L295 Regulation of Gene Expression

Question 1

How many % of the genome do exons make up?

Answer 1

~1-2%

Question 2

Hetero vs euchromatin (4)

Answer 2

• Heterochromatin: condensed dark bands (Giemsa), mostly inactive, A + T rich, late S-phase rep
• Euchromatin: light bands, more active, C + G rich, early S-phase rep

Question 3

Gene expression can be … (2 types)

Answer 3

1. Constitutive
   
   • ‘housekeeping’ genes: products made by all cells all the time
   • Expression is constant
2. Regulated
   
   • Time (developmental), place (cell type), amount, in response to signals
     
     • Can be under very tight, complex control

Question 4

Different classes of RNA genes

Answer 4

1. Coding RNA (mRNA) → translated into protein
2. Non-coding RNAs e.g. roles in RNA maturation and gene reg
3. rRNA and tRNA: involved in protein synthesis

Question 5

RNA splicing of protein-coding genes: how does it occur?

Answer 5

1. Spliceosome binds to intron at donor splice and acceptor splice sites
2. Cleavage of splice sites by spliceosome → splicing of gene

Question 6

What is the spliceosome?

Answer 6

= large ribonucleoprotein complex that splices primary transcripts to remove introns

Question 7

How might splicing contribute to protein diversity?

Answer 7

Alternative splicing: process by which different combos of introns/exons can be spliced together from one gene

Question 8

Points of regulation of gene expression: which were covered in the lecture (4)?

Answer 8

1. Conformation of chromatin (localised only)
2. Transcription
3. Post-transcriptional processing
4. Non-coding RNA regulation

Question 9

Chromatin =

Answer 9

= DNA and associated protein (histone and non-histone)

Question 10

Which conformation of chromatin is needed for gene expression?

Answer 10

Open conformation

Question 11

How is the conformation of chromatin regulated?

Answer 11

Epigenetic changes

Question 12

Examples of epigenetic changes regulating conformation of chromatin

Answer 12

1. Histone variants
   
   • e.g. acetylation, methylation, ubiquitination, phos…
2. DNA methylation
3. Nucleosome occupancy
4. Nuclear localisation of chromosome

Question 13

Describe ‘nucleosome occupancy’ and how it is regulated

Answer 13

• Distances between nucleosomes can vary to allow greater access
• Regulated by ATP-driven chromatin modifying complexes, that change position of nucleosomes along DNA

Question 14

‘Nuclear localisation of chromosome’: where are non-transcriptionally active chromosomes located?

Answer 14

Chromosomes that are not transcriptionally active are located peripherally in the nucleus

Question 15

DNA methylation generally means…

Answer 15

↓ gene expression

Question 16

Where at DNA does methylation occur?

Answer 16

at cytosine of CpG islands

Question 17

CpG islands - where are they often clustered and in what form? What does this mean?

Answer 17

• Often surround promoter regions, but are usually unmethylated there - even when genes aren’t expressed
• i.e. not all CpG motifs are methylated

Question 18

DNA methylation and DNA replication: what happens to the methylation pattern with new DNA strands?

Answer 18

• New DNA strands initially lack methyl groups, but original pattern is soon transmitted to daughter cells

Question 19

Examples of transcriptional regulation of gene expression

Answer 19

1. Multiple promoter sites
2. RNA polymerase and transcription factors
3. Interaction with other cis-acting DNA sequences, ncRNAs and trans-acting proteins

Question 20

What does interaction with other cis-acting DNA sequences entail?

Answer 20

• Looping DNA together brings regions on the same chromosome together, and allow interaction with other cis-acting DNA sequences (‘enhancers’ or ‘silencers’ of transcription)

Question 21

What does ‘cis-acting’ mean?

Answer 21

On the same chromosome as the gene to be transcribed

Question 22

Example of post-transcriptional regulation of gene expression

Answer 22

Alternative splicing of different exons can lead to different protein products

Question 23

What must we note about alternative splicing?

Answer 23

• alternative splicing does not necessarily just involve taking out an intervening intron between exons
• Parts of introns can be included, and parts of exons can even be excluded!

Question 24

Examples of non-coding RNAs regulating gene expression

Answer 24

1. Long non-coding RNAs (lncRNAs)
2. Short interfering RNAs (siRNA)
3. Micro RNAs (miRNA)

Question 25

4 possible ways long non-coding RNAs might act to regulate gene expression

Answer 25

1. Decoy - takes away enzymes that would usually act for transcription
2. Scaffold - can bring proteins together
3. Guide - guide molecules together
4. Enhance - make proteins bind better

Question 26

How do siRNAs act to regulate gene expression?

Answer 26

• siRNA is ds - each has sequence complementary to specific mRNA
  1. Form complex with RNA-induced silencing complex (RISC) and becomes ss
  2. Binds to complementary sequence on mRNA
  3. RISC cleaves mRNA before translation
     
     4. → mRNA degradation

Question 27

How do miRNAs act to regulate gene expression?

Answer 27

• miRNA only partially complementary to mRNA sequence

1. miRNA forms complex with RISC
2. Multiple proposed mechanisms of repression 
3. → repressed mRNA translation