Quiz 2 : Transcriptional control Flashcards
Describe chromatin structure
- refers to how tightly the nucleosomes are packed
- determines whether DNA is assessable to transcription factors
Condensed chromatin structure
- inaccessible to TFs; transcription is blocked
- heterochromatin
relaxed chromatin structure
- open conformation, transcription possible
- euchromatin
Open Promoters
- nucleosome depleted region (NDR) (no nucleosomes are present, promotor open)
- constitutive transcription
Constitutive transcription
- constant transcription, constitutive genes transcribed continually
inducible transcription
- transcribed when needed, related to regulated genes which are only transcribed under certain conditions
Housekeeping genes
- gene that is required to maintain basic cellular function, typically expressed in all types of organisms
Covered promoters
- regulated transcription
- inducible: off or can be uncovered to be on
- tata box is covered by a histone and the polymerase cannot get to it
describe transcriptional activation of covered promoters
transcription factors cause the nucleosome to slide and open a binding region
- once the nucleosomes are displaces, activator can bind
WHat is the purpose of DNase I sensitivity assays?
- detect open/closed chromatin regions
Closed chromatin: DNase I is insensitive and transcriptionally silent
Open chromatin: DNase hypersensitivity detected following nucleosome displacement
results of a DNase I assay in closed chromatin?
DNase I is insensitive and transcriptionally silent
Results of a DNase I assay in open chromatin
- nucleosomes are displaced, activator binds
- RNA pol II and transcription factors bind promotor
- DNase I hypersensitivity detected following nucleosome displacement
What is chromatin structure determined by?
- chromatin remodeling and modifications
- may up or down-regulate the expression of a gene
Epigenetic regulation
- inheritable chromatin modifications
Chromatin remodelers and chromatin modifiers are…
- recruited to specific sites in chromatin by trans-acting factors that bind to specific DNA sequences
- mediate the reversible transition from inactive, heterochromatic DNA to active, euchromatic DNA
chromatin REMODELERS…
- change the POSITIONING of histones by sliding nucleosomes along the DNA to expose sequences of transcription
- changes the COMPOSITION of histones
Chromatin MODIFIERS…
- CHEMICALLY ALTER HISTONE PROTEINS in the nucleosomes by adding or removing chemical groups
- ENZYMES INVOLVED IN DNA METHYLATION may also be considered chromatin modifiers
Chromatin remodelling is done by
- position and distribution of nucleosomes
- 1) nucleosome sliding (displacement)
- 2) repositioning
- 3) eviction (ejection)
- 4) changing composition (histone variants)
Histone variants
- non-allelic (different gene altogether) variants of histones
- expressed at low levels
- specific expression, localization and species-distribution patterns
- affect chromatin remodeling and modifications
How does SWI/SNF play a role in chromatin remodelling
- SWI/SNF is responsible for nucleosome EJECTION in order to uncover the specific binding site for TFs
Chromatin modifiers can:
- CHEMICALLY ALTER proteins and histone proteins
modifications: - acetylation, methylation, phosphorylation, ubiquitination
- occurs at N-terminal
- relax or condense DNA
Describe histone acetylation
- addition of acetyl group
- promotes loose chromatin structure
- permits transcription
Describe histone methylation
- addition of a methyl group… outcome varies with amino acid position
- euchromatin: open… involves methylation, demethylation and acetylation
- Heterochromatin: closed… involves deacetylation, demethylation and methylation
H3K4
- euchromatin
- Histone 3, lysine 4
H3K27
- heterochromatin
- histone 3, lysine 27
Most frequently targeted residue for acetylation
- lysine (K)
most frequently targeted for methylation
- lysine
- arginine (R)
Phosphorylation
- promote activation or repression depending on location
- Targets: Serine (S), Threonine (T)
Ubiquitination
- may promote activation or repression depending on location
- target: Lysine (K)
Histone modifying enzymes
- reader
- writer
- eraser
Chromatin readers:
Effector of modification
- (uses it)
Chromatin writers:
- adds modifications
Eraser:
- removes modifications
Acetylation writers and erasers
- histone acetyltransferase (HAT) : writer (gene on)
- histone deactylase (HDAC) : eraser (gene off)
Methylation writers and erasers
- histone methyltransferase (HMT): open (gene on)
- histone demethylase (HDMT) : closed (gene off)
DNA methylation can regulate the ability of TFs to bind by
- adding methyl groups to cytosines located in CpG dinucleotides
- CpG are clustered at the promoters in mammals
- when CpG unmethylated: chromatin open… transcription
- CpG methylated: chromatin closed… no transcription
Deactivating transcription:
1 ) DNA in promotor region methylated by HMT
2 ) Methyl-CpG-binding protein (MECP2) binds to methylated DNA
3) MECP2 recruits HDAC
4) acetyl groups removed, histones condense, chromatin closes
main approaches to study DNA methylation:
- sodium bisulfite modification
- sequence-specific enzyme digestion
- capture/quantification of methylated DNA
