Gene Regulation During Development Flashcards
How do cells progressively become different from each other
Changes in gene expression
Process of differentiation basic
Series of Hierarchical fate decisions
Before reaching a final nondifferentiatable state
TFs to convert fibroblast to neuron
Ascl1
Brn2
Myt1I
Change gene expression - altering cell type
Gene regulation - activation
DNA demethylation (permissive)
Active histone marks (permissive?)
Transcriptional activator proteins (instructive)
Transcription release
RNA processing
RNA stabilisation (via proteins or absence of miRNA)
Translation (& protein modification)
Gene regulation - repression
DNA methylation
Repressive histone marks
Transcriptional repressor proteins
Transcription pausing
RNA processing
RNA destabilisation (via proteins or miRNA)
Translation (and protein modification)
Regulation at chromatin level - histones
DNA wrapped around histone octamer of 4 core histones
H3
H4
H2A
H2B
Have n terminal tails that can be modified (acetylation, methylation)
Certain modifications correlate activation or repression
Catalysed by particular enzymes
These marks change dynamically during development
Histones keep DNA packaged
Can actively influence expression
Histone acetylation
Usually on lysine
Neutralises lysines +ve charge
Weakens histone’s interaction with -ve charged DNA backbone
Losses DNA association
Makes genes more accessible to transcription machinery
Deacetyltransferases remove the acetylation
Reinstating the interaction of lysine with DNA backbone
repressive again
Histone deacetylase complexes
Histone deacetylases are part of complexes
Recruit other factors that also repress transcription
Eg NuRD complex
Sin3 complex
REST complex
Polycomb complex
Contain enzymes that catalyse H3K27 METHYLATION
Represses transcription
By enabling recruitment of proteins that modulate chromatin and transcription
Is important for maintaining correct gene expression in differentiated cells
Polycomb mutants
Fail to establish cell identity - homely if transformations
Mine. With mutations in PRC2 component fail to gastrulate
Can’t see in embryo but mutant ES cells in dish -
ES cells are fine and can differentiate OK
But differentiated cells don’t have the correct expression profile
So mouse fails to gastrulate as differentiated cells at gastrulation have wrong gene profile so act incorrectly
NuRD component mutations
Mutant ES cells can renew but are unable to initiate differentiation unless v strong cues are given
NuRD complex important for establishing correct gene expression so cells CAN differentiate
Role of repressive complexes in development
Transcription factors initiate changes in gene expression
Then chromatin modifications stabilise these changes by enforcing on/off state
LOCKING IN
Or alternatively:
Chromatin modifiersser particular gene activation threshold
SETTING THRESHOLDS
Epigenetic marks
Epigenetic marks: accessibility of binding sites on DNA
-help regulate gene expression and can help cells remember their history
Important as allows cell to integrate information that arrived at different times
And because same signals are often Used to generate different cell types
Epigenetic marks and Locking in
2 genes In development
1st signal
Initiates gene expression change
Chromatin modification Locks In the change
2nd signal comes that can potentially activate both of these genes
But gene 2 cannot activate due to the Epigenetic marks from chromatin modification
Epigenetic marks let the same signal have a different effect in different contexts
Allows the cells to integrate into that arrived at different times because same signals often used to generate diff cell types
Setting a threshold for lineage commitment
Depending on the modification, DNA is tighter or looser
Influences access by transcription machinery
Tighter = decreased probability of transcription
So will need more transcription signal/signal to stay longer
Allows for MORPHOGEN GRADIENTS
Morphogen gradients and thresholds in developmental patterning
Different modifications in different genes
Different tight/losseness in different genes
So different reaction to morphogen signal depending on its concentration
(Only cells closest to source will have highest thresholds crossed)
Regulation at transcriptional level - promoters and enhancers
Depends on recruitment of RNA pol II
TFs bind promoter
Can help to recruit/stabilise the machinery
Can also bind long way upstream, downstream, within introns - and stil control expression (far away binding is binding at enhancers)