Quiz 2 : Transcriptional control Flashcards
(38 cards)
1
Q
Describe chromatin structure
A
- refers to how tightly the nucleosomes are packed
- determines whether DNA is assessable to transcription factors
2
Q
Condensed chromatin structure
A
- inaccessible to TFs; transcription is blocked
- heterochromatin
3
Q
relaxed chromatin structure
A
- open conformation, transcription possible
- euchromatin
4
Q
Open Promoters
A
- nucleosome depleted region (NDR) (no nucleosomes are present, promotor open)
- constitutive transcription
5
Q
Constitutive transcription
A
- constant transcription, constitutive genes transcribed continually
6
Q
inducible transcription
A
- transcribed when needed, related to regulated genes which are only transcribed under certain conditions
7
Q
Housekeeping genes
A
- gene that is required to maintain basic cellular function, typically expressed in all types of organisms
8
Q
Covered promoters
A
- 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
9
Q
describe transcriptional activation of covered promoters
A
transcription factors cause the nucleosome to slide and open a binding region
- once the nucleosomes are displaces, activator can bind
10
Q
WHat is the purpose of DNase I sensitivity assays?
A
- detect open/closed chromatin regions
Closed chromatin: DNase I is insensitive and transcriptionally silent
Open chromatin: DNase hypersensitivity detected following nucleosome displacement
11
Q
results of a DNase I assay in closed chromatin?
A
DNase I is insensitive and transcriptionally silent
12
Q
Results of a DNase I assay in open chromatin
A
- nucleosomes are displaced, activator binds
- RNA pol II and transcription factors bind promotor
- DNase I hypersensitivity detected following nucleosome displacement
13
Q
What is chromatin structure determined by?
A
- chromatin remodeling and modifications
- may up or down-regulate the expression of a gene
14
Q
Epigenetic regulation
A
- inheritable chromatin modifications
15
Q
Chromatin remodelers and chromatin modifiers are…
A
- 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
16
Q
chromatin REMODELERS…
A
- change the POSITIONING of histones by sliding nucleosomes along the DNA to expose sequences of transcription
- changes the COMPOSITION of histones
17
Q
Chromatin MODIFIERS…
A
- CHEMICALLY ALTER HISTONE PROTEINS in the nucleosomes by adding or removing chemical groups
- ENZYMES INVOLVED IN DNA METHYLATION may also be considered chromatin modifiers
18
Q
Chromatin remodelling is done by
A
- position and distribution of nucleosomes
- 1) nucleosome sliding (displacement)
- 2) repositioning
- 3) eviction (ejection)
- 4) changing composition (histone variants)
19
Q
Histone variants
A
- non-allelic (different gene altogether) variants of histones
- expressed at low levels
- specific expression, localization and species-distribution patterns
- affect chromatin remodeling and modifications
20
Q
How does SWI/SNF play a role in chromatin remodelling
A
- SWI/SNF is responsible for nucleosome EJECTION in order to uncover the specific binding site for TFs
21
Q
Chromatin modifiers can:
A
- CHEMICALLY ALTER proteins and histone proteins
modifications: - acetylation, methylation, phosphorylation, ubiquitination
- occurs at N-terminal
- relax or condense DNA
22
Q
Describe histone acetylation
A
- addition of acetyl group
- promotes loose chromatin structure
- permits transcription
23
Q
Describe histone methylation
A
- 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
24
Q
H3K4
A
- euchromatin
- Histone 3, lysine 4
25
H3K27
- heterochromatin
- histone 3, lysine 27
26
Most frequently targeted residue for acetylation
- lysine (K)
27
most frequently targeted for methylation
- lysine
- arginine (R)
28
Phosphorylation
- promote activation or repression depending on location
- Targets: Serine (S), Threonine (T)
29
Ubiquitination
- may promote activation or repression depending on location
- target: Lysine (K)
30
Histone modifying enzymes
- reader
- writer
- eraser
31
Chromatin readers:
Effector of modification
- (uses it)
32
Chromatin writers:
- adds modifications
33
Eraser:
- removes modifications
34
Acetylation writers and erasers
- histone acetyltransferase (HAT) : writer (gene on)
- histone deactylase (HDAC) : eraser (gene off)
35
Methylation writers and erasers
- histone methyltransferase (HMT): open (gene on)
- histone demethylase (HDMT) : closed (gene off)
36
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
37
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
38
main approaches to study DNA methylation:
- sodium bisulfite modification
- sequence-specific enzyme digestion
- capture/quantification of methylated DNA
