Epigenetics

Question 1

What does DDT correlate to in terms of genetic difference?

Answer 1

It leads to inheritance of obeisity

Question 2

What does tighter DNA in mitosis lead to?

Answer 2

Lower expression and transcription levels

Question 3

Do epigenetic effects have the ability to be heritable?

Answer 3

Yes

Question 4

How can epigenetics be explained from a stem cell viewpoint?

Answer 4

Epigenetics leads to differentiation of stem cells into different cells.

Question 5

What are epigenetics?

Answer 5

The study of DNA sequence combined with variable gene expression

Question 6

What are the 4 most recognized epigenetic regulations?

Answer 6

DNA tagging
Histone Modifications
Non-coding RNAs
RNA modifications (post transcriptional)

Question 7

What is DNMT and what does it do?

Answer 7

DNA methyltransferase is a family of enzymes that catalyzes the methylation of DNA

Question 8

What are the three properties of CpG islands?

Answer 8

1. They are 200-2000 base pairs long
2. They are typically found near promotors of genes
3. They play a large role in gene regulation

Question 9

What is a CpG site?

Answer 9

A cytosine followed by guanine in linear sequence

Question 10

When does CpG lead to gene expression silencing?

Answer 10

When it is methylated, the genes are silences

Unmethylated = expression

Question 11

What is the difference in function between DNMT1, and DNMT 2/3?

Answer 11

1 - Preserves methylation pattern during cell division

2/3 - Induces de novo methylation to control differentiation

Question 12

What can be said about the heritability of histone modifications?

Answer 12

They are inherited through cell division, which can maintain an expression pattern across cell generations

Question 13

What does de novo DNA methylation include to effect expression?

Answer 13

The methylation of new CpG sites, or increased methylation of a site

Question 14

What is the mechanism with which DNMT1 adds methyl groups to DNA?

Answer 14

It recognizes hemimethylated DNA and adds methyl groups to the unmethylated strand, ensuring patterns are copied

Question 15

What is hemimethylated DNA?

Answer 15

It is when one strand is unmethylated

Question 16

How does methylation interfere with DNA expression?

Answer 16

It interferes with the docking of the TM (transcriptional machinery)

Question 17

What is transcriptional control by methylation highly dependent on?

Answer 17

location of methylation relative to the gene

Question 18

What is the difference in expression when different parts of the gene are methylated?

Answer 18

It is repressed if the methylation is near a promotor region or start site, and expression is correlated with methylation of the gene body

Question 19

What other genetic process is gene body myelination hypothesized to be involved in?

Answer 19

Gene splicing

Question 20

What are transposons?

Answer 20

They are jumping genes that change their position in the genome

Question 21

How is DMNT linked to transposons?

Answer 21

Transposons are upregulated in DNMT-1 deficient mice

Question 22

How are transposons silenced in mammals?

Answer 22

1. Bulk de novo methylation of old transposons from DNMT3A/L
2. PIWI proteins recruit DNMT3A/L enzymes

Question 23

What is X chromosome inactivation (XCI)?

Answer 23

A process in female mammals where one of the two x chromosomes is silenced to achieve dosage compensation

Question 24

When are sexual dimorphisms observed due to DNA methylation?

Answer 24

When there is low methylation on a promotor CpG region of the X chromosome in females.

Question 25

In terms of histones, what does gene expression depend on?

Answer 25

Nucleosome position, mobility, and packaging

Question 26

What structure is critical to the knowledge of chromatin properties on gene mechanisms?

Answer 26

The nucleosome core particle NCP

Question 27

What are the four properties of histones with impact on DNA expression?

Answer 27

1. Chromatin structure - condensed or relaxed structure 2. Recruitment of regulatory proteins - activate or repress transcription 3. Histone code hypothesis - modifications can make a code that regulating proteins read 4. Histones are dynamic and reversible

Question 28

What type of RNA is responsible for epigenetics?

Answer 28

Non-coding RNA, NCRs

Question 29

What important complex processed NCRs?

Answer 29

The RISC, RNA-induced silencing complex And AGO protein

Question 30

What does AGO do?

Answer 30

It loads a small RNA- duplex to make pre-RISC

Question 31

What is mature RISC?

Answer 31

It is the red (guide) strand of DNA with the blue (passenger) strand ejected

Question 32

What guides RISC to its complementary RNAs?

Answer 32

small RNA

Question 33

What three types of ways does RISC use to stop gene expression?

Answer 33

1. mRNA cleavage 2. degradation 3. translational repression

Question 34

What types of RNA are involved in silencing?

Answer 34

Micro RNA (miRNA) and silencing RNA (siRNA)

Question 35

What is the process that miRNA takes to get to its RISC form?

Answer 35

pre-miRNA is produced in the nucleus, it is sent to the dicer, which turns it into miRNA, which then is loaded into protein AGO2 to make RISC

Question 36

What is the process that siRNA takes to get to its RISC form?

Answer 36

double stranded RNA is cut by the dicer and loaded to AGO2 to make RISC

Question 37

What does siRNA do to mRNA?

Answer 37

Degradation

Question 38

At what levels do non coding RNA act?

Answer 38

At the gene and chromosome level

Question 39

How man RNA modifications have been discovered, and what accounts for two thirds of these cases?

Answer 39

More than 170 modifications have been found, with 2/3 of these bring from methylation

Question 40

What does histone tail methylation do in a 2023 study?

Answer 40

It allows for the control of muscle specific genes during myogenesis

Question 41

What DNA process is correlated with age?

Answer 41

Methylation of DNA