Basics of gene regulation during development and cell differentiation Flashcards
What is the purpose of asymmetric cell division?
To diversify cell functions and differentiate.
What happens in cell proliferation?
The total number of cells increases but the size of the cell does not change.
What are the two stages in embryonic gene transcription?
The first stage is zygotic gene activation and the second stage is mid preimplantation gene activation.
What are the three stages of differentiation?
Activation of gene expression, modifying the chromatin status to stabilize gene expression and removal of existing gene products to clear out the previous cellular program.
What are the two bases behind gene expression?
Genetic based and epigenetic based.
What are the differences between the two types of gene expression?
Genetic based involves sequence determinants whereas epigenetic based involves non-sequence based aspects such as the environment.
What is epigenetics?
A level of gene regulation that is not determined solely by the gene sequence. It is a sudden change in the way the genome is working that doesnt involve genetic mutation/genome changes.
What are some examples of epigenetic factors?
Nucleosome phasing and remodelling, DNA methylation, nucleosome phasing and remodelling.
What are writers in epigenetics?
Things that pit marks on such as transferases, acetylases, enzymes.
What are the erasers in epigenetics?
Things that remove markers.
What are the readers in epigenetics?
Transcription factors - proteins that bind to DNA depending on the markers.
What are some of the combinatorial epigenetic marks?
Active, permissive, repressed, inactive.
What is the inactive state of DNA?
DNA is tightly wound and histones are close together.
What are some active markers?
H3K4me3, H3 and H4 acetylation, DNA hydroxymethylation.
What are some silent markers?
H3K9me3, H3K27me3, DNA methylation.
What is asymmetric proliferation?
Two daughter cells are divided but the two resulting cells are not the same - one resulting cell will continue to differentiate.
What are progenitors?
Committed cells that are will become the differentiated cells.
What does the prescence of active and silent markers on the same nucleosome result in?
The flexibility to divide asymmetrically.
When is epigenetic asymmetry present in the embryo?
The 4 cell stage.
When does polarisation and compaction occur in the embryo?
The 8-cell stage.
What are the two fates of cells in the embryo?
Inner cell mass or trophectoderm.
What does it mean that stem cells have bivalent poised genes?
They contain histone modifications that are associated with gene activation and suppression. The genes are repressed in progenitors and silent in differentiated cells. This gives the ability of cells to divide asymmetrically.
What does epigenetic heterogenity allow?
It biases a cell towards one fate or another.
At what stage do blastomeres retain the capacity to differentiate into ICM or trophectoderm?
The 16 cell stage.
Why do biases in cell fate arise at the 4 cell stage?
Biological noise and early heterogeneities in blastomeres in epigenetic modifications and transcription factor binding to DNA. These differences can be amplified until two lineages are defined.
What marks the first major morphological changes in the embryo?
The onset of polarisation and compaction at the 8 cell stage.
What is significant about the cells before the 8 cell stage?
They are all morphologically similar.
What happens to cells once they have reached the 8 cell stage?
Within 1-3 hours, blasomeres begin to display the first outward signs of radial polarity with the establishment of distinct apical and basolateral domains.
What mechanisms is polarisation thought to be regulated by?
Post-translational mechanisms.
What does compaction result in?
Maximisation of cell-cell contact area and flattening of the outer surface of the blastomeres to form a tightly packed mass of cells with indistinct cell boundaries.
What is apical/basal polarisation?
When transcription factors vary between the apical and basal portion of the embryo.
What are compaction and polarisation followed by?
The first spatial segregation of cells into two separate populations that will establish the first distinct cell lineages.
What are the inner cells surrounded by between the 8 and 16 cell stage?
They are completely surrounded by basolateral membrane and cell-cell contacts.
What will the inner cells between teh 8 and 16 cell stage differentiate to form?
The primitive endoderm - this gives rise to extra-embryonic structures and the pluripotent epiblast - which the entire embryo proper is derived from.
What happens to the cells on the outside surface between the 8 and 16 cell stage?
They retain an apical surface which is devoid of cell-cell contacts and exposed to the exterior. These cells will then differentiate to form the trophectoderm, which gives rise to the placenta.
What factors promote proliferation?
Oct4, Sox2, Nanog.
What factors promote differentiation?
Tead4, KLF5, CDX2, GATA3, EOMES.
What are important factors in promoting and maintaining trophectoderm differentiation?
Gata2, Gata3 and Cdx2.
What maintains the expression of Gata3 and Cdx2 in outer cells?
Tead4 and Yap1.
What does Yap1 do?
It shuttles between the nucleus and the cytoplasm. Its phosphorylation state determines its subcellular localisation.
When does Cdx2 become present in the embryo?
8 cell stage - in all cells at the 8 cell compacted morula stage. OCt4, Sox2, Nanog and Tead4 are still present at this stage.
What other factors are expressed in the embryo at later cell stages?
Sox17, Gata4, Sox7.
What happens in zygotic gene activation?
Several trophectoderm specific factors (including TEAD4) are induced.
What is present at the 8 cell stage, in terms of trophectoderm development?
Cells are located in an inside vs. outside position - this instigates the trophectoderm development. This continues until the TE-determination phase.
What is the TE determination phase important in?
It ensures the development of the functional TE-lineage in a matured blastocyst.
What is Oct4 required for?
Formation of the ICM.
What is Cdx2 required for?
Trophectoderm development.
What are transcription factors?
A protein that controls the rate of transcription. They are proteins with different domains.
What can be used to stabilise DNA binding domains?
Zinc.
What are zinc fingers?
When zinc is in the middle of a molecule and histones bind around them to create different types of fingers. They can bind in the major and minor groove in the DNA.
What are the function of zinc fingers?
The can bind in and twist and bend the DNA - they act as paper clips to hold the DNA in specific places.
What is GATA?
A transcription factor that can bridge two DNA fragments.
What are pou domains?
Regions that have a bipartite DNA-binding domain with two helix-turn-helix subdomains, a POU specific domain (POUs) and a homeodomain (POUhd) connected by a variable linker region.
What in the POU domain binds to the major groove of DNA?
The globular region of POUs and POUhd.
What in the POU domain binds to the minor groove of DNA?
The N-terminal tail of POUhd.
Where is the POU domain found?
In Oct4.
What are HMG box factors?
They are domains which contain three alpha helices separated by loops. They alter DNA architecture by inducing bends upon binding.
What type of DNA conformation do HMG box factors bind?
B-type DNA conformations (kinked or unwound_ with high affinity.
What are pioneering factors?
They open up that the chromatin so that other factors can get there.
What is the MCAT element?
A consensus DNA sequence 5’-CATTCCA-3’.
What is a consensus sequence?
A sequence of DNA having similar structure and function in different organisms.
Where is Yap produced?
In the inner cell mass.
What happens when Yap translocates to the nucleus?
SOx2 is expressed.
What happens if there is no Sox2 present/Yap in the nucleus?
These cells will die due to apoptosis.
What pathway does yap belong to?
The hippo pathway.
What is the hippo pathway?
It is a pathway that controls organ size in animals through regulation of cell proliferation apoptosis. The protein kinase hippo is a key factor. It is evolutionary conserved and important in development.
What is YAP?
Yes-associated protein 1. Do not bind to DNA themselves.
What is TAZ?
Transcriptional covactivator with PDZ binding motif. Do not bind to the DNA themselves.
What do YAP and TAZ have in common?
They are both transcriptional coactivators that do bind to DNA themselves.
What do TAZ and YAP interact with?
Tead - the TEA family of TF.
What does the hippo pathway result in the activation of?
Proliferation genes.
