Regulation of Transcription in Eukaryotes

What affects the availability of DNA (mostly promoters) to transcription machinery?

chromatin structure

What is required to improve contact between RNA pol and the promoter to achieve high rate of transcription and allow gene regulation?

activation factors

What initiates transcription at low frequency?

Basel transcription complex

What are the five types of proteins RNA polymerase II requires?

1. Activator proteins

2. Architectural regulators of looping

3. Coactivators

4. Chromatin modification/remodeling proteins

5. Basal transcription factors

Are enhancers cis-acting or trans-acting?

cis-acting

Are promoters cis-acting or trans-acting?

cis-acting

What needs to form for contact of promoter and enhancer?

DNA loops

What does Pol II and activators bind to?

Pol II: binds to promoter

Activators: enhancer

Transcription activators can bind thousands of nucleotides away from the ______ of the promoter

TATA box

What is the function of activators besides binding to the enhancer?

recruit histone modification/ nucleosome remodeling complexes and coactivator such as Mediator

What is the function of the mediator?

Multi-subunit co-activator complex that facilitate the binding and/or function of Pol II at the core promoter

How does mediator interaction affect transcription?

they help recruit and stabilize RNA polymerase II near specific genes that are then transcribed

Mediator complex binds to what part of RNA pol II?

carboxyl-terminal domain (CTD)

Why are most genes inactive?

most promoters are inaccessible

Does transcription depend on RNA pol affinity or activator proteins?

activator proteins

What are three features of transcriptionally active chromatin?

1. nucleosome repositions (or evicted)

2. histone variants

3. covalent modifications to nucleosomes

What is the protypical chromatin remodeling complex called?

SWI/SNF complex

(SWItch/Sucrose non-fermentable)

Describe the function of the SWI/SNF complex

ATP dependent, multi-subunit complex that can open chromatin structure by repositioning or ejecting nucleosomes

Do chromatin remodeling complexes directly interact with DNA?

coactivator of transcription but does not directly interact with DNA or machinery

What do histone modifiers do?

add or remove chemical groups to histones

Lysine (K) and arginine (R) are _________-charged R groups

positively

What is the effect of adding an acetyl group to the positively charged histone tails?

neutralizes charge and makes DNA less tightly coiled

What are histone codes?

combinations of modifications to histone tails that activate or silence genes

Compare HMTs to HDMTs

HMT: histone methyltransferases that add methyl groups

HDMT: histone demethylases that remove methyl groups

Does methylation always activate or repress transcription?

No, it depends

Compare HATs to HDACs

HAT: histone acetylation transferases that add acetyl groups

HDAC: histone deacetylases that remove acetyl groups

Describe estrogen

sex hormones essential for mammalian reproduction

What are glucocorticoids?

a type of steroid hormone that plays a role in metabolism, stress response, and inflammation

What is a nuclear receptor superfamily?

proteins that bind specific small lipophilic signaling molecules

What are monomeric type 1 nuclear receptors?

receptors for sex hormones and glucocorticoids

What do hormone-receptor complexes bind to after travelling to nucleus?

hormone response element (HRE)

What are examples of type II nuclear receptors?

thyroid hormone receptor and estrogen receptor

How does the thyroid hormone receptor turn a target gene on or off?

always bound to HRE and corepressor to turn gene off

turns gene on when thyroid hormone binds to heterodimer and corepressor dissociates

What does estrogen bind to?

estrogen response elements (EREs)

What happens after estrogen binds to estrogen hormone receptor?

conformational change leads to recruitment of coactivator

What happens after coactivator is recruited?

Histone acetyltransferase (HAT) acetylates lysine of histone tails to decrease binding of histones and DNA

What are the four key mechanisms that regulate translation initiation?

1. phosphorylation of initiation factors

2. translational repressors

3. disruption of eIF4E and eIF4G interactions by eIF4E binding proteins

4. ncRNA-mediated regulation (gene silencing)

What is Rett syndrome?

mutations in MECP2 gene, a chromatin modifier "reader" protein recognizes and binds 5-methylcytosine in 5-meCG dinucleotides.

What is AID?

activation-induced cytidine deaminase

What is the effect of too much AID?

ssDNA nicks and DSB

Describe the cMyc oncogene

-activates transcription of genes controlling cell proliferation

-overexpressed in majority of human cancers

-contributes to the cause of at least 40% of tumors