
• histones aggregate

Question 22

Genomic imprinting characteristics:

Answer 22

• as in the inheritance of methylated sequence
• happens in random
• methylated maternal allele can be inherited (vice versa)
• the methylated allele is silenced (could be either mat or pat)
• the difference of inheritance of methylated mat/pat alleles can cause two totally different diseases
• however some inheritance of methylated alleles is fixed

Question 23

Detrimental effects of hypomethylation:

Answer 23

• hypomethylation causes overactivity of genes

- can cause activation and expression of unnecessary gene sequence (parasitic seq)

Question 24

Detrimental effects of hypermethylation:

Answer 24

• hypermethylation causes inactivity of genes

- cause inactivation of genes necessary for DNA repairing and cell cycle control

Question 25

Relation between importance of imprinting and failure of cloning:

Answer 25

The fact that donor nucleus does not go through the germ line state results in NO IMPRINTING, hence why cloning is inefficient

Question 26

2 kinds of selective expression (mechanism of monoallelic expression of biallelic genes):

Answer 26

1. Allelic exclusion according to parent of origin (imprinting) - for some genes, the repressed allele is always paternally inherited allele (vice versa)
2. Allelic exclusion independent of parent of origin - choice of either expressing the maternally/paternally inherited allele is at random

Question 27

X chromosome inactivation:

Answer 27

• one of the X chrom in EACH CELL of the female is inactivated early in development
• by using methylation of DNA
• HOWEVER, there is a gene in the (supposedly) inactivated X chrom (Xist) that will still be transcribed into a NON-TRANSLATING mRNA
• this mRNA will bind to the (going to be) inactivated X chrom itself and hence triggers inactivation