Ch 17: Eukaryotic Gene Regulation

• more genes and not organized in operons

• diploid content (two alleles)

• DNA found in chromatin

• spatial separation of transcription and translation

• cellular differentiation in eukarytoes

Why is gene regulation in eukaryotes more complex?

GTFs bind to promoter while TFs bind to enhancer sites

GTFs vs TFs

formation of pre-initiation complex

rate limiting step

packing of genes in chromatin, nucleosome placement can inhibit transcription

availability of genes influenced by…

TF_IID binds to TATA via TBD —> recruits other GTFs —> recruit and bind RNA pol II —> interacts with other TFs to increase association with promoter DNA

PIC formation

GTFs

position RNA pol II at transcription start site

activators

proteins that bind to genes at enhancers, determining which genes will be turned on via promotion of PIC or modification of chromatin

Repressors

proteins that bind to silencer genes, interfere with function of activation by slowing/stopping transcription and interfering with chromatin

Mediator

mediates interaction between activator and repressors and RNA Pol II

non-phosphorylated CTD of RNA Pol II

how does mediator interact with RNA Pol II

activators binding to enhancers

enhanceosome

TAF role

help GTFs bind and stabilize PIC + RNA Pol II

enhancers

cis-acting DNA elements that promote transcription

silencers

cis-acting elements that repress the level of transcription

• promote PIC assembly

• organize chromatin

What do TF factors do

metaphase

when does chromatin condensation occur?

solenoid

nucleosome fibers coil into a compact, helical fiber

Epigenetics

heritable information that is not encoded in DNA sequences

through mitosis between cells

through meiosis between generations

how are epigenetic marks inherited?

chromatin remodeling

step of gene regulation involving changes either to the nucleosome or DNA

• ATP hydrolysis to relocate nucleosomes

• modification of histone proteins

• methylation of DNA at CpG dinucleotide

Chromatin remodeling types

histone acetylation of nucleosome catalyzed by histone acetyltransferase enzymes (HAT)

Increased transcription

histone deacetylation (HDAC) and DNA methylation

Decreased transcription

differential chromosomal regions to be accessible by transcription proteins

What does repositioning of nucleosomes allow for?

ATP

how are nucleosomes repositioned

• altering contacts between DNA and histones

• alternating path of DNA around nucleosome

• altering structure of nucleosome core

Nucleosome remodeling alters nucleosome structure how?

Cytosine on carbon-5 of base, CpG

Where does DNA methylation occur

• remodel chromatin

• interact with GTFs to help them assemble at promoters

• interact with RNA Pol II through mediator to form PIC

what do activators do?

remodel chromatin —> increase DNA methylation to inhibit PIC formation

What do repressors do?

SWI/SNF

opens up chromatin for gene activation by disassembling nucleosomes and creating accessible regions (ATP-dependent)

ISWI

creates regular, tightly spaced nucleosome arrays, often leading to gene silencing or stability (ATP-dependent)

• methylation

• proteins that bind methylated DNA

• histone deacetylase

Euchromatin —> heterochromatin

Mig1

galactose silencer TF

UAS_G

enhancer for galactose that binds Gal4

• Gal80 doesn’t inhibit Gal4

• Gal4 interacts w/ GTFs, chromatin remodeling machinery and RNAP II to activate transcription

ON

Galactose induction (only galactose present)

Gal80 inhibits Gal4

OFF

No glucose or galactose present

TF Mig1 binds to silencing elements and interacts with Tup1/Ssn6 to make heterchromatin

Glucose present (catabolite repression)

• activation domain

• DNA binding domain

TF domains

• GTF (TF_IID and TF_IIB)

• RNA Pol II mediator

• SAGA (histone acetyltransferase)

what transcriptional machinery does Gal4 interact with?

1. Gal4 recruits SAGA complex to genes promoter

2. Gal4 and SAGA recruit TF_IID/TBP, TF_IIB, and mediator complex

3. stable PIC formation and RNA Pol II recruitment —> transcription occurs

PIC formation by Gal4