Evolutionary Biology 11: Signals, molecules, genes, epigenetics

Question 1

Describe features of:
mp mutant,
bdl mutant,
tpl mutant

Answer 1

mp (monopteros) mutant

• encodes TF ARF5 which binds to auxin responsive promotor elements
• loss of function meaning auxin responsive genes aren’t activated
• works in auxin regulated pathway to control early division of cell specification in embryo

bdl (bodenlos) mutant

• encodes IAA12
• gain of function - BDL binds to MP that prevents target gene activation
• BDL would normally be degraded in response to auxin, bdl is stabilising mutation

tpl (topless) mutant

• encodes wd40 transcriptional co-repressor of root meristem identity
• switches SAM to RAM, results in double root seedling, no SAM
• TPL protein required for SAM identity + suppression of RAM identity

Question 2

Notable features of bdl/tpl double mutant?

Answer 2

tpl rescues patterning defects of bdl
-> formation of root and hypocotyl

BDL, MP and TPL form complex that prevents MP from activating target genes

Question 3

How does DNA methylation effect gene expression? How?

Answer 3

DNA methylation

• add methyl group to cytosine base, involved in gene silencing
• promoters can be hypomethylated to become transciptionally active
• regulated by DNA methyl transferases (DNMTs) and DNA glycolases

Can also lead to histone modification

Question 4

Mechanism of histone modification and resulting repression through DNA methylation?

Answer 4

DNA methylation by DNMTs

• DNMTs recruit HDACs
• Histone deacetylation by HDAC complex
• Transcriptional repression

Question 5

How are histones modified in epigenetic mechanisms?

Answer 5

Histone tails are acetylated and deacetylated

• by HATs and HDACs respectively
• HATs activate, HDACs repress

Acetylation means TFs can access promoters more readily

Both modulate reversible changes in gene expression

Question 6

Example of gene deactivation via deacetylation? What molecules mediate this process?

Answer 6

X chromosome inactivation (XCI) in female mammalian cells

• 2 X copies, one X copy must be silenced, example of DOSAGE COMPENSATION (equalising expression of genes)

deacetylation mediated by lncRNAs, specifically Xist

Xist recruits PRC complexes that mediate methylation of histones -> spreads through chromosome leading to inactivation

Question 7

Function of Polycomb proteins and Trithorax proteins? How do the do this?

Answer 7

Polycomb - maintain gene repression

Trithorax (Trx) - maintain gene expression

both recognise specific DNA motifs PRE, TRE and regulate many genes

Trx have histone methyltransferase activity and prevent polycomb mediated silencing of homeotic genes

Question 8

types of ncRNAs - what are they?

Answer 8

non-coding RNAs

• microRNAs
• smallRNAs
• medium/large RNAs (lncRNAs)

Question 9

Main roles of miRNAs in development? examples?

Answer 9

Regulate genes and TFs that regulate development

• can also bind to target sites on RNA to impede translation (post-transcriptional regulation)
• > ‘fine-tunes’ gene activity

e.g. spatial restriction, (restricts expression domain) 
buffering function, (stabilise expression levels)
temporal regulation (control levels over time)