Genomic imprinting 2

Question 1

Why can women suffer from haemophilia?

Answer 1

The mutant x chromosome may be activated and the normal one inactivated

Question 2

Four stages of inactivation?

Answer 2

Establishment, maintenance, reading, erasure

Question 3

Three stages of x inactivation in diploid cells?

Answer 3

Counting, choice, stabilisaiton

Question 4

Why is the counting phase necessary in x inactivation?

Answer 4

Must inactivate all X chromosomes except 1 (might have 3 and so need to inactivate 2)

Question 5

What happens regarding the progeny of a cell that has done the x inactivation?

Answer 5

They will all have the same x chromosome(s) inactivated and the same x chromosome activated

Question 6

Which gene is the x inactivation centre near?

Answer 6

Xist

Question 7

Which gene is the x inactivation centre opposite?

Answer 7

Tsix

Question 8

How far on either side of the Xist gene is the critical region for x inactivation?

Answer 8

150kB

Question 9

What happens if there is a deletion or mutation in the x inactivation centre?

Answer 9

That x chromosome does not become inactivated

Question 10

What happens if the choice component of the x inactivation centre is put into other regions of the genome?

Answer 10

They can inactivate other genes

Question 11

What type of RNA is Xist transcribed into?

Answer 11

lncRNA

Question 12

What type of RNA is Tsix transcribed into?

Answer 12

lncRNA

Question 13

What is the locational relationship between Tsix and Xist regarding their transcription?

Answer 13

They are expressed in opposite orientation to one another

Question 14

How much of Tsix and Xist are produced prior to inactivation?

Answer 14

Very low levels

Question 15

Role of Tsix?

Answer 15

Reduce Xist expression

Question 16

What role does Xist have in gene activation?

Answer 16

a gene with high levels of Xist expression is an inactive gene

Question 17

What happens to Tsix expression on the active X once the inactive X is turned off?

Answer 17

Tsix is no longer required

Question 18

Why is Tsix no longer required once inactivation has occured?

Answer 18

Epigenetic mechanisms lock the inactive X into being silenced

Question 19

Which stage of X inactivation doesn’t require Xist?

Answer 19

Maintainance

Question 20

X inactivation state in pluripotent embryonic stem cells?

Answer 20

Both Xs are active

Question 21

Tsix and Xist expression in embryonic stem cells?

Answer 21

Both are expressed

Question 22

What happens to Xist and Tsix expression in stem cell differentiation?

Answer 22

One chromosome expresses a lot more Xist

Question 23

What does Xist RNA do to the inactive X chromosome?

Answer 23

Coats it

Question 24

Sex of tortoiseshell cats?

Answer 24

Always female

Question 25

What are DMRs?

Answer 25

Differentially methylated regions (where one allele of a gene on one chromosome is more/less methylated than the sister allele on the other chromosome)

Question 26

Full "lollipop" on gene expression diagram?

Answer 26

Methylated gene

Question 27

Hollow "lollipop" on gene expression diagram?

Answer 27

Non-methylated gene

Question 28

When do primordial germ cells lose their methylation?

Answer 28

When they are migrating to the genital ridge

Question 29

What are the most hypomethylated cells?

Answer 29

Primordial germ cells on their way to the genital ridge

Question 30

What helps imprints to be maintained after fertilization and ensures they won't be erased?

Answer 30

Maternal zygotic factors

Question 31

Role of ZFP57?

Answer 31

Maintains maternal imprints

Question 32

Role of Pgc7 (stella, DPPA3)?

Answer 32

Protecting maternal imprints from demethylation

Question 33

How do maternal zygotic factors ensure imprinting is maintained?

Answer 33

Bind to DNA at specific methylated sequences (high preference for imprinted regions) and they stop TET enzymes from demethylating the imprinted regions

Question 34

What are the three ways by which a TF can "read" an imprint and transcribe from only one parental allele?

Answer 34

Differential promoter selection Differential inhibition by noncoding RNA Differential boundaries

Question 35

Which level of methylation makes it easier for a TF to bind?

Answer 35

Low levels of methylation

Question 36

How does noncoding RNA expression work in imprinting?

Answer 36

If a noncoding RNA is expressed (low methylation of it) then it can affect a downstream gene and repress that gene. If a noncoding RNA isnt expressed (high methylation) then it cant affect a downstream gene and so that gene is active

Question 37

What is cotranscriptional interference?

Answer 37

Two polymerases on either side in opposite directions cant squeeze past one another, so interference with transcription happens

Question 38

What can noncoding RNA do regarding bringing in other molecules?

Answer 38

It can bring in repressive promoters, histone methylation etc to act as a scaffold to create a silencing effect

Question 39

Where are insulators spaced in the genome?

Answer 39

40kB-100kB

Question 40

How does CTCF cause a silencing effect?

Answer 40

It has zinc fingers which wind the DNA into a knot so their genes cannot be accessed by TFs or other regulatory mechanisms

Question 41

What level of methylation is required for CTCF binding?

Answer 41

Unmethylated DNA

Question 42

Which sex's allele expresses IGF2?

Answer 42

Paternal

Question 43

Which sex's allele expresses H19?

Answer 43

Maternal

Question 44

What type of RNA is H19?

Answer 44

noncoding

Question 45

Role of H19?

Answer 45

Suppresses IGF2

Question 46

What type of gene is IGF2?

Answer 46

Growth factor

Question 47

Why are beckwith wiedermann syndrome affected people larger than average?

Answer 47

They express too much IGF2

Question 48

What happens, regarding CTCF, if an imprinting control region is methylated?

Answer 48

CTCF cannot bind

Question 49

What happens if CTCF isnt bound to an imprinted control region?

Answer 49

A gene can access its enhancer on the other side of the ICR, leading to expression of the gene

Question 50

How many zinc fingers does CTCF have?

Answer 50

7

Question 51

Role of cohesin in combination with CTCF?

Answer 51

Can hold sister chromatids together, or create a boundary in the middle of a chromatid

Question 52

Role of KCNQ1OT1?

Answer 52

Coating the chromosome in the area where it acts, preventing those genes from being expressed

Question 53

Effect of uniparental dispmy?

Answer 53

Both maternal and paternal chromosome look like they are a paternal chromosome (appears you have two paternal chromosomes)

Question 54

Origins of uniparental disomy?

Answer 54

Trisomy rescue, monosomy rescue

Question 55

Trisomy rescue?

Answer 55

Disomic oocyte (2 egg chromosomes instead of 1) and 1 haploid sperm--> the two egg chromosomes are what are passed onto the offspring instead of 1 egg and 1 sperm. Leads to maternal heterodisomy

Question 56

Monosomy rescue?

Answer 56

Nullisomic oocyte (0 egg chromosomes) so haploid sperm duplicates to ensure there is enough chromosomes. Leads to paternal isodisomy