Quiz 2 : Transcriptional control

Question 1

Describe chromatin structure

Answer 1

• refers to how tightly the nucleosomes are packed
• determines whether DNA is assessable to transcription factors

Question 2

Condensed chromatin structure

Answer 2

• inaccessible to TFs; transcription is blocked
• heterochromatin

Question 3

relaxed chromatin structure

Answer 3

• open conformation, transcription possible
• euchromatin

Question 4

Open Promoters

Answer 4

• nucleosome depleted region (NDR) (no nucleosomes are present, promotor open)
• constitutive transcription

Question 5

Constitutive transcription

Answer 5

• constant transcription, constitutive genes transcribed continually

Question 6

inducible transcription

Answer 6

• transcribed when needed, related to regulated genes which are only transcribed under certain conditions

Question 7

Housekeeping genes

Answer 7

• gene that is required to maintain basic cellular function, typically expressed in all types of organisms

Question 8

Covered promoters

Answer 8

• 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

Question 9

describe transcriptional activation of covered promoters

Answer 9

transcription factors cause the nucleosome to slide and open a binding region
- once the nucleosomes are displaces, activator can bind

Question 10

WHat is the purpose of DNase I sensitivity assays?

Answer 10

• detect open/closed chromatin regions
  Closed chromatin: DNase I is insensitive and transcriptionally silent
  Open chromatin: DNase hypersensitivity detected following nucleosome displacement

Question 11

results of a DNase I assay in closed chromatin?

Answer 11

DNase I is insensitive and transcriptionally silent

Question 12

Results of a DNase I assay in open chromatin

Answer 12

• nucleosomes are displaced, activator binds
• RNA pol II and transcription factors bind promotor
• DNase I hypersensitivity detected following nucleosome displacement

Question 13

What is chromatin structure determined by?

Answer 13

• chromatin remodeling and modifications
• may up or down-regulate the expression of a gene

Question 14

Epigenetic regulation

Answer 14

• inheritable chromatin modifications

Question 15

Chromatin remodelers and chromatin modifiers are…

Answer 15

• 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

Question 16

chromatin REMODELERS…

Answer 16

• change the POSITIONING of histones by sliding nucleosomes along the DNA to expose sequences of transcription
• changes the COMPOSITION of histones

Question 17

Chromatin MODIFIERS…

Answer 17

• CHEMICALLY ALTER HISTONE PROTEINS in the nucleosomes by adding or removing chemical groups
• ENZYMES INVOLVED IN DNA METHYLATION may also be considered chromatin modifiers

Question 18

Chromatin remodelling is done by

Answer 18

• position and distribution of nucleosomes
• 1) nucleosome sliding (displacement)
• 2) repositioning
• 3) eviction (ejection)
• 4) changing composition (histone variants)

Question 19

Histone variants

Answer 19

• non-allelic (different gene altogether) variants of histones
• expressed at low levels
• specific expression, localization and species-distribution patterns
• affect chromatin remodeling and modifications

Question 20

How does SWI/SNF play a role in chromatin remodelling

Answer 20

• SWI/SNF is responsible for nucleosome EJECTION in order to uncover the specific binding site for TFs

Question 21

Chromatin modifiers can:

Answer 21

• CHEMICALLY ALTER proteins and histone proteins
  modifications:
• acetylation, methylation, phosphorylation, ubiquitination
• occurs at N-terminal
• relax or condense DNA

Question 22

Describe histone acetylation

Answer 22

• addition of acetyl group
• promotes loose chromatin structure
• permits transcription

Question 23

Describe histone methylation

Answer 23

• 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

Question 24

H3K4

Answer 24

• euchromatin
• Histone 3, lysine 4

Question 25

H3K27

Answer 25

• heterochromatin
• histone 3, lysine 27

Question 26

Most frequently targeted residue for acetylation

Answer 26

• lysine (K)

Question 27

most frequently targeted for methylation

Answer 27

• lysine
• arginine (R)

Question 28

Phosphorylation

Answer 28

• promote activation or repression depending on location
• Targets: Serine (S), Threonine (T)

Question 29

Ubiquitination

Answer 29

• may promote activation or repression depending on location
• target: Lysine (K)

Question 30

Histone modifying enzymes

Answer 30

• reader
• writer
• eraser

Question 31

Chromatin readers:

Answer 31

Effector of modification
- (uses it)

Question 32

Chromatin writers:

Answer 32

• adds modifications

Question 33

Eraser:

Answer 33

• removes modifications

Question 34

Acetylation writers and erasers

Answer 34

• histone acetyltransferase (HAT) : writer (gene on)
• histone deactylase (HDAC) : eraser (gene off)

Question 35

Methylation writers and erasers

Answer 35

• histone methyltransferase (HMT): open (gene on)
• histone demethylase (HDMT) : closed (gene off)

Question 36

DNA methylation can regulate the ability of TFs to bind by

Answer 36

• 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

Question 37

Deactivating transcription:

Answer 37

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

Question 38

main approaches to study DNA methylation:

Answer 38

• sodium bisulfite modification
• sequence-specific enzyme digestion
• capture/quantification of methylated DNA