15: Transcription, activator

Question 1

What are the stages of transcription? (4)

Answer 1

• Pol II Recruitment
• Initiation and Early elongation
• Productive elongation
• Termination

Question 2

What are the regulatory regions of the structure of a protein-coding gene

Answer 2

• Core promoter
• Promoter/proximal promoter
• Cis-regulatory element (CRE)

Question 3

What is the role of the core promoter?

Answer 3

The DNA sequence at which the general transcription factors bind and recruit RNA Pol II. Close to the TSS

Question 4

What is the role of the promoter/proximal promoter

Answer 4

The entire regulatory region around the start site, including the core promoter

A region of upstream DNA that facilitates the transcription of a particular gene (1-2 kb)

Question 5

What is the role of the cis-regulatory element (CRE):

Answer 5

Short DNA sequences (sequence motifs) involved in regulation of transcription

cis means on the same molecule (as is being regulated)

Question 6

What are chromatins?

Answer 6

DNA + Proteins

• Chromatin is a form of “primary packaging”
• Chromatins are quite dynamic and modified continuously

Question 7

What are two examples of histone tail modifications?

Answer 7

• Acetylation (ac)

- Methylation (me)

Question 8

Describe acetylation of histone proteins

Answer 8

• Added by histone acetyltransferases (HATs), removed by histone deacetylases (HDACs). -WRITERS
• The lysine residues get acetylated
• Removes a positive charge
- Histones are positively charged, which is useful as DNA are negatively charged
- Lysine has a positive amino group
- When we acetylate this amino group, it loses the positive charge.
- There is still an electrostatic information, but it is weaker
Bound by proteins with a bromodomain -READERS

Question 9

Describe methylation of histone proteins

Answer 9

• Added by histone methyltransferase (HMTases), removed by histone demethylases -WRITERS
• Lysine and arginine residues
• One, two, or three groups added
Bound by proteins with a chromodomain -READERS

Question 10

Describe nucleosome (chromatin) remodelers)

Answer 10

slides (draw out)

• ATP dependent
• ATP is used to disrupt the electrostatic relationship between DNA and histones
• Slide or eject (fully or partially) nucleosome to expose regions of DNA
• Maintain packaging while making DNA accessible to transcriptional machinery and DNA binding proteins Work in conjunction with histone chaperones

Question 11

Describe Activator-dependent recruitment

Answer 11

slides -draw this out

will be very long

Question 12

What are activators

Answer 12

• Proteins that recognise and bidn CRE based on DNA sequence (target specific genes)
• Promote transcription
• Activators are transcription factors (not all transcription factors are activators)
• Also called trans-acting factors -trans means on a different molecule (as is being regulated)

Question 13

Activators consist of which two domains?

Answer 13

• Activation domain

- DNA binding domai

Question 14

What is the role of the activation domain?

Answer 14

-Protein-protein interactions
Other activators
Co-activators

• Can also act as repressors
• Not conserved

Question 15

What is the role of the DNA binding domain?

Answer 15

• Recognises a cis-regulatory element
• Hold the activator domain in the vicinity of the promoter
• Conserved
• Used to classify activators into families

Question 16

Describe co-activators

Answer 16

• Protein complexes
• The components of these complexes usually have diverse roles (2 below)

Protein-protein interactions involving recruiting:

• One co-activator interacts with a range of activators (many genes)
• General transcription factors/RNA Pol II

Chromatin modifications

• HAT activity (histone H3 and histone H4 acetylation)
• Other histone-tail modifications

Question 17

Describe chromatin remodeling of the core promoter

Answer 17

slides