19.01.01 dna structure packaging histone modification and chromatin

Question 1

nucleoside

Answer 1

one of four nitrogenous bases ((adenine, guanine, cytosine or thymine) attached to the carbon 1’ of the 5 carbon sugar deoxyribose

Question 2

nucleotide

Answer 2

nucleoside + phosphate

Question 3

What type of bond joins nucleotides?

Answer 3

phosphodiester

Question 4

What makes RNA more unstable than DNA?

Answer 4

Additional hydroxyl group at the 2’ position which makes it more unstable

Question 5

What type of bond holds the two DNA strands in a duplex helix structure?

Answer 5

Hydrogen bonds

Question 6

How many hydrogen bonds between A and T?

Answer 6

2

Question 7

How many hydrogen bonds between C and G?

Answer 7

3

Question 8

Size of complete turn of DNA helix

Answer 8

3.6nm

Question 9

What is chromatin?

Answer 9

DNA/histone complexes

Question 10

What gives histones affinity to DNA?

Answer 10

Rich in positively charged arginine and lysine

Question 11

nucleosome

Answer 11

a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones (~8histones).

Question 12

solenoid

Answer 12

secondary 30nm chromatin fibre structure

Question 13

chromatosome

Answer 13

Nucleosome plus H1 histone

Question 14

How much is DNA condensed in chromatin fibre

Answer 14

50 fold

Question 15

How much is DNA condensed in chromatin fibre during metaphase

Answer 15

1/10,000 of stretched out length

Question 16

Interphase chromatin in a relatively extended conformation. Marked by weak binding of H1 histones and acetylation of the 4 nucleosomal histones. Contains transcriptionally active DNA.

Answer 16

Euchromatin

Question 17

Heterochromatin

Answer 17

highly condensed throughout cell cycle. Genes not expressed. Associated with tight H1 histone binding. Heterochromatin silencing shown to be linked to miRNAs

Question 18

2 classes of Heterochromatin

Answer 18

▪ Constitutive: condensed and generally inactive. Consists largely of repetitive DNA.
▪ Facultative: sometimes inactive (condensed) and sometimes active (decondensed), e.g. X-inactivation

Question 19

Where does methylation commonly take place

Answer 19

lysines and arginines

Question 20

What do histone methyltransferases (HMTs) do?

Answer 20

recruit S-adenosylmethionine as a co-substrate for transfer of the methyl group

Question 21

What effects does methylation have?

Answer 21

Affects basicity and hydrophobicity of histones and their affinity with certain proteins, such as transcription factors

Question 22

Ubiquitination

Answer 22

Ubiquitin (a 76 aa polypeptide) is attached to histone lysines

Question 23

Sumoylation

Answer 23

attachment of addition of SUMOs (small ubiquitin-like modifiers) to histone lysines. Functions by antagonizing acetylation and ubiquitination which may occur on the same lysine. Associated with repressive functions.

Question 24

Deamination

Answer 24

Converts arginine to a citrulline. Neutralises positive charge of arginine.

Question 25

ADP-ribosylation

Answer 25

ADP ribose can be added to lys/arg/glu/asp/cys/phosphoSer/Asn and mono ADP ribose can be further ribosylated to form a poly-ADP-ribose protein

Question 26

Proline isomerisation

Answer 26

Peptidyl-proline isomerases alter the orientation of proline

Question 27

H-DNA

Answer 27

Triple helix structure which can be caused by inverted repeats of polypurine/polypyrimidine DNA stretches

Question 28

G4-DNA

Answer 28

quadruplex DNA. Double stranded GC rich DNA can fold back onto itself and form base pairing between 4 G’s.. Often found near promoters of genes and at telomeres. Linked to transcription inhibition in C-MYC

Question 29

CTCF (CCCTC-binding factor) domains

Answer 29

CTCF domains, Bound by CTCF (CCCTC-binding factor), pair to each other and are then further bound with rings of cohesin to form chromatin loops, involved in gene regulation (acts as an insulator, blocking enhancers from gene target)

Question 30

sub TADs

Answer 30

sub-topologically associated domains. When chromatin loops interact with each other.

Question 31

Acetylation

Answer 31

Occurs on lysines; almost always associated with activation of transcription (e.g. acetylated H3K9 is found in actively transcribed promoters.

Question 32

Addition of an acetyl group to lysine does what?

Answer 32

neutralises its positive charge and weakens interactions between histones and DNA, de-stablising chromatin architecture

Question 33

Acetylation is regulated by

Answer 33

histone acetyl-transferases (HATs) and histone deacetylases (HDACs)

Question 34

Phosphorylation

Answer 34

serines, threonines and tyrosines. Controlled by kinases (adds phosphates) and phosphatases (removes phosphates).

Question 35

Addition of phosphate to amino acid does what?

Answer 35

adds significant negative charge to the histone and influences chromatin structure

Question 36

Competitive antagonism

Answer 36

if more than one modification is targeting the same site. Lysines can be acetylated, methylated or ubiquitinated

Question 37

SATB1 (Special AT-rich binding protein 1)

Answer 37

global chromatin organiser and transcription factor, recruits chromatin remodeling factors in order to regulate chromatin structure and gene expression. Increased expression level correlates with poor prognosis in breast cancer.

Question 38

Mutation of CTCF binding site near a repeat leads to

Answer 38

increased genomic instability and increased repeat length. Mutations in CTCF binding sites have been found in Silver-Russell and Beckwith-Wiedemann syndromes.

Question 39

Cohesin

Answer 39

multi-protein complex involved in establishment and maintenance of pairing of sister chromatids during DNA replication and into mitosis

Question 40

Mutations in cohesin

Answer 40

likely to weaken association with target sites throughout genome and result in wide-spread misexpression of genes, e.g. Cornelia de Lange syndrome and Roberts syndrome.

Question 41

C-MYC

Answer 41

prototypical oncogene involved in proliferation, cell cycle regulation and apoptosis.

Question 42

C-MYC in disease

Answer 42

Loss of C-MYC results in reduction of histone H3 and H4 acetylation and increase in tri-methylation of H3K9 (consistent with increase in heterochromatin). C-MYC is mis-regulated in a wide range of tumours.

Question 43

MLL or KMT2A (lysine-specific methyltransferase 2A)

Answer 43

regulates gene expression during early development and hematopoiesis via its SET domain (facilitates the histone H3K4 methyltransferase activity). Translocations cause acute leukemias

Question 44

HP1 (heterochromatin protein 1)

Answer 44

prominent structural component of heterochromatin. Acts as platform for variety of chromatin-modifying proteins

Question 45

HP1 in disease

Answer 45

Usually has a Repressive action by condensing chromatin regulatory regions of target genes. Reduced expression of HP1 reported in breast, brain, colon and ovarian cancer.

Question 46

MECP2 (Methyl CpG binding protein 2

Answer 46

MECP2 protein binds to methylated DNA and recruits repressive complexes that contain HDACs and/or HMTs

Question 47

MECP2 in disease

Answer 47

Rett Syndrome, genes that are normally repressed by MeCP2 remain active

Question 48

Brachydactyly-TAD boundary deletion

Answer 48

TAD boundary deletion between the PAX3 gene and an enhancer causes enhanced transcription of PAX3 and therefore PAX3 is upregulated causing

Question 49

Polydactyly

Answer 49

caused by a deletion of a TAD boundary near the IHH gene leading to a long distance interaction with an enhancer element