Genet 302 lec 39 & 40
What 2 dosage-compensation systems do mammals use?
They upregulate X-linked gene expression and also inactivate one X chromosome in females
Why do mammals need 2 dosage-compensation systems instead of 1?
Upregulation makes one active X produce enough product in both sexes, and X inactivation prevents females with 2 X chromosomes from overexpressing X-linked genes
What evidence from mouse genetics supports X upregulation in mammals?
An X-linked gene in one mouse species and an autosomal version in another can produce similar mRNA levels in males
What gene was used in the mouse-genetics example for X upregulation?
Clc4
Which species had Clc4 on the X chromosome in the lecture example?
Mus spretus
Which species had Clc4 on chromosome 7 in the lecture example?
Mus musculus
Which male makes more Clc4 mRNA in the lecture example?
They make the same amount
Why is X-linked disease often milder in gene+/− females than in gene−/Y males?
Because females are mosaics, so some cells express the normal allele
Why are heterozygous females mosaics for X-linked gene expression?
Different cells inactivate different X chromosomes
What human example was used to show mosaic X-linked expression can reduce severity?
X-linked disorders such as muscular dystrophy are usually milder in heterozygous females than in affected males
What cat-coat example was used to show mosaic X inactivation?
Black versus orange coat color
What gene was identified in 2025 as responsible for black versus orange fur in cats?
ARHGAP36
What alleles were used for the cat color example?
A^O for orange and A^B for black
What is the phenotype of A^O/A^O cats?
Orange female
What is the phenotype of A^B/A^B cats?
Black female
What is the phenotype of A^O/Y cats?
Orange male
What is the phenotype of A^B/Y cats?
Black male
What is the phenotype of A^O/A^B cats?
Tortoiseshell or calico female
What is the allele interaction between A^O and A^B?
Codominant
Why are A^O/A^B females tortoiseshell instead of blended in color?
Random X inactivation creates patches of cells expressing one allele or the other
In the kangaroo example, what color are the male joeys from A^O/A^O mother × A^B/Y father?
Orange
In the kangaroo example, what color are the female joeys from A^O/A^O mother × A^B/Y father?
Orange
Why are the female kangaroos not tortoiseshell in this lecture example?
Because the paternal X is preferentially inactivated, so the maternal orange X stays active
How did the mouse experiment visualize X inactivation patterns?
Using Cre-lox with fluorescent reporter transgenes on the 2 X chromosomes
How does the Cre-lox system work in this context?
Cre removes a loxP-stop-loxP cassette so the fluorescent reporter can be expressed
What were the 3 transgenes in the mouse mosaic experiment?
A cell-type-specific Cre transgene, a maternal X reporter, and a paternal X reporter
What fluorescent reporters were used on the 2 X chromosomes?
nls-tdTomato on one X and nls-GFP on the other
What does Cre do to the reporter transgene?
It excises the stop sequence between the loxP sites and turns the reporter on
Why do different cells end up red or green in the female mouse?
Because different cells keep different X chromosomes active
What do mixed red and green patches in tissues show?
Mosaic X inactivation
What is similar about sex determination in humans, mice, and kangaroos?
All are mammals and use an XY system with SRY on the Y chromosome for male sex determination
What is similar about dosage compensation in humans, mice, and kangaroos?
All upregulate X-linked gene expression and inactivate one X chromosome in females
What is a key difference in X inactivation between humans and mice?
Human females are random mosaics for maternal versus paternal X activity, while mice have strong experimental evidence for random mosaicism and are often used to visualize it directly
What is a key difference involving kangaroos in this lecture?
Kangaroos tend to inactivate the paternal X, so female offspring are not random mosaics like typical human tortoiseshell examples
What base is methylated in mammalian DNA methylation?
Cytosine
What DNA sequence context is usually methylated in mammals?
CpG sites
What is 5-methylcytosine?
A cytosine with a methyl group attached
About what fraction of human cytosines are 5-methylcytosine in this lecture?
About 2 to 7%
What does CpG mean in this lecture? where does the major groove come from?
A cytosine followed by guanine on the same DNA strand, linked by phosphate. the methylation causes bulging--> major groove
What enzyme adds methyl groups to DNA?
DNA methyltransferase
What are de novo DNA methyltransferases?
DNMTs that methylate previously unmethylated DNA
What are maintenance DNA methyltransferases?
DNMTs that methylate hemi-methylated DNA after replication
How is DNA methylation passively removed in this lecture?
Turn off de novo DNMTs and maintenance DNMTs and allow DNA replication to dilute the mark
Why do mammals use DNA methylation to repress transposable elements?
It blocks excision and insertion, reducing damage from TE movement by essentially turning of the TE's ability to move locations
Why do mammals use DNA methylation in developmental gene regulation?
It reinforces shutdown of genes that a cell type does not need
How does DNA methylation help keep tissue-specific genes off?
It helps convert genes from off but leaky to completely off
How can DNA methylation repress genes mechanistically?
Methyl-CpG-binding proteins such as MeCP2 recruit histone modifiers such as HP1
Why is methylation of tumor-suppressor genes bad?
It can silence them and contribute to cancer
Why is methylation of Xi genes good?
It is a normal part of X chromosome inactivation
Why do mammals use DNA methylation in genomic imprinting?
To mark specific maternal or paternal regions differently during oogenesis or spermatogenesis
What DNA-testing use of methylation was mentioned in the lecture?
Older mammals tend to have more DNA methylation, which can help estimate age
List the main reasons mammals use DNA methylation from this lecture
To repress transposable element mobilization, reinforce developmental gene regulation, help maintain X chromosome inactivation, and establish genomic imprinting. also more methylation of dna--> older mammal