Lecture 3 - Regulation Of Chromatin Structure

Question 1

What are centromeres characterised by?

Answer 1

Specific histone H3 variant (CenpA or CenH3)?

Question 2

What do centromeres in higher eukaryotic chromosomes contain in large amounts?

Answer 2

Repetitive DNA and unique histone variants

Question 3

What type of structure does a centromere have?

Answer 3

Heterochromatin

Question 4

What is the structure of heterochromatin like?

Answer 4

The structure is inaccessible and repressive No Replication No Transcription No DNA repair

Question 5

What is the structure of Euchromatin like?

Answer 5

The structure is accessible and extended Replication Transcription DNA repair

Question 6

What is chromatin remodelling?

Answer 6

The energy-dependent displacement of reorganisation of nucleosomes that occurs in conjugation with activation of genes for transcription There are numerous ATP-dependent chromatin remodelling dimpled that use energy provided by hydrolysis of ATP

Question 7

What can remodelling complexes do?

Answer 7

Alter, slide or displace nucleosomes

Question 8

What are histone post translational modification?

Answer 8

Covalent in nature Lysine methylation Lysine acetylation Lysine ubiquitilation Lysine sumolyation
Arginine methylation Glutamate ADP ribosylation Threonine phosphorylation.
Serine phosphorylation Tyrosine phosphorylation Arginine deimination (citrullination)

Question 9

What is side chain modification?

Answer 9

Histone tails are highly conserved and are modified on specific amino acids Modification of amino acid side chains can alter structure/function

Question 10

What is direct effect of side chain modification?

Answer 10

Change in charge

Question 11

What is the indirect effect of side chain modification?

Answer 11

Change in charge

Question 12

Histone modification

Answer 12

Histone modifications are mutually exclusive e.g. lysine cannot be methylated if already acetylated and vice versa Marks are reversible

Question 13

What does chromatin modification function depends on?

Answer 13

Specific modification ‘reader’

Question 14

Methylation

Answer 14

KMTs

Question 15

Demethylation

Answer 15

KDMs

Question 16

Acetylation

Answer 16

HDACs

Question 17

De acetylation

Answer 17

HATs

Question 18

Phosphorylation

Answer 18

Kinase

Question 19

Dephosphorylation

Answer 19

Phosphatases

Question 20

What is HAT?

Answer 20

Histone acetyltransferase

Question 21

What is Lysine acetylation/deacetylation of histone tails?

Answer 21

Acetylation of Lysine residues in histone tails Loss of positive charge Reduction in binding to DNA Opening up of chromatin Access to DNA

Question 22

HDAC

Answer 22

Histone deacetylase

Question 23

What is TAFII250 bromodomain?

Answer 23

Acetylates Transcriptional activation

Question 24

Histone modifying complexes have several components

Answer 24

Histone modification enzymes have little, if any, specificity other than for Lysine, they have the ability to acetylation/deaceytlate ANY Lysine on ANY histone or nucleosome

Question 25

What is histone acetylation associated with?

Answer 25

Transcription activation

Question 26

What is Lysine (K) acetyltransferase (KAT) ?

Answer 26

An enzyme present in large complexes that acetylates Lysine residues in histones AKA histone acetyltransferase

Question 27

What is transcription activators associated with?

Answer 27

Histone acetylase activities in large complexes

Question 28

What is histone deacetylase (HDAC)?

Answer 28

Enzyme that removes acetyl groups from histones May be associated with repressors of transcription

Question 29

Where are deacetylase present ?

Answer 29

Complexes with repressor activity

Question 30

Where do distinct enzyme activities exist ?

Answer 30

Both methylation for and demethylating Lysines (mono, di, tri)

Question 31

What is context dependent?

Answer 31

Different methylated Lysine’s can recruit activators or repressors

Question 32

What is methylation catalysed by?

Answer 32

Histone methyltransferase (KMTs)

Question 33

What is demethylation catalysed by?

Answer 33

Histone demethyltransferase (KDMs)

Question 34

What is HP1 chromodomain?

Answer 34

Methylates Heterochromatin assembly Transcriptional silencing

Question 35

How can processes such as transcription be regulated?

Answer 35

By switching modifications

Question 36

What is DNA methylation?

Answer 36

Covalent addition of a methyl group onto 5th position of cytosine within self complementary CpG dinucleotides Catalysed by DNA methyltransferase

Question 37

What does DNA methyltransferase do ?

Answer 37

Flip bases out of the double helix

Question 38

What are examples of highly methylated sequences?

Answer 38

Satellite DNA Repetitive element (transposons and relic) Non-repetitive intergenic DNA and exons of genes

Question 39

What is the percentage of CpG in human somatic cells that are methylated (global methylation)?

Answer 39

70-80%

Question 40

Approximately how many CpG islands in human genome?

Answer 40

45,000

Question 41

Where are CpG islands present?

Answer 41

Nearly all constitutively active house keeping genes

Question 42

What are CpG islands in normal tissue?

Answer 42

Unmethylated

Question 43

What does DNA methylation do?

Answer 43

Compact chromatin and is associated with Transcriptional repression

Question 44

What are the 3 types of modification that affect chromatin?

Answer 44

1. Acetyltransferase/deacetylase 2. Histone methyltransferase/demethylase 3. DNA demethylase/ DNA methyltransferase

Question 45

Acetyltransferase/deacetylase

Answer 45

Remodelling complexes can facilitate binding of acetyltransferase complexes

Question 46

Histone methyltransferase/demethylase

Answer 46

Histone methylation can also recruit chromatin-modifying complexes

Question 47

What do different modifications and complexes facilitate?

Answer 47

Transcription, initiation and elongation

Question 48

DNA demethylase/ DNA methyltransferase

Answer 48

DNA methylation and histone modification act in concert to regulate transcription in the chromatin environment

Question 49

What are modification?

Answer 49

Reversible and therefore dynamic

Question 50

Inactive to active state

Answer 50

Histone acetyltransferase Histone demethylase DNA demethylase

Question 51

Active to inactive state

Answer 51

Histone deacetylase Histone methyltransferase DNA methyltransferase