BIO230 L4 eukaryotic gene regulation

just the names of things

TFIID

general transcription factor

recognizes TATA box and other DNA sequences (other consensus sequences) near the transcription start point for initiation

bends DNA to highlight it for RNA polymerase recognition

TFIIH 

general transcription factor

unwinds DNA at the transcription start point 

phosphorylates Ser5 of the RNA polymerase C-terminal domain (CTD)

• allowing the recruitment and release of various protein factors required for mRNA processing

releases RNA polymerase from the promoter to initiate transcription

RNA polymerase II

transcribes protein coding genes in eukaryotes

general transcription factors

help position RNA polymerase at promoters

TFIID, TFIIB, TFIIF, TFIIE, TFIIH for eukaryotes

sigma factor for prokaryotes

difference between eukaryotic genomes and prokaryotic genomes

eukaryotic genomes

• lack operons

• 1 gene, 1 RNA molecule, 1 protein

• packaged into chromatin (additional mode of regulation)

prokaryotic genomes

• operons 

• multiple genes encoded on 1 RNA molecule

mediator

acts as an intermediate between many regulatory proteins and RNA polymerase in eukaryotes

regulatory proteins for eukaryotic gene expression

both activators and repressors

can act over very large distances, sometimes >10,000 bp away by DNA looping

often function as protein complexes on DNA

includes co-activators and co-repressors that do not directly bind DNA

coactivators and corepressors

only bind to proteins that are already bound to DNA, do not directly bind to DNA

works in a complex and aids activators and repressors with regulating gene expression

DNA binding domain (DBD)

a module of eukaryotic activator protein that recognizes specific DNA sequence

very specific about binding

binds to activation domain (AD) to adjust frequency/rate of transcription

activation domain (AD)

a module of eukaryotic activator protein that accelerates frequency/rate of transcription

tends to be general about binding

binds to DNA binding domain (DBD) to recognize specific DNA sequence

how activator proteins activate transcription

attract, position, and/or modify

• general transcription factors, mediator, RNA polymerase II

by either

• directly interacting with them

• indirectly modifying chromatin structure

how activator proteins directly activate transcription

bind directly to transcriptional machinery or the mediator and attract them to promoters (like prokaryotic activators)

how activator proteins indirectly activate transcription

alter chromatin structure and increase promoter accessibility in 4 ways

nucleosomes

the basic structure of eukaryotic chromatin

DNA wound around a histone octamer with 2 sets of H2A, H2B, H3, H4 creates a compact chromatin fibre

can be unwound or altered to increase promoter accessibility

histone tails are modified over the course of a cell’s life to meet its particular gene expression needs

4 major ways activator proteins can alter chromatin

using chromatin remodeling complex:

1. nucleosome sliding

2. histone removal

3. histone replacement

histone-modifying enzyme:

4. specific pattern of histone modification

nucleosome sliding

nucleosome structure altered by ATP-dependent chromatin remodeling complexes to increase promoter accessibility

nucleosome removal

requires cooperation with histone chaperones

ATP-dependent chromatin-remodeling complex removes a histone core interfering with accessibility of target gene

ATP-dependent chromatin remodeling complex dissociates

transcription machinery assembles on nucleosome-free DNA

histone exchange/replacement

requires cooperation with histone chaperones

exchange:

• ATP-dependent chromatin-remodeling complex creates a variant of histone dimer(s)

replacement:

• ATP-dependent chromatin remodeling complex removes histone core, then histone chaperone exchanges for a new nucleosome core

histone variants allow greater access to nucleosomal DNA

chromatin remodeling complex

an ATP-dependent protein that modifies chromatin to regulate transcription

attracted to chromatin by transcription regulator

3 main functions:

• nucleosome sliding

• histone removal

• histone replacement

histone modifying enzymes

AKA “writers”

produce specific patterns of histone modifications on specific amino acids of histone tails

patterns of histone modifications can increase/decrease gene accessibility 

• can destabilize compact forms of chromatin

• can attract components of transcription machinery

types of modifications in histone code

addition of phosphate group (phosphorylation)

• performed by kinase enzyme

addition of acetyl group (acetylation)

• performed by acetyltransferase enzyme

addition of methyl group (methylation)

• performed by methyltransferase enzyme

histone code

specific modifications to histone tails by histone modifying enzymes nicknamed “writers”

code “reader” proteins can recognize specific modifications and provide meaning to the code

writer proteins

histone modifying enzymes that specifically modify histone tails for transcription regulation

part of the histone code

reader proteins

histone modifying enzymes that recognize specific modifications and provide meaning to the code

human interferon gene regulation as a histone code example

1. activator protein attracts histone acetyltransferase 

2. HA acetylates H3K9 and H4K8

3. activator protein attracts histone kinase

4. histone kinase phosphorylates H3S10 (can only occur after acetylation of H3K9)

5. serine phosphorylation signals the acetyltransferase to acetylate H3K14

6. TFIID and a chromatin remodeling complex bind to modified tails and initiate transcription

the code for transcription initiation is written

transcriptional repression

1. competitive DNA binding

2. masking the activation surface

3. direct interaction with the general transcription factors

4. recruitment of chromatin remodeling complexes

5. recruitment of histone deacetylases

6. recruitment of histone methyl transferase

repressor proteins: competitive DNA binding

a mechanism of transcriptional repression where activator and repressor compete to bind to DNA (occurs if binding sites overlap)

repressor proteins: masking the activation surface

a mechanism of transcriptional repression where the repressor prevents the activator’s activation surface from binding with transcription machinery

repressor proteins: direct interaction with the general transcription factors

a mechanism of transcriptional repression where the repressor interacts with the general transcription factors to prevent proper transcription

repressor proteins: recruitment of chromatin remodeling complexes

a mechanism of transcriptional repression where the repressor recruits the chromatin remodeling complex to restrict access to the promoter sequence

repressor proteins: recruitment of histone deacetylases

a mechanism of transcriptional repression where the repressor recruits histone deacetylases to interfere with histone code for transcriptional activation

repressor proteins: recruitment of histone methyl transferase

a mechanism of transcriptional repression where the repressor recruits histone methyl transferase to interfere with histone code for transcriptional activation

proteins can bind to these methylated histones that further compact chromatin

epigenetic inheritance

a process where gene expression patterns can be inherited by daughter cells, maintaining specialization across a lineage of cells

occurs by DNA methylase and DNA methyl-binding proteins that create inheritable structures

DNA methylase enzyme in epigenetic inheritance

attracted by reader and methylates nearby cytosines

the reader-writer chain reaction (one reader for every next histone) allows DNA methylase enzyme to methylate several linker DNAs in a row

methylation can be inherited in daughter cells

DNA methyl-binding proteins in epigenetic inheritance

bind methyl groups and stabilize structure, repressing genes that may not be necessary for certain specialized cells

because methylation is inheritable, these proteins will be attracted again to same genes in daughter cells

reader-writer complexes

writers are bound by transcription regulator and can recruit a reader protein

sets off a chain reaction where readers attract writers, and writers create a signal to attract readers

this complex spreads the histone code along chromatin and can stabilize it

DNA methylase and DNA methyl-binding proteins work together to further stabilize this structure, creating an inheritable gene expression pattern