Genetics Chapter 11: Gene Expression in Eukaryotes

Transcriptional level: General Transcription Factors (GTF)

-TFIID -TBP - lures the RNAP to the promoter

Octamer histome cores

2 (H2A) 2 (H2B) 2 (H3) 2 (H4)

histomes

HI (linker) H2 -H2A -H2B H3 H4

nucleosome arrangements in the vicinity of a protein encoding gene

a nucleosome free region (NFR) is found at the beginning and end of many genes. nucleosomes tend to be precisely positions near the beginning and end of a gene, but are less regularly distributed elsewhere

modulation of RTF functions

a) binding of small effector molecules such as hormone - hormone binds to allosteric site of transcription factor which binds to enhancer (response elements) b) protein protein interaction - 2 transcription factors bind to enhancer (dimerize) c) covalent modifications such as phosphorylation - phosphorylating transcription factors can enhance them

Activation via TFIID

activator/coactivator complex recruits TFIID to the core promoter and/or activates its function. Transcription will be enhanced. Job is to lure RNAP and then leave

Transcriptional level 2:

activators can recruit chromatin remodeling complexes plus histone modifying enzymes

Methylation (lysine and arginine)

add histone methyl transferases (HMT) remove histone demethylates results are variable lysine can only be methylated 3x arginine can be methylated 2x

phosphorylation- serine, tyrosine, threonine

add kinase transcription favorable Dna becomes less tightly bound to histones remove phosphatase transcription less favorable dna becomes more tightly bound to histones

Acetylation (lysine gets acetylated)

addition of acetyl group HAT (histone acetyl transferase) transcription favorable DNA becomes less tightly bound to histones "open system" removal of acetyl group HDAC (histone deactylase) transcription not favorable DNA becomes more tightly bound to histones "closed system"

chromatin remodeling and histomes

atp dependent chromatin remodeling refers to dynamic changes in chromatin structure these changes range from a few nucleosomes to large scale changes

chromatin remodeling complexes

atpase subunit called DNA translocase changes structure in one of two ways 1) change in the position or composition of nucleosomes 2) eviction of histome octamers

Transcriptional level: Repressors

can stop transcription, suppresses transcription - binds to regions called silencers

chromatin structure

closed confirmation - chromatin more compacted, tightly packed, not favorable for transcription open confirmation - chromatin not as tightly packed, chromatin easily accessible to transcription factors, favorable for transcription DNA PREFERS AN OPEN SYSTEM requires ATP by changing structure, chromatin becomes more/less favorable for transcription SW1/SNF

transcriptional level 3:

dna methylation - block activators from binding to enhancer sequences - help recruit chromatic compaction structures

Transcriptional level: Regulatory (specific) Transcription Factors (RTF)

enhances genes to stop or start transcription activators: enhance transcription binding to enhancer sequences - some enhancers are closer to the promoter: proximal - some enhancers are farther from the promoter: distal - upstream: left of TSS

CPG islands in tissue specific genes

expression of these genes may be silenced by methylation of CPG island methylation may influence the binding of transcription factors methyl-CPG- binding proteins may recruit factors that lead to the compaction of chromatin methylating DNA blocks activator from enhancer methylated CPG binding proteins recruits other proteins that change the chromatin to a closed confirmation

Introduction

if we have our DNA tightly wrapped around histomes, it might not be available for DNA to bind to the promoter - we can unwrap it making the promoter available to bind

DNA methylation

inhibits transcription by methylating certain sequences, we block the activators helps recruit chromatin remodeling complex dna methylation creates closed system, blocks enhancer sequence, doesn't allow progression

mediator (activator)

mediator interacts with the enhancer and phosphorylates the CTD activator interacts with mediator allowing mediator to phosphorylate CTD. - mediator has kinase activity - phosphorylation of CTD causes GTF to fall off, start elongation - RNAP is in place starting initiation, mediator gets past initiation into elongation - mediator causes GTF to fall off starting elongation

histone code

modification through acetylation, methylation, phosphorylation these modifications may affect the level of transcription - may influence interactions b/w nucleosomes - occur in patterns recognized by proteins called the histone code pattern modifications: provide binding sites for proteins that specify alterations too be made to chromatin structure these protein bind based on the code and affect transcription occur on histone tails

TFIID and Mediator

most RTFs do not bind directly to RNAP 3 ways to communicate signal: 1) regulation via TFIID (GTF works closely with TATA Box) directly or through coactivators. 2) regulation via mediator 3) regulation via changes in chromatin structures

combinational control

most eukaryotic genes are regulated by many factors. combinational factors are - one or more activators may stimulate transcription - one or more repressor proteins may inhibit transcription - activators and repressors may be modulated by --> binding of small effector molecules --> protein protein interactions (dimerize) --> covalent modifications (phosphate binding)

histone eviction

removes histones so that the can be open as binding sites for activators a few histone genes have accumulated that alters the amino acid sequence - called histone variants - some histone variants are incorporated into a subset of nucleosomes to create specialized chromatin

mediator (repression)

repressor protein binding to mediator prevents phosphorylation of CTD which hinders transcription and delays it.

chromatin remodeling complex 2

such as sw1/snf, recruited for doing everything such as chromatin remodeling and histone modification histone acetyl transferase recruited CREATES SPACE RNAP, GTF in place allowing elongation as we move forwards, we create more space to make DNA available for RNAP

CPG Islands

tend to be near promoters (where RNAP binds to start transcription ) in housekeeping genes, CPG islands are unmethylated genes tend to be expressed in most cell types in very specific genes, we methylate CPG islands inhibiting transcription

enhancers and silencers

the binding of a transcription factor to an enhancer increases the rate of transcription - called up regulation - can be 10-1000 fold - speeds up process, faster the binding of a transcription factor to a silencer decreases the rate of transcription - this is called down regulation - slows down Many elements are found upstream, some are found downstream

Repression via TFIID

the repressor protein inhibits the binding of TFIID to the core promoter or inhibits its function. transcription is silenced. stops from compiling, luring RNAP.

Structural Features of Regulatory Transcription Factors

transcription factor proteins contain regions called domains, that have specific functions - one domain could be for DNA binding -another could provide a binding site for effector molecules

Nucleosome-free region (NFR)

unwraps as we move forward because RNAP needs to be able to read a free template strand, once we're done we put everything back where it was