Gene Expression II

Question 1

Chromatin

Answer 1

Can affect the ability of trx factors to bind to DNA

DNA winds around histones, which make nucleosomes, which make chromatin

Question 2

2 classes of chromatin remodeling factors

Answer 2

1. ) DNA-dependent ATPases (SWI/SNF) disrupt histone octamers and DNA
2. ) Factors that reversible modify histones through acetylation (HATs and HDACs)

Question 3

Where can histones be modified?

Answer 3

The N-termini of histones are rich in lysine residues, which can be reversibly modified by acetylation, phosphorylation, methylation, and ubiquination

Acetylation: associated with gene control

Question 4

Activators and repressors can recruit

Answer 4

histone acetyltransferases (HATs) or deacetylases (HDACs)

Question 5

HATs

Answer 5

Acetylate N-termini of histones.
Acetylating the N-termini of histones neutralizes the positively charged ends and eliminates electrostatic interactions with DNA phosphates…
SO nucleosomal DNA is OPENED up for general trx factors/ the Pol II transcriptional apparatus

NOW we know: acetylating lysines allows for binding of specific trx factors, and the pattern of histone acetylation serves as a “code” to recruit different factors that affect the transcriptional state.

co-activators (generally)

Question 6

HDAC

Answer 6

In presence of HDACs, histones keep their positive charge at the N-terminal ends (HDACs remove acetyl groups).

co-repressors (generally)

Question 7

Trans-acting factors

Answer 7

Can switch from repressors to activators by recruiting either HATs or HDACs (ex: thyroid hormone receptor)

they are DNA sequences that encode trx factors. (vs. cis-acting which are non-coding)

Question 8

Rubinstein-Taybi Syndrome

Answer 8

A rare genetic multi-system disorder.
Craniofacial dysmorphism, broad thumbs and great toes, growth retardation etc.
Mutation in one copy of CREB binding protein (CBP) which is an essential trx coactivator for many different trx factors and is a HAT. Normally recruited to many genes to activate trx … so it causes lots of trx issues.

Question 9

Leukemia

Answer 9

Can result from fusions of trx regulators (HATs or HDACs), altering activity of regulators

Question 10

2 ways trx activators and repressors work

Answer 10

1. ) Interact with general trx. factors/ polymerase II associated proteins to influence initiation of elongation of the primary transcript
2. ) Interact with chromatin to regulate accessibility of DNA to Pol II trx. apparatus

Question 11

Basic principles of trx. regulation

Answer 11

1. ) Specificity depends on binding of trx activators/repressors to DNA control elements
2. ) Regulation depends on DNA-protein and protein-protein interactions
3. ) The interactions affect the conformation of DNA, the modification of chromatin structure, and the formation of the initiation complex
4. ) Control is combinatorial, so thousands of trx factors can combine differently to differently affect the expression of genes in diff cell types/ in response to diff stimuli