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Vertebrate development > Basics of gene regulation > Flashcards

Basics of gene regulation Flashcards

1
Q

Zygotic gene activation

A

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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2
Q

Initiation of embryonic gene transcription

= maternal to zygote transiton

A

2 stages:
1. ZGA
= zygotic gene activation

  1. MGA
    = mid-preimplantation gene activation
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3
Q

ZGA commences…?

A

2 cell stage - mice

4-8 cell stage in humans, cows, sheep

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4
Q

Cellular transitions

3 stages

A
  1. activation of gene expression
  2. modify the chromatin status to stabilise gene expression
  3. remove existing gene products to clear out previous cellular program

Can occur simultaneously or in different order

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5
Q

Cellular transitions occur..?

A

Throughout life

- from conception to adult regeneration

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6
Q

2 types of gene expression

A

Genetic based
- sequence determinants

Epigenetic based

  • non-sequence based
  • enviro influenced
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7
Q

Epigenetic modifications

A

DNA methylation

Histone modification

Nucleosome phasing + remodelling

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8
Q

Epigenetic writers

Epigenetic erasers

Epigenetic readers

A

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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9
Q

Combinatorial epigenetic marks

A

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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10
Q

Active marks

A

H3K4me3
= creates a + charge

H3 + H4 acetylation

DNA hydroxymethylation (5hmc)

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11
Q

Silent marks

A

H3K27me3

H3K9me3

DNA methylation (5mc)

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12
Q

Stem cell differentiation

A

Must decide whether to proliferate or differentiate

1 daughter cell divides
1 differentiates

Can form committed progenitors
(divide or differentiate)

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13
Q

Stem cells

- bivalent poised genes

A

= 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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14
Q

1st major morphological changes in embryo

A

4 cell stage
= epigenetic asymmetry

8 cell stage
= polarisation + compaction

16 cell stage
= blastomeres differentiate into ICM or TE

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15
Q

Epigenetic heterogeneity…

A

biases cells toward 1 fate or another

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16
Q

8 cell stage

- polarisation

A

Blastomeres begin to establish apical + basolateral domains

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

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17
Q

8 cell stage

- compaction

A

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

18
Q

What follows compaction + polarisation?

A

1st spatial segregation of cells

  • > 2 separate populations
  • > will establish the 1st distinct cell lineages
19
Q

Formation of pluripotent ICM + TE

A

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)

20
Q

Primitive endoderm forms

A

Extra-embryonic membranes

21
Q

Pluripotent epiblast forms

A

Entire embryo

22
Q

Differentiating primitive endoderm + epiblast cells

A

Gata6 cells
= PE

Nanog cells
= EPI

23
Q

TFs that promote proliferation

A

Oct4
Sox2
Nanog

24
Q

TFs that promote differentiation

A 
Gata3
Tead4
Cdx2
Klf5
EOMES
25
Q

Gata2, Gata 3 + Cdx2 role

A

Promote + maintain TE differentiation

26
Q

Tead4 + its co-activator Yap1 role

A

Maintain expression of Gata3 + Cdx2 in outer cells

Yap1 shuttles between nucleus + cytoplasm

  • its phosphorylation state determines its location
27
Q

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

A

ICM
- Oct4

ICM
- Cdx2

28
Q

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

A

Tead4

29
Q

Transcription factor

- structure

A

DNA-binding domain
= recognises sequence

Activation domain
= activates other proteins

Interaction domain
= interacts w/ other TFs or chromatin modifiers

30
Q

TF families

A

Share common DNA-binding domain

31
Q

Zinc finger

C2H2

A

TFs use Zinc to stabilise their DNA-binding domains

  • most have at 3-14 fingers
  • > increasing the contact with DNA
32
Q

Zinc finger

C2H2

A

2 cysteine residues + 2 histidine residues interact w/ a zinc ion

-> stabilises the finger of amino acids associated w/ the DNA

33
Q

Gata

A

Can bridge 2 DNA fragments

34
Q

POU proteins

e.g.

A

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

35
Q

HMG-box domain factors

A

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

36
Q

Pioneering TFs

A

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

37
Q

TEA domain

= TEAD family

A

This DNA binding domain has a consensus DNA sequence:
5’-CATTCCA/T-3’

= the MCAT element

38
Q

YAP + Sox2

A
  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
39
Q

Hippo pathway

A
  • evolutionary conserved

- important in growth + organ size + development

40
Q

Hippo pathway proteins

A

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

41
Q

Fewer TFs than cell types…

A

Key is the combo of TFs + chromatin

Vertebrate development (12 decks)

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