Epigenetics in Cancer I

Question 1

What is epigenetics?

Answer 1

The study of changes in gene expression or cellular phenotype, caused by mechanisms other than changes in the underlying DNA sequence

Question 2

What is gene regulation?

Answer 2

A process that leads to a gene being turned on or off

Cellular homeostasis is achieved by the proper balance of regulatory networks

Question 3

Why do epigenetic mechanisms play an important role in cancer progression?

Answer 3

The ultimate cause of cancer is alteration of the balanced harmony of cellular networks and gene expression programs that maintain cellular homeostasis

Question 4

What are the basic components of a gene?

Answer 4

Exons whose sequences encode the protein
Introns that are removed from the mRNA before translation
A transcription start site where RNA transcription begins
Promoters including basal promoters within 40 bp of the start site and upstream promoters which may extend up 200 bp farther upstream
Enhancers some transcription factors bind to these regions of DNA that are thousands of bp away from the gene they control, binding to these regions increases the rate of gene transcription
Silencers are regions of DNA which act like enhancers however they suppress expression of this gene

Question 5

What are the epigenetic changes that alter gene expression without changing the underlying DNA sequence?

Answer 5

DNA methylation, histone modification and remodelling and non-coding RNAs

Question 6

How does DNA methylation suppress gene expression?

Answer 6

For some transcription factors such as AP-2, c-myc, CREB/ATF, E2F and NFkB DNA methylation can create a physical barrier, abolishing access to promoter binding sites
It is also an initiation step for establishing the inactive chromatin state, followed by methyl-CpG binding proteins which recruit histone deacetylases causing repressive epigenetic modification enzymes

Question 7

What are CpG islands?

Answer 7

This is the name given to a CpG sequence after it exceeds a certain length of methylated bases

Question 8

What is the CpG sequence?

Answer 8

The region where methyl groups bind to C and supresses gene expression

Question 9

What role does methylation play in cancer?

Answer 9

If a tumour suppressor gene is methylated it will not be expressed leading to cancer progression
If an oncogene is unmethylated it will be expressed and lead to tumour progression

Question 10

How can DNA become methylated?

Answer 10

There are three active DNA methyl transferase which have identified in mammals including DNMT1, DNMT2/TRDMT1 and DNMT3

Question 11

What are DNA methyltransferases?

Answer 11

DNA methyl-transferases catalyse the transfer of the methyl group from S-adenosyl-methionine onto cytosine-S-adenosyl-methionine

Question 12

Can DNA methylation lead to a heritable change in DNA expression?

Answer 12

During DNA replication the parents methylation pattern is copied to the newly synthesized strand ensuring that a parents strand passes on its methylation pattern to its daughter strand

Question 13

What are the features of DNMT1?

Answer 13

The most abundant DNA methyltransferase in mammalian cells and considered to be the key maintenance methyltransferase in mammals

Question 14

What are the features of the DNMT2/TRDMT1?

Answer 14

Strong sequence similarities with 5-methylcytosine methyltransferases of both prokaryotes and eukaryotes. It methylates position 38 in aspartic acid transfer RNA and does not methylate DNA so it is also called TRDMT1, this is the first RNA cytosine methyltransferase to be identified in humans

Question 15

What are the features of DNMT3?

Answer 15

Could methylate hemimethylated and unmethylated CpG ate the same rate, this is a family with three known members: DNMT3a, DNMT3B and DNMT3L

Question 16

How does DNA demethylation occur?

Answer 16

This can occur through two processes,active which depends on the ability of enzymes to hydroxylate, further oxidise or deaminate 5mC this is independent to the DNA replication prcess
In the passive process the maintenance of DNA methylation is impaired during DNA replication

Question 17

What are the enzymes involved in the process of DNA demethylation?

Answer 17

TET (Ten-eleven translocation), AID (activation induced cytidine deaminase) and TDG (Thymine DNA glycosylation)

Question 18

What is the stepwise reaction leading to DNA demethylation?

Answer 18

Hydroxylation of 5mC by TET occurs first, followed by deamination by AID or carboxylation and base excision repair pathway

Question 19

What is chromatin?

Answer 19

Mass of DNA and proteins that condense to form chromosomes

Question 20

What are the primary functions of chromosomes?

Answer 20

Package DNA into a smaller volume to fit into the cell strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, control of gene expression

Question 21

What is the nucleosome?

Answer 21

The building blocks of chromatin consisting of a segment of DNA sequence around eight core histone proteins (2 copies of H2A, H2B, H3 and H4)
These can later be interacted with by linker histones such as H1 and its isoforms which are involved in chromatin compaction and sit at the base of the nucleosome near the DNA entry and exit the binding to the linker region of the DNA

Question 22

What is the difference between euchromatin and heterochromatin?

Answer 22

Euchromatin is when DNA is expressed sand more loosely packed to allow RNA polymerase and other protein access to the DNA while in heterochromatin the DNA is densely packed preventing this access causing it to be transcriptionally silent

Question 23

How does chromatin regulate DNA transcription?

Answer 23

Chemical modification such as methylation and acetylation of the histone structure alter chromatin structure changing the access of the transcription factors to the DNA

Question 24

What are chromatin remodelling complexes?

Answer 24

Nucleosome occupancy is a key mechanism for gene expression and chromatin remodelling complexes are responsible for regulating this process
ATP dependent chromatin remodelling enzymes are generally a part of multiprotein complexes which are highly conserved using ATP to non-covalently alter chromatin structure to cause changes in nucleosome postion, composition or confirmation along DNA to change the status of chromatin

Question 25

What are histone modification?

Answer 25

Nucleosomes carry epigentically inherited information in the form of covalent modifications of core histones
These include active promoter region containing trimethylated H3 at Lys4 (H3K4me3), inactive promoter regions containing trimethylated H3 at Lys 27 (H3K27me3 or H3K9me3)
Regulatory enhancers are enriched in H3K4me1 and/or H3K27ac

Question 26

What are the enzymes involved in histone modification?

Answer 26

Histone acetyltransferase and Histone deacetylases

Histone methyltransferase and histone demethylases

Question 27

What are the polycomb group of repressor proteins?

Answer 27

The polycomb group of repressor proteins controls the accessibility of gene regulatory elements to the transcription machinery

Question 28

What makes up polycomb repressor complex 2?

Answer 28

EZH2, SUZ12, PCL and EED form PCR2 which methylates H3K27

Question 29

What makes up polycomb repressor complex 1?

Answer 29

CBX, PHC, BMI and RING1A/B form PCR1 that contains Bmi-1 and Ring1B proteins which are able to ubiquitylate histone H2A, PCR1 is also able create a compacted chromatin state that is refractory to ATP dependent remodelling

Question 30

What is the trithorax group proteins?

Answer 30

The trithorax group proteins are a heterogenous collection of proteins whose main action is to maintain gene expression though other components seem to be recruited to chromatin in an activation dependent manner
TrxG proteins also not only change chromatin marks but also help to recruit transcription factors and transcription elongation

Question 31

What are the three general classes that the trithorax group proteins can be placed into?

Answer 31

These classes are based on molecular function and are
Histone-modifying TrxG proteins
Chromatin-remodeling TrxG proteins
DNA-binding TrxG proteins

Question 32

What is the relationship between the Polycomb repressor complex and the trithorax group?

Answer 32

The TrxG are antagonists to the polycomb repressor complexes