[W6-7] Eukaryotic gene expression regulation

Question 1

How does eukaryotic gene regulation differ from prokaryotic regulation?

Answer 1

Eukaryotic regulation occurs at multiple levels (chromatin, transcription, RNA processing, translation); transcription and translation are separated in space and time.

Question 2

What are the key components required for transcription initiation in eukaryotes?

Answer 2

• RNA polymerase
• Core promoter
• General transcription factors
• Regulatory transcription factors (activators/repressors)

Question 3

What are DNase I hypersensitive sites?

Answer 3

Open chromatin regions accessible to DNase I, typically found upstream of active genes.

Question 4

What is the effect of histone acetylation?

Answer 4

Neutralizes positive lysines, loosens chromatin structure, increases transcription factor access.

Question 5

What enzymes acetylate and deacetylate histones?

Answer 5

• HATs (histone acetyltransferases) add acetyl groups
• HDACs (histone deacetylases) remove them.

Question 6

What is the role of FLD in Arabidopsis flowering?

Answer 6

FLD encodes a histone deacetylase that represses the flowering repressor gene FLC.

Question 7

What is the difference between core and regulatory promoters?

Answer 7

• Core promoter: binds general TFs and RNA pol for basal transcription.
• Regulatory promoter: binds activators/repressors that modulate transcription levels.

Question 8

What are general transcription factors?

Answer 8

Proteins required for transcription of all genes; they form the basal transcription apparatus.

Question 9

What are specific transcription factors?

Answer 9

Factors that regulate individual genes or gene sets, often binding enhancers/silencers.

Question 10

What are trans-acting factors?

Answer 10

Proteins (activators, repressors) that bind cis-acting DNA sequences to control transcription.

Question 11

What are coactivators?

Answer 11

Proteins that do not bind DNA but mediate interaction between activators and the basal machinery (e.g., Mediator complex).

Question 12

What are architectural proteins?

Answer 12

Proteins (e.g. YY1) that bend DNA to bring distant regulatory elements into contact.

Question 13

How do repressors act?

Answer 13

By blocking activators, preventing RNA pol recruitment, or promoting chromatin compaction.

Question 14

What two domains do transcriptional activators have?

Answer 14

• DNA-binding domain
• Activation domain (interacts with transcription machinery)

Question 15

Can activators work without an activation domain?

Answer 15

Yes, by recruiting coactivators with activation domains.

Question 16

What is the Mediator complex?

Answer 16

A large coactivator complex that conveys signals from DNA-bound TFs to RNA pol II.

Question 17

Name six common DNA-binding motifs in eukaryotic TFs.

Answer 17

• Zinc finger
• Helix-turn-helix
• Homeodomain
• Helix-loop-helix (HLH)
• Leucine zipper (bZIP)
• Basic helix-loop-helix (bHLH)

Question 18

What is an enhancer?

Answer 18

A DNA sequence that increases transcription from a distance by binding activators.

Question 19

What is an insulator?

Answer 19

A DNA element that blocks the influence of enhancers on promoters.

Question 20

What is dosage compensation?

Answer 20

Mechanism that equalizes gene expression from X chromosomes in males and females.

Question 21

What is X-inactivation?

Answer 21

In females, one X chromosome is randomly inactivated during embryogenesis.

Question 22

What is the Xic?

Answer 22

X-inactivation center; a cis-acting region that includes Xist, which coats the inactive X.

Question 23

How does Xist RNA induce inactivation?

Answer 23

Xist RNA coats the future inactive X chromosome and recruits Polycomb complexes to modify histones.

Question 24

What regulates mRNA stability?

Answer 24

• 5′ cap presence
• Poly(A) tail length
• Sequences in UTRs
• RNA-binding proteins
• miRNAs

Question 25

What are P bodies?

Answer 25

Cytoplasmic sites for mRNA storage and degradation.

Question 26

How does shortening of the poly(A) tail affect mRNA?

Answer 26

Prevents binding of PABP and leads to removal of 5′ cap → degradation.

Question 27

What is RNAi?

Answer 27

A regulatory mechanism involving miRNAs and siRNAs that silence gene expression post-transcriptionally.

Question 28

What does Dicer do?

Answer 28

Processes double-stranded RNA into ~21–25 nt siRNAs or miRNAs.

Question 29

What is RISC?

Answer 29

RNA-induced silencing complex that uses small RNAs to target mRNAs for silencing or degradation.

Question 30

What is the role of Argonaute in RISC?

Answer 30

Binds small RNAs and cleaves or represses target mRNAs.

Question 31

What are four mechanisms of RNAi gene silencing?

Answer 31

* mRNA cleavage (siRNA) * Translation inhibition (miRNA) * Transcriptional silencing (via chromatin) * Slicer-independent degradation (e.g. AU-rich elements)

Question 32

Where do miRNAs/siRNAs bind on mRNA?

Answer 32

Typically the 3′ UTR.

Question 33

What affects translation rate?

Answer 33

* Availability of ribosomes, tRNAs, initiation factors * Phosphorylation of initiation factors * RNA-binding proteins in 5′ UTR

Question 34

How do miRNAs inhibit translation?

Answer 34

By blocking initiation or causing ribosome stalling.

Question 35

List key differences between bacterial and eukaryotic gene control.

Answer 35

* Eukaryotes regulate at many levels; bacteria mostly at transcription. * Eukaryotes use chromatin structure; bacteria don’t. * Operons are rare in eukaryotes. * Enhancers common in eukaryotes, rare in bacteria. * Eukaryotic transcription and translation are separated.