What is an epigenetic effect?
When the (heritable) expression of a gene is affected by factors other than the primary DNA sequence.
Covalent alterations such as
*cytosine methylation
*modification or substitution in chromatin of specific histone types (Thank you Dr. Ford!)
What is genomic imprinting?
Differences in gene expression between the allele inherited from the mother and the allele inherited from the father.
Individual is functionally hemizygous for the gene.
What is the epigenetic mark that mediates genetic imprinting?
DNA methylation
Briefly outline the DNA methylation —> gene silencing pathway
- A locus is methylated following replication
- Selective interaction of MeCP2 with metylated DNA
- ATP hydrolysis
- Histone deacetylation followed by histone methylation (H3)
- Chromatin is now compacted, histones are hypoacetylated
- Transcription is now repressed
What enzyme maintains the methylation of DNA after replication?
Maintenace Methyltransferase
At each round of replication, the newly synthesized strand of DNA is not methylated until maintenace methyltransferase comes in to selectively methylate the C in CpG’s
Where are the CpG dinucleotides that are methylated generally found in relation to a gene?
Within the promoter region of an imprinted gene.
What are two proposed mechanisms by which DNA methylation silences genes?
- directly inhibiting trxn by repelling trxn factors
2. methylation actively recruits trxn repression factors
What is a proposed mechanism by which DNA methylation acts as a gene activator?
may prevent binding of trxn repressors
Imprinted genes tend to be __________ rather than __________. (location along the DNA)
clustered together rather than spread apart
Imprinted genes contain maternally or paternally derived genes?
Both
Do imprinted genes encode only proteins?
No. proteins and non-coding RNA’s
When are epigenetic marks applied to the genome?
in gametes. when maternal and paternal DNA are still separate and can be modified differentially.
Why does DNA methylation need to be reversible in genetic imprinting?
So that it can be reset during gametogenesis to transmit the appropriate sex-specific imprint to progeny
What are the three “rules” that genetic imprinting follows?
DNA methylation marks…
- are established in the gamete
- are stably maintained in the somatic cells after fertilization
- are reversible so can be reset at gametogenesis
There are _______ major types of histones in human DNA.
________ copies of the ________ core histones (list them) make up the _________ around which DNA winds like thread around a spool.
5
2
4 (H2A, H2B, H3, H4)
octamer (nucleosome)
What is the H1 histone?
The 5th histone that binds the DNA to the edge of the nucleosome.
The pattern of major and specialized histone types along with their modifications is known as the _______________.
histone code
Describe the distribution of imprinted genes throughout the genome.
Clustered together on a small subset of the autosomes rather than dispersed
What do maintenance methyltransferase enzymes do?
They recognize hemi-methylated (newly synth) DNA and restores the methylation state on the new strand.
In genetic imprinting, which gene is silenced: the methylated allele or the unmethylated allele?
Why?
The methylated allele is silenced. The CpG repeat region is located in the promoter region of a gene. When methylated, Methyl Cpg Binding Proteins bind and effectively block trxn machinery. So the methylated gene is OFF and the unmethylated gene is ON.
What happens to imprinted genes in gametogenesis?
Methylations are erased effectively resetting the imprinting. Then, if the individual is a female, one set of “imprinted” genes are methylated (= silenced). If the individual is a male, the complimentary set of “imprinted” genes are methylated (=silenced).
If erasure and resetting of imprinted genes does not occur during gametogenesis what would be observed in the resulting offspring?
Offspring could have one of the following:
1. no active copies of a gene
2. two active copies of a gene
(it could also happen by chance that the correct imprinting is carried through in some gametes)
A deletion on which chromosome will lead to either Prader-Willi syndrome or Angleman syndrome
on the long arm of chromosome 15 interval q11 - a13 is deleted
del(15q11-q13)
Del(15q11-q13) on Mom’s chromosome 15 results in what syndrome?
Angleman’s syndrome
Del(15q11-q13) on Dad’s chromosome 15 results in what syndrome?
Prader-Willi syndrome
On the __________ allele, the Prader-Willi gene is normally transcriptionally silenced.
maternal
The expression of the Prader-Willi gene normally comes ONLY from the ________ allele.
paternal
The expression of the Angleman gene normally comes ONLY from the __________ allele.
maternal
Angleman syndrome is caused by defects in the expression of __________ which encodes a ______________ involved in early brain development.
UBE3A
ubiquitin ligase
Prader-Willi syndrome is (currently thought to be) caused by defects in ____________ which may be involved in mRNA modification, possibly by modulating_____________.
SNORD116 snoRNA genes (non-coding RNA’s typically involved in guiding modifications of other RNA’s)
alternative splicing.
What is Uniparental Disomy?
Both autosomes are inherited from one parent.
What would be a likely cause of uniparental disomy?
- Nondisjunction during meiosis I, resulting in a diploid gamete from parent 1.
- Upon fertilization, zygote is now trisomic
- If mitotic nondisjunction then results in the loss of the chromosome from parent 2, leaving only parent 1’s two copies, the conceptus now has two copies of the chromosome, but both are from parent 1.
Nondisjunction is more likely during maternal or paternal meiosis?
maternal
Whys is uniparental disomy a more common cause of Prader-Willi syndrome than of angelman syndrome?
Meiotic nondisjunction is more likely in the maternal gameteogenesis.
It is thus more likely that Mom contributes two transcriptionally silent PW genes. If Dad’s chromosome 15 is not present, PW syndrome results.
What percent of PW syndrome cases are due to uniparental disomy and which parent do the two chromosome 15’s come from?
25%
both maternal chromosome 15’s (which are trxn’ly silent for SNORD116)
What percent of Angelman syndrome cases are due to uniparental disomy and which parent do the two chromosome 15’s come from?
s (which are trxnly silenced for UBE3A)
What percentage of the genes in the human genome are subject to genetic imprinting?
1%
Histone 3, Lysine 4 (H3K4) is a(n) ____________ methylation.
activating
What region on the DNA initiates the imprinting process and what do we know about the mechanism of action?
Imprinting centers - DNA elements located within imprinted genes are the governing elements of imprinting.
We know very little about their mechanism of action…
What is Albright Hereditary Osteodystrophy?
AHO is a fully penetrant autosomal dominant trait
obesity, short stature, subcutaneous calcifications, brachydactyly (4th, 5th metacarpals)
Often, but not always, associated with PHP (pseudohypoparathyroidism)
GNAS gene is defective
*** is an example of maternal / paternal imprinting only in certain tissues
(see p. 137-139 from reading list in Megee’s L3)
