Tijmen Lourens Summary Epigenetics and Gene Editing
Epigenetics and Gene Editing
Lecture 1
Epigenetics:
- Heritable, yet reversible changes in genome functioning, not encoded in the DNA
sequence
-
Induced Pluripotent Stem Cells: iPSCs: cell from human can be reprogrammed to stem cell
state.
Centromere: keeping the two chromatids together during mitosis.
Interphase is the most common phase, here the DNA is packed in
nucleosomes. During Mitosis (M-phase) the DNA is fully condensed.
Organization of chromatin:
- Interphase chromatin: fibers, roughly two types:
o Heterochromatin → very dense
o Euchromatin → more loose
- Tail of histone H3 is heavily subjected in post-translational
modification
o For all histones the tail sticks out
- Dimer of histones is formed between two different types of
histones, then these two bind again to form tetramer.
Nucleosomal DNA:
- No particular sequence, affected by DNA binding protein
- Tight association DNA-histones
- Breathing Is unregulated, protein is
regulated
o This breathing happens really short
and makes the DNA accessible for a
short period of time.
Chromatin remodelling:
- ATP dependent (controlled)
- Need to be recruited, need to know what to
do
o Nucleosome sliding makes sure some
parts become accessible / inaccessible
,Tijmen Lourens Summary Epigenetics and Gene Editing
Chromatin compaction: linker histone H1
- 1 molecule present per nucleosome core
- Binds DNA and protein
- Larger than other (individual) core histones
o Determines direction ‘nucleosome-outgoing’ DNA
- Histone 1 plays a role in compaction in bead on string configuration
- Tentacles seek contact with each other in order to come closer
o Can cause DNA around complex to get closer or farther away
Conclude this part:
- DNA is organized in nucleosomes
- Nucleosomes form chromatin fibers
- Chromatin compaction differences
o (euchromatin <-> heterochromatin (condensed))
- Chromatin is dynamic (+/- ATP):
o remodeling influences accessibility DNA
- Next:
→ chromatin types can be passed on to next generation of cells
→ Þ chromatin types associate with gene expression levels
EXAM! Very important to realise: 40% = fast majority (euchromatin) of DNA is open but not
actively expressed.
Also:
- Facultative heterochromatin: regulated if it is active/inactive
- Constitutive heterochromatin: permanent inactive
,Tijmen Lourens Summary Epigenetics and Gene Editing
Heterochromatin structure spreading:
- Position effect: active gene translocated to heterochromatin area → inactive
(silencing)
- Barrier: chromatin likes to spread until it comes across a barrier
o If there is no barrier between hetero- and euchromatin after translocation --.
Spreading of heterochromatin
Heterochromatin spreading and maintenance:
position effect variegation (PEV)
Variegation = “to make varied in appearance”
different appearance within one tissue
- White gene active = red pigment
- White gene inactivated = white spots
Acetylation: removing positive charge results in more ‘open’ chromatin structure →
expression activation (DNA is negatively charged)
Phosphorylation: introduces negative charge = ‘open’ chromatin structure → loosening up
its compaction by making the compound less positive!!!
Mutually excluded: if there is one modification the other one does not fit. (if a lysin is
acetyled it cannot be methylated also)
Methylation does not mean silencing directly, it can also associated with activation →
different tags recruiting proteins
, Tijmen Lourens Summary Epigenetics and Gene Editing
Summary:
- DNA in nucleosomes
o Packaging
o Controlling accessibility
- Nucleosomes exist in different forms:
o Histone modification (writers/erasers)
o Histone variants
- Different chromatin types: dynamic
o Eu-versus heterochromatin (chromatin
remodellers)
o Spreading, maintenance, transcription
Histone acetylation (in contrast to methylation) is always
associated with active gene expression.
Reader-writer complex binds to DNA sequence → reader-writer
complex spreads heterochromatin-specific histone tail
modifications and heterochromatin-specific protein bind →
heterochromatin spreads until it encounters a barrier DNA
sequence
- Reader-writer mitigates the process of heterochromatin
spreading over Reader Complex
- Reader-eraser protein binds and removes
heterochromatin-specific marks
- Erasers can also erase activating modifications to induce
silencing
Epigenetics and Gene Editing
Lecture 1
Epigenetics:
- Heritable, yet reversible changes in genome functioning, not encoded in the DNA
sequence
-
Induced Pluripotent Stem Cells: iPSCs: cell from human can be reprogrammed to stem cell
state.
Centromere: keeping the two chromatids together during mitosis.
Interphase is the most common phase, here the DNA is packed in
nucleosomes. During Mitosis (M-phase) the DNA is fully condensed.
Organization of chromatin:
- Interphase chromatin: fibers, roughly two types:
o Heterochromatin → very dense
o Euchromatin → more loose
- Tail of histone H3 is heavily subjected in post-translational
modification
o For all histones the tail sticks out
- Dimer of histones is formed between two different types of
histones, then these two bind again to form tetramer.
Nucleosomal DNA:
- No particular sequence, affected by DNA binding protein
- Tight association DNA-histones
- Breathing Is unregulated, protein is
regulated
o This breathing happens really short
and makes the DNA accessible for a
short period of time.
Chromatin remodelling:
- ATP dependent (controlled)
- Need to be recruited, need to know what to
do
o Nucleosome sliding makes sure some
parts become accessible / inaccessible
,Tijmen Lourens Summary Epigenetics and Gene Editing
Chromatin compaction: linker histone H1
- 1 molecule present per nucleosome core
- Binds DNA and protein
- Larger than other (individual) core histones
o Determines direction ‘nucleosome-outgoing’ DNA
- Histone 1 plays a role in compaction in bead on string configuration
- Tentacles seek contact with each other in order to come closer
o Can cause DNA around complex to get closer or farther away
Conclude this part:
- DNA is organized in nucleosomes
- Nucleosomes form chromatin fibers
- Chromatin compaction differences
o (euchromatin <-> heterochromatin (condensed))
- Chromatin is dynamic (+/- ATP):
o remodeling influences accessibility DNA
- Next:
→ chromatin types can be passed on to next generation of cells
→ Þ chromatin types associate with gene expression levels
EXAM! Very important to realise: 40% = fast majority (euchromatin) of DNA is open but not
actively expressed.
Also:
- Facultative heterochromatin: regulated if it is active/inactive
- Constitutive heterochromatin: permanent inactive
,Tijmen Lourens Summary Epigenetics and Gene Editing
Heterochromatin structure spreading:
- Position effect: active gene translocated to heterochromatin area → inactive
(silencing)
- Barrier: chromatin likes to spread until it comes across a barrier
o If there is no barrier between hetero- and euchromatin after translocation --.
Spreading of heterochromatin
Heterochromatin spreading and maintenance:
position effect variegation (PEV)
Variegation = “to make varied in appearance”
different appearance within one tissue
- White gene active = red pigment
- White gene inactivated = white spots
Acetylation: removing positive charge results in more ‘open’ chromatin structure →
expression activation (DNA is negatively charged)
Phosphorylation: introduces negative charge = ‘open’ chromatin structure → loosening up
its compaction by making the compound less positive!!!
Mutually excluded: if there is one modification the other one does not fit. (if a lysin is
acetyled it cannot be methylated also)
Methylation does not mean silencing directly, it can also associated with activation →
different tags recruiting proteins
, Tijmen Lourens Summary Epigenetics and Gene Editing
Summary:
- DNA in nucleosomes
o Packaging
o Controlling accessibility
- Nucleosomes exist in different forms:
o Histone modification (writers/erasers)
o Histone variants
- Different chromatin types: dynamic
o Eu-versus heterochromatin (chromatin
remodellers)
o Spreading, maintenance, transcription
Histone acetylation (in contrast to methylation) is always
associated with active gene expression.
Reader-writer complex binds to DNA sequence → reader-writer
complex spreads heterochromatin-specific histone tail
modifications and heterochromatin-specific protein bind →
heterochromatin spreads until it encounters a barrier DNA
sequence
- Reader-writer mitigates the process of heterochromatin
spreading over Reader Complex
- Reader-eraser protein binds and removes
heterochromatin-specific marks
- Erasers can also erase activating modifications to induce
silencing
