Gene Regulation 4 - Regulation of eukaryotic gene expression Packing and unpacking of DNA Flashcards
Learning Outcomes
Students will be able to
➢ explain experimental evidence that shows that almost all cell have the same
genome and that this genome is sufficient to give rise to a fully functional
eukaryotic organism.
➢ relate development and differentiation of a multicellular eukaryote to the
regulation of gene expression.
➢ discuss why eukaryotic control of gene expression is more complex than
prokaryotic gene expression.
➢ list levels at which gene expression is regulated in eukaryotes
➢ describe eukaryotic DNA packaging into chromosome structures
➢ relate packaging of DNA to gene expression.
If two cells share the same genome, how come they look
different and have different functionalities?
- Different cells differ in structure and
function.
➢ A neuron cells from the retina
receives electrical signals from
many other neurons and carries
them to many neighbouring
neurons via neurotransmitters.
➢ A liver cell is involved in many
metabolic processes. One of those
is the detoxification of alcohol via
the enzyme alcohol
dehydrogenase - The two cells have the same genes,
same genome. - They express different subsets of
genes leading to different subsets of
proteins which determine their
different shapes and functions.
Differentiation as a consequence of changes in gene expression
- In multicellular organisms, life begins as a single cell.
- In development, cells commit to specific fates & differentially express subsets of genes.
- Daughter cells may differ with respect to regulatory instructions & developmental fate, so new cells become different to
their parent cell.
Frog Embryo Development
Frog embryogenesis is characterised by cell division and cellular differentiation of pluripotent cells (in plants
meristem cells).
Pluripotent cell: immature stem cell that has the potential to differentiate into any of the three germ layers:
endoderm (gut, lungs and liver), mesoderm (muscle, skeleton, blood vascular, urogenital, dermis), or ectoderm
(nervous, sensory, epidermis), but not into extra-embryonic tissues like the placenta or yolk sac
Are losses or gains of genes driving changes during development?
Undifferentiated and Differentiated cells produce different specific mRNAs and proteins
Consider:
▪ A single fertilised egg cell develops into a multicellular organism with trillions of cells, ~ 200 different cell types.
▪ These cells are organised into tissues & organs performing different, specialised functions and morphologies.
▪ This requires that different cell types make different sets of proteins.
* The early embryo is characterised by rapid cell division followed by differentiation ➔ genes expressed will enable
the embryo to fulfil functions associated with division and differentiation appropriate to its developmental state.
* Differentiated cells will express genes that enables them to fulfil a specific function within an organism.
Let’s look at levels of Gene Expression
- Control of gene expression in eukaryotes occurs at
several levels:
1) Packing or unpacking DNA
2) Transcription
3) mRNA processing
4) mRNA export
5) Translation, mRNA stability and degradation
6) Post-translation protein modification
7) Protein stability and degradation
How is gene expression regulated in
Eukaryotes?
- Regulation of gene expression in eukaryotes is more complex than in
prokaryotes. - Control of gene expression in eukaryotes occurs at many levels:
How long is my DNA ?
DNA in each of our cells is about 2 to 3 meters long based on 3.2 x 109 nucleotides and
a length of 0.6 nanometers (10-9 m) per nucleotide.
This DNA has to fit into the cellular nucleus which is about 6 µm in size (10-6 metres)
Image result for eukaryotic cell microscope
If we would magnify the nucleus 1000 x to 6 mm, the total length of all the DNA in the
cell’s nucleus would be 2 - 3 km long
DNA in our whole body is about 2.04 x 1010 km ➔ 66.5 trips from
the earth to the sun and back
How to fit 2 meters of DNA into a nucleus of 6 µm diameter:
Package DNA around add histone H1
- The ‘string’ part of the beads on a string is formed by
unbound linker DNA DNA ~ 20 bp between nucleosomes. - The linker DNA is bound by the linker histone protein H1.
- The nucleosome plus the linker DNA and the linker histone
form the chromatosome. - The chromatosome contains about 166 bp of DNA.
- This condenses DNA from 2 nm to 11 nm.
How to fit 2 meters of DNA into a nucleus of 6 µm diameter:
Package DNA around core histones
Chromosome structure is regulated
- Gene expression, DNA replication, DNA repair requires access of proteins to the DNA.
- Along an interphase chromosome we can find regions that are:
– densely packed: heterochromatin ➔ DNA less accessible ➔ silent genes
– less densely packed: euchromatin ➔ DNA is more accessible ➔ expressed genes. - Eukaryotic cells have several ways to adjust the local structure of chromatin rapidly.
– Chromatin remodelling complex
– Reversible chemical modifications of histones
How to fit 2 meters of DNA into a nucleus of 6 µm diameter:
Using scaffold proteins
- Multiple nucleosomes wrap into a 30 nm fibre forming
heterochromatin or chromatin. - During mitosis and meiosis DNA can be packaged even more
into the metaphase chromosome (~1400 nm diameter). This
requires other sets proteins:
– Scaffold proteins determine and maintain the authentic
chromosome shape
– ensure that DNA winds up and unwinds without tangling.
– Packaged DNA molecule in a mitotic chromosome is
10,000 fold shorter than its fully extended length.
Visualising transcribed areas of chromosomes
▪ Chromosomes transform into the
lampbrush form in the growing
oocytes of most animals, except
mammals, during the diplotene stage
of meiotic prophase I.
▪ Opened loops of varying length are
areas of active transcription of many
genes.
▪ The light line in the centre of the
chromosome is scaffold made up of
non-histone scaffold protein
Chromatin Remodeling Complexes
- Chromatin Remodelling Complex: Regulatory proteins that use ATP (energy) to alter chromatin structure without
changing histone chemistry. - Bind directly to DNA and reposition nucleosomes ➔ DNA is accessible to proteins, e.g. to transcription factors.
- Example of ways in which remodeling occurs:
– Nucleosome slides along DNA, DNA that would normally be wrapped around the histones becomes exposed.
– Conformational change of nucleosomes, DNA or both, so the DNA is more exposed. - May work in unison with histone acetylation (see next slides)
Histone tail modifications determine active and repressive chromatin
- Histone tail modifications are Post-translational modifications (PTMs).
- PTMs are covalent modifications of a protein after protein biosynthesis (after translation).
- These modifications are done by enzymes (proteins).
- PTMs can regulate protein activities, localization, structure etc.
- PTMs of histone tails can lead to
- active, less densely packed DNA in euchromatin
- or to densely packed DNA in repressive heterochromatin
How do histones interact with DNA?
- Chromatin: DNA packaged with protein
- Most abundant proteins are histones
- Histone proteins contain basic amino
acids which are positively charged
– Lysine
– Arginine - The positive charges of these amino
acids can interact strongly with the
negative charges of the phosphate
groups in DNA = ionic interactions
Visualising histone modifications and chromatin structure
Chromatin during meiosis prophase:
* Pink shows histone modifications, here methylation of histone
proteins at lysins (K) of histone protein 3
* LEFT (H3K4me3): active chromatin, radially, loop-like structures.
* Bottom (H3K27me3): inactive, repressive chromatin
Acetylation of basic amino acids
Amino Acid Acetylation:
– Addition of an acetyl (CH3C=O-
) group to Lysine
▪ Acetylation of lysines is done by enzymes called
histone acetyltransferases = HATs
▪ Acetyl groups can be removed by other enzymes
called histone deacetylases = HDACs or HDs
➢Histone modification influences gene expression without changing the nucleotide sequence of the
DNA = type of epigenetic regulation
➢Epi means above or over
Decondensed chromatin
– Acetylated, active
– Acetylation neutralising positive charge of lysine
– Loose association of less positive histone with negative DNA ➔ prevents
ionic interaction of lysins with DNA
– DNA is accessible for proteins involved in gene transcription (RNA
polymerases, transcription factors…)
Histone modifications are a form of Epigenetic Regulation of
eukaryotic gene expression
Epigenetic
Modifications:
Heritable alterations that
are not due to changes
in DNA sequence.
▪ DNA methylation
▪ Histone modifications
Acetylation of histone protein tails
remodels chromatin
Condensed chromatin
– hypo-acetylated, inactive
– Tight ionic interaction of positively charged histone protein tails with
negative DNA
– Inaccessible DNA, not transcribed
Can you …
➢ … relate regulation of gene expression to the creation of a fully functional eukaryotic organism with many
different cell types?
➢ … compare levels of the regulation of gene expression in pro – and eukaryotes?
➢ … list levels at which gene expression is regulated in eukaryotes?
➢ … explain the necessity of DNA packaging into chromosomes?
➢ … describe levels of DNA packaging?
➢ … relate packaging of DNA to gene expression?
➢ … describe different ways in which DNA packaging occurs for example by chromatin remodeling or histone
protein modifications?
➢ … explain the definition for “Epigenetic Regulation” and relate this to histone modifications?
