Evolution of gene regulation

Question 1

Why does RNA sequencing help to understand gene expression?

Answer 1

Higher levels of RNA indicate a gene is being transcribed and thus expressed.

Question 2

What affects organismal complexity, gene number or gene regulation?

Answer 2

Gene regulation. Humans and nematodes have similar numbers of genes.

Question 3

The same genes can be expressed differently across different tissues. True or false?

Answer 3

True.

Question 4

Gene expression underlies adaptive evolution. What is adaptive evolution?

Answer 4

Variation between very closely related organisms.

Question 5

Give an examples of adaptive evolution.

Answer 5

Darwin’s finches.

Question 6

In Darwin’s finches, those with broad, crushing beaks have higher levels of what expression?

Answer 6

Bmp

Question 7

In Darwin’s finches, those with pointy, narrow beaks have higher levels of what expression?

Answer 7

Calmodulin

Question 8

There are 2 regulatory mechanisms in transcription. What are they?

Answer 8

1. Cis

2. Trans

Question 9

Define cis-regulation.

Answer 9

The region of DNA that regulates transcription is on the same chromosome.

Question 10

Define trans-regulation.

Answer 10

The region of DNA that regulates transcription is distant.

Question 11

Give examples of trans-regulation?

Answer 11

TSFs and signalling molecules can move to faraway regions of DNA.

Question 12

What does a promoter do?

Answer 12

Initiate transcription.

Question 13

What does an enhancer do?

Answer 13

Increase transcription.

Question 14

What does a repressor do?

Answer 14

Prevent transcription.

Question 15

If you changed the sequence of the promoter/enhancer/repressor, which regulatory mechanism would be affected?

Answer 15

Trans regulation. This is because it changes the affinity of the site and its regulatory components, e.g. TSFs.

Question 16

If you changed the recognition site for a promoter/enhancer/repressor, which regulatory mechanism would be affected?

Answer 16

Cis regulation.

Question 17

If divergence is a) rapid and b) gradual, what is assumed to have caused the variation?

Answer 17

a) Adaptive evolution

b) Genetic drift

Question 18

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

Answer 18

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.

Question 19

What has a larger effect on gene regulation, genomic location or gene function?

Answer 19

Genomic location.

Question 20

X is the major sex chromosome and Y is the minor. True or false?

Answer 20

True.

Question 21

What caused the divergence of the sex chromosomes?

Answer 21

Inversions.

Question 22

Define orthologues.

Answer 22

Divergents that originate from the same chromosome.

Question 23

Copy number correlates to what?

Answer 23

Transcription/translation rate: if there are more copies of a gene, it will be transcribed more.

Question 24

Why do males have reduced fitness in terms of the X chromosome?

Answer 24

They only produce 50% of the original gene products as the Y has diverged.

Question 25

The lack of recombination on the Y chromosome has caused the decay of many genes in sequence. Which genes on the Y still persist?

Answer 25

Those involved in male fertility and fitness.

Question 26

Define Ohno’s hypothesis.

Answer 26

Sex-linked genes are overexpressed in the heterogametic sex to compensate for dosage imbalance.

Question 27

By what mechanism are genes overexpressed?

Answer 27

Hyper-transcription.

Question 28

Which chromosome is hyper-transcribed in human males?

Answer 28

The X.

Question 29

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?

Answer 29

Unwind so that TSFs can better access it.

Question 30

What is XCI?

Answer 30

X-Chromosome Inactivation: one in every XX pair is switched off in all body cells.

Question 31

Which animals display XCI?

Answer 31

All therians (marsupials and placental mammals)

Question 32

Every therian female is a chimera. Why?

Answer 32

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.

Question 33

XCI did not used to be random, in monotremes the paternal X was always inactivated. What caused XCI to become random?

Answer 33

The evolution of the Xist gene that drives XCI in therians.

Question 34

What is characteristic about mice XCI?

Answer 34

The paternal X is inactivated until blastocyst stage, after then it changes to random XCI.

Question 35

How does the Xist gene work?

Answer 35

It produces non-coding RNA and causes excessive winding of the DNA around the histones so transcription regulators cannot access the genes.

Question 36

Even if the Xist gene itself is switched off it is proliferated in cell division. How?

Answer 36

It has coding that spreads across the chromosome.

Question 37

Which gene represses Xist to keep the other X switched on?

Answer 37

Tsix.

Question 38

Recap: what is the primary dosage correction in a) males and b) females?

Answer 38

a) Hyper-transcription of the X

b) XCI

Question 39

What kind of gene expression do organisms display if there is no dosage compensation?

Answer 39

Female bias, i.e. there is an overrepresentation of female gene products in all tissues

Question 40

Define hypo-transcription.

Answer 40

Under-expression of particular genes. This is another method of dosage correction seen in nematodes (C. elegans).

Question 41

Dosage compensation is conserved across all species. True or false?

Answer 41

False: it has evolved convergently across species, there are no relationships across taxa.