Evolution of gene regulation Flashcards
Why does RNA sequencing help to understand gene expression?
Higher levels of RNA indicate a gene is being transcribed and thus expressed.
What affects organismal complexity, gene number or gene regulation?
Gene regulation. Humans and nematodes have similar numbers of genes.
The same genes can be expressed differently across different tissues. True or false?
True.
Gene expression underlies adaptive evolution. What is adaptive evolution?
Variation between very closely related organisms.
Give an examples of adaptive evolution.
Darwin’s finches.
In Darwin’s finches, those with broad, crushing beaks have higher levels of what expression?
Bmp
In Darwin’s finches, those with pointy, narrow beaks have higher levels of what expression?
Calmodulin
There are 2 regulatory mechanisms in transcription. What are they?
- Cis
2. Trans
Define cis-regulation.
The region of DNA that regulates transcription is on the same chromosome.
Define trans-regulation.
The region of DNA that regulates transcription is distant.
Give examples of trans-regulation?
TSFs and signalling molecules can move to faraway regions of DNA.
What does a promoter do?
Initiate transcription.
What does an enhancer do?
Increase transcription.
What does a repressor do?
Prevent transcription.
If you changed the sequence of the promoter/enhancer/repressor, which regulatory mechanism would be affected?
Trans regulation. This is because it changes the affinity of the site and its regulatory components, e.g. TSFs.
If you changed the recognition site for a promoter/enhancer/repressor, which regulatory mechanism would be affected?
Cis regulation.
If divergence is a) rapid and b) gradual, what is assumed to have caused the variation?
a) Adaptive evolution
b) Genetic drift
What can be said about variation within and between species in
a) neutral evolution via genetic drift
b) purifying selection
c) Positive selection via adaptive evolution
a) Lots of variation both within and between species. Random process.
b) Little variation within and between species. Selection removes variation as it is deleterious.
c) Little variation within but extreme variation between species. Adaptive evolution leads to divergence.
What has a larger effect on gene regulation, genomic location or gene function?
Genomic location.
X is the major sex chromosome and Y is the minor. True or false?
True.
What caused the divergence of the sex chromosomes?
Inversions.
Define orthologues.
Divergents that originate from the same chromosome.
Copy number correlates to what?
Transcription/translation rate: if there are more copies of a gene, it will be transcribed more.
Why do males have reduced fitness in terms of the X chromosome?
They only produce 50% of the original gene products as the Y has diverged.
The lack of recombination on the Y chromosome has caused the decay of many genes in sequence. Which genes on the Y still persist?
Those involved in male fertility and fitness.
Define Ohno’s hypothesis.
Sex-linked genes are overexpressed in the heterogametic sex to compensate for dosage imbalance.
By what mechanism are genes overexpressed?
Hyper-transcription.
Which chromosome is hyper-transcribed in human males?
The X.
There is also transcription in drosophila to correct dosage. The MSL1 & 2 genes form a complex that binds to the X, causing it to do what?
Unwind so that TSFs can better access it.
What is XCI?
X-Chromosome Inactivation: one in every XX pair is switched off in all body cells.
Which animals display XCI?
All therians (marsupials and placental mammals)
Every therian female is a chimera. Why?
The process of XCI is random, thus in some cells the maternal X is switched off, in others it will be the paternal X etc.
XCI did not used to be random, in monotremes the paternal X was always inactivated. What caused XCI to become random?
The evolution of the Xist gene that drives XCI in therians.
What is characteristic about mice XCI?
The paternal X is inactivated until blastocyst stage, after then it changes to random XCI.
How does the Xist gene work?
It produces non-coding RNA and causes excessive winding of the DNA around the histones so transcription regulators cannot access the genes.
Even if the Xist gene itself is switched off it is proliferated in cell division. How?
It has coding that spreads across the chromosome.
Which gene represses Xist to keep the other X switched on?
Tsix.
Recap: what is the primary dosage correction in a) males and b) females?
a) Hyper-transcription of the X
b) XCI
What kind of gene expression do organisms display if there is no dosage compensation?
Female bias, i.e. there is an overrepresentation of female gene products in all tissues
Define hypo-transcription.
Under-expression of particular genes. This is another method of dosage correction seen in nematodes (C. elegans).
Dosage compensation is conserved across all species. True or false?
False: it has evolved convergently across species, there are no relationships across taxa.
