Genomic imprinting 2 Flashcards
Why can women suffer from haemophilia?
The mutant x chromosome may be activated and the normal one inactivated
Four stages of inactivation?
Establishment, maintenance, reading, erasure
Three stages of x inactivation in diploid cells?
Counting, choice, stabilisaiton
Why is the counting phase necessary in x inactivation?
Must inactivate all X chromosomes except 1 (might have 3 and so need to inactivate 2)
What happens regarding the progeny of a cell that has done the x inactivation?
They will all have the same x chromosome(s) inactivated and the same x chromosome activated
Which gene is the x inactivation centre near?
Xist
Which gene is the x inactivation centre opposite?
Tsix
How far on either side of the Xist gene is the critical region for x inactivation?
150kB
What happens if there is a deletion or mutation in the x inactivation centre?
That x chromosome does not become inactivated
What happens if the choice component of the x inactivation centre is put into other regions of the genome?
They can inactivate other genes
What type of RNA is Xist transcribed into?
lncRNA
What type of RNA is Tsix transcribed into?
lncRNA
What is the locational relationship between Tsix and Xist regarding their transcription?
They are expressed in opposite orientation to one another
How much of Tsix and Xist are produced prior to inactivation?
Very low levels
Role of Tsix?
Reduce Xist expression
What role does Xist have in gene activation?
a gene with high levels of Xist expression is an inactive gene
What happens to Tsix expression on the active X once the inactive X is turned off?
Tsix is no longer required
Why is Tsix no longer required once inactivation has occured?
Epigenetic mechanisms lock the inactive X into being silenced
Which stage of X inactivation doesn’t require Xist?
Maintainance
X inactivation state in pluripotent embryonic stem cells?
Both Xs are active
Tsix and Xist expression in embryonic stem cells?
Both are expressed
What happens to Xist and Tsix expression in stem cell differentiation?
One chromosome expresses a lot more Xist
What does Xist RNA do to the inactive X chromosome?
Coats it
Sex of tortoiseshell cats?
Always female
What are DMRs?
Differentially methylated regions (where one allele of a gene on one chromosome is more/less methylated than the sister allele on the other chromosome)
Full “lollipop” on gene expression diagram?
Methylated gene
Hollow “lollipop” on gene expression diagram?
Non-methylated gene
When do primordial germ cells lose their methylation?
When they are migrating to the genital ridge
What are the most hypomethylated cells?
Primordial germ cells on their way to the genital ridge
What helps imprints to be maintained after fertilization and ensures they won’t be erased?
Maternal zygotic factors
Role of ZFP57?
Maintains maternal imprints
Role of Pgc7 (stella, DPPA3)?
Protecting maternal imprints from demethylation
How do maternal zygotic factors ensure imprinting is maintained?
Bind to DNA at specific methylated sequences (high preference for imprinted regions) and they stop TET enzymes from demethylating the imprinted regions
What are the three ways by which a TF can “read” an imprint and transcribe from only one parental allele?
Differential promoter selection
Differential inhibition by noncoding RNA
Differential boundaries
Which level of methylation makes it easier for a TF to bind?
Low levels of methylation
How does noncoding RNA expression work in imprinting?
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
What is cotranscriptional interference?
Two polymerases on either side in opposite directions cant squeeze past one another, so interference with transcription happens
What can noncoding RNA do regarding bringing in other molecules?
It can bring in repressive promoters, histone methylation etc to act as a scaffold to create a silencing effect
Where are insulators spaced in the genome?
40kB-100kB
How does CTCF cause a silencing effect?
It has zinc fingers which wind the DNA into a knot so their genes cannot be accessed by TFs or other regulatory mechanisms
What level of methylation is required for CTCF binding?
Unmethylated DNA
Which sex’s allele expresses IGF2?
Paternal
Which sex’s allele expresses H19?
Maternal
What type of RNA is H19?
noncoding
Role of H19?
Suppresses IGF2
What type of gene is IGF2?
Growth factor
Why are beckwith wiedermann syndrome affected people larger than average?
They express too much IGF2
What happens, regarding CTCF, if an imprinting control region is methylated?
CTCF cannot bind
What happens if CTCF isnt bound to an imprinted control region?
A gene can access its enhancer on the other side of the ICR, leading to expression of the gene
How many zinc fingers does CTCF have?
7
Role of cohesin in combination with CTCF?
Can hold sister chromatids together, or create a boundary in the middle of a chromatid
Role of KCNQ1OT1?
Coating the chromosome in the area where it acts, preventing those genes from being expressed
Effect of uniparental dispmy?
Both maternal and paternal chromosome look like they are a paternal chromosome (appears you have two paternal chromosomes)
Origins of uniparental disomy?
Trisomy rescue, monosomy rescue
Trisomy rescue?
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
Monosomy rescue?
Nullisomic oocyte (0 egg chromosomes) so haploid sperm duplicates to ensure there is enough chromosomes. Leads to paternal isodisomy
