Basics of gene regulation Flashcards by Rosie Liddell

Zygotic gene activation

When moving from a terminally differentiated oocyte
to a zygote

Then maintaining balance between increasing cell no.s + changing cell functions

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Initiation of embryonic gene transcription

= maternal to zygote transiton

2 stages:
1. ZGA
= zygotic gene activation

MGA
= mid-preimplantation gene activation

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ZGA commences…?

2 cell stage - mice

4-8 cell stage in humans, cows, sheep

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Cellular transitions

3 stages

activation of gene expression
modify the chromatin status to stabilise gene expression
remove existing gene products to clear out previous cellular program

Can occur simultaneously or in different order

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Cellular transitions occur..?

Throughout life

- from conception to adult regeneration

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2 types of gene expression

Genetic based
- sequence determinants

Epigenetic based

non-sequence based
enviro influenced

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Epigenetic modifications

DNA methylation

Histone modification

Nucleosome phasing + remodelling

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Epigenetic writers

Epigenetic erasers

Epigenetic readers

Put marks on
e.g. methylases

Take marks off
e.g. demethylases

Bind to DNA but don’t change marks
- interpret info conveyed by epigenetic marks

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Combinatorial epigenetic marks

Active
= histones far apart
so TFs can bind to DNA
= euchromatin

Permissive

Repressed

Inactive
= DNA tightly wrapped around close together histones
= heterochromatin

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Active marks

H3K4me3
= creates a + charge

H3 + H4 acetylation

DNA hydroxymethylation (5hmc)

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Silent marks

H3K27me3

H3K9me3

DNA methylation (5mc)

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Stem cell differentiation

Must decide whether to proliferate or differentiate

1 daughter cell divides
1 differentiates

Can form committed progenitors
(divide or differentiate)

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Stem cells

- bivalent poised genes

= simultaneous presence of histone modifications that activate and repress genes
- give flexibility to be able to divide asymmetrically

e.g.
Stem cell = bivalent gene
Committed progenitor = repressed gene
Differentiated cell = silent gene

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1st major morphological changes in embryo

4 cell stage
= epigenetic asymmetry

8 cell stage
= polarisation + compaction

16 cell stage
= blastomeres differentiate into ICM or TE

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Epigenetic heterogeneity…

biases cells toward 1 fate or another

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8 cell stage

- polarisation

Blastomeres begin to establish apical + basolateral domains

Doesn’t require transcription or translation
- regulated via post-translational mechanisms

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8 cell stage

- compaction

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Maximisation of cell-cell contact area
+ flattening of blastomere outer surface
-> forms tightly packed mass of cells w/ indistinct cell boundaries

What follows compaction + polarisation?

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1st spatial segregation of cells

> 2 separate populations
> will establish the 1st distinct cell lineages

Formation of pluripotent ICM + TE

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Cells on inside

surrounded by cell-cell contacts + basolateral membrane
form ICM (primitive endoderm + pluripotent epiblast)

Cells on outside
- an apical surface exposed to the exterior
- form TE
(gives rise to placenta)

Primitive endoderm forms

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Extra-embryonic membranes

Pluripotent epiblast forms

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Entire embryo

Differentiating primitive endoderm + epiblast cells

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Gata6 cells
= PE

Nanog cells
= EPI

TFs that promote proliferation

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Oct4
Sox2
Nanog

TFs that promote differentiation

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Gata3
Tead4
Cdx2
Klf5
EOMES

Gata2, Gata 3 + Cdx2 role

Promote + maintain TE differentiation

Tead4 + its co-activator Yap1 role

Maintain expression of Gata3 + Cdx2 in outer cells Yap1 shuttles between nucleus + cytoplasm - its phosphorylation state determines its location

In mice, which TFs are required for ICM and TE formation?

ICM - Oct4 ICM - Cdx2

Which TE-specific factor is induced during zygotic gene activation?

Tead4

Transcription factor | - structure

DNA-binding domain = recognises sequence Activation domain = activates other proteins Interaction domain = interacts w/ other TFs or chromatin modifiers

TF families

Share common DNA-binding domain

Zinc finger | C2H2

TFs use Zinc to stabilise their DNA-binding domains - most have at 3-14 fingers - > increasing the contact with DNA

Zinc finger | C2H2

2 cysteine residues + 2 histidine residues interact w/ a zinc ion -> stabilises the finger of amino acids associated w/ the DNA

Gata

Can bridge 2 DNA fragments

POU proteins | e.g.

Have a bipartite DNA-binding domain w/ 2 helix-turn-helix subdomains - globular regions bind to major groove - N-terminal tail of the hoemodomain binds to the minor groove e.g. Oct4

HMG-box domain factors

Contain 3 alpha helices separated by loops Only bind non-B-type DNA conformations (kinked or unwound) w/ high affinity Alter DNA architecture by inducing bends upon binding

Pioneering TFs

Look for their binding site and pull apart the chromatin via nucleosomes so other factors can bind -> activates genes

TEA domain | = TEAD family

This DNA binding domain has a consensus DNA sequence: 5'-CATTCCA/T-3' = the MCAT element

YAP + Sox2

1. Cytoplasmic YAP w/ low pluripotency 2. YAP translocates to nuclei in ICM 3. Variable TEAD activity + pluripotency 4. Cells not expressing Sox2 (unspecified cells) die via apoptosis 5. Formation of high quality EPI

Hippo pathway

- evolutionary conserved | - important in growth + organ size + development

Hippo pathway proteins

YAP = Yes-associated Protein 1 TAZ = Transcriptional co-activator with PDZ binding motif Both transcriptional activators - don't bind to DNA Interact w/ TEAD when they move into nucleus after being phosphorylated

Fewer TFs than cell types...

Key is the combo of TFs + chromatin

Basics of gene regulation Flashcards

(41 cards)