Epigenetics + Histone Modification Flashcards
1
Q
Nucleosomes
A
- block RNA polymerase II from gaining access to promoters
- need to decondense DNA to open
- addition of acetyl groups to histone tails remodel it so that the DNA is accessible for transcription
2
Q
Changing chromatin template to allow access of TFs
A
-opening chromatin through directed modification of histone tails (acetylation and methylation)
Histone modification by HAT and HMT
- opening of chromatin through directed nucleosome mobilization
- ATP-dependent process
- positioning of nucleosomes creates promoters with different requirement for remodelling
- enrichment of nucleosomes in promoter region
- Swi/Snf: removal of nucleosome with histone variants
- histone variants can direct function
- recruit remodelling factors/assembly factors
- HDACs: suppression of genes
- HATs: expression of genes
3
Q
Conrad Hal Waddington
A
- coined term epigenetics to mean above or in addition to genetics to explain differentiation (1942)
- myoblasts can only form muscle cells
- keratinocytes only form skin cells
- hematopoietic cells can only become blood cells
- but all have identical DNA sequence
4
Q
Epigenetics
A
- described phenomena in which genetically identical cells or organisms express their genomes differently, causing phenotypic variance
- information coded beyond the DNA sequence
- covalent modifications to DNA
- modifications to chromatin structure
-heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in underlying DNA sequence
5
Q
Epigenomics
A
- the same of genome wide epigenetic patterns, distinguishes and defines one tissue from another, stem cells from somatic cells, and ages from young cells
- cloning not just DNA but also epigenomic profile
6
Q
Pathways for environmental gene programming
A
- epigenator (differentiation signals, temperature variations)
- extracellular environment
- epigenetic initiator (DNA binding factors, non-coding RNA) in nucleus
- epigenetic maintainer (histone/DNA modifiers, histone variants)
7
Q
Epigenetic mechanisms
A
-key determinants for organization and expression of the genome
- RNA interference
- Histone modification
- DNA methylation
8
Q
Biological examples of epigenetic phenotypes
A
- twins
- Barr body
- polythene chromosomes
- yeast mating types
- blood smear
- tumor tissue
- mutant plant
- cloned cat
9
Q
Genetically identical - epigenetically variable
A
- almost all cells in our body are genetically identical but generates different cell types
- organized into different tissues and organs and express different proteins
- epigenetically variable
-
10
Q
Histone tails
A
-N-terminal tails point outward and is available for interaction with cell signalling pathways
11
Q
Histone modifications
A
- covalent attachments to amino acids of histones (usually side chain groups)
- affect affinity of histone to DNA and other proteins
- affect nucleosome and higher order DNA structures
- predominantly added to histone tail
- histone modifications are POST TRANSLATIONAL modifications
12
Q
Types of histone modifications
A
- Acetylation
- modifies lysine
- Methylation
- modifies lysine and arginine
- Phosphorylation
- serine and threonine
- before acetylation “primes”
- Ubiquitination
- lysine
- cell death/degradation
13
Q
Evidence for a histone code
A
- specific modifications correlate with specific processes
- specific modification patterns and sequences
- interactions of specific modified residues with classes of protein domains
- epigenetic code includes
1. Stable (not transient) through cell cycle (possible source of inheritance)
2. Heritable (through cell generations)
3. Consistent (always associated with defined chromatin behaviour)
4. Predictive (upon discover of new modification)
14
Q
Links between histone acetylation and gene activation (transcription)
A
- acetylated histone tails enriched in transcribed chromatin
- immunofractionated chromatin: acetylated fraction enriched in active chromatin
- neutralizing mutations in histone tails affect gene expression
- changes in levels of acetylation using inhibitors of deacetylation enhance gene expressions
- chromatin immunoprecipitations (ChIP) assays show enrichment of acetylated histone in active promoters
- acetylation makes nucleosomes DNA more accessible for TF binding
- a role in potentiation towards the gene being transcribed
15
Q
Chromatin Immunoprecipitation
A
- Cross-link protein to DNA in living cells with formaldehyde
- increase sulfur bonds to make tissue stick together
- fixing brain tissue to remove blood so it doesn’t contaminate DNA you want to look at
- Break open cells and shear DNA
- 200bp
- Add pre-blocked Protein G agarose beads
- Add primary antibody of interest
- Immunoprecipitate to enrich fragments bound by protein of interest
- Reverse cross-links and treat with proteinase K
- purifying DNA associated with acetyl-histone protein
- Detect and quantify precipitated DNA through PCR and hybridization methods
