What is a nucleosome?
Necessary to package genomic DNA into nucleus in the form of chromosomes
- Tightly wound DNA is around histones forming nucleosomes
What is Heterochromatin?
The transcriptionally inactive region of a genome
- stains heavily and is very dense
- Localizes at nuclear envelope, often near the nuclear pore
What is euchromatin?
Actively transcribing region of the genome
- delicate, stains lightly
- May represent unwound DNA
What does it mean for regions to be in a “heterochromatinized” state?
A transcriptionally inactive region
Explain how yeast mating types are used to understand transcriptional repression
- Mating type is controlled by 3 genetic loci on the chromosome
- HML alpha and HMLa loci must first be silenced, otherwise cells will be diploid and cannot mate
Shows how silent mating type must be repressed so cells don’t become diploid and can still mate
What does transcriptional represssion depend on?
- Silencer sequences - can even block RNA pol III
- Histones affect repression, but regions around telomeres behave similarly
What 3 factors are required for silent mating type repression?
- RAP1: binds to DNA in the region of the silencer, also binds to repetitive sequence in telomeres
- SIR1: cooperates with RAP1 and is important for binding the silencer region in silent mating type loci
- SIR2, 3, and 4 bind to histone tails and recruit SIR2, and form large complexes with telomeric DNA
Sir 2 is also believed to play a major role in aging
How are histones important?
Histones have positive charged inner region and disordered internal tails
- Histone tails are sometimes modified post translation: phosphorylation, methylation, ubiquitination, acetylation
H3K4 vs H3K9
- H3K4 - when methylated is associated with activation of transcription
- H3K9 - methylation is associated with inactivation of transcription
What does H3K9me3 do?
Methylates neighbouring histones - acts as an epigenetic reader and writer
Ensures daughter cell has some marks after cell division
What antibodies can be used for cHIP?
Proteins bound to chromatin can be isolated using antibodies - sequences can be determined
- Use of known primers to know whether a specific gene is affected
- Entire genome can be analyzed using NGS
- Compare cHIPS contained after NGS is carried out, can identify regions bound by TFs
What are histone acetyl transferases?
- Positive charge of N-terminal histone tail interacts electrostatically with DNA phosphate groups
- Inducing acetylaton of histone tails allows some transcriptional activators to overcome being repressed
*Induces acetylation, allowind some transcriptional activators to overcome repression
What happens when you acetylate a histone tail?
Give exmple with GCN4
You neutralize charge, allowing for chromatin to decondense
GCN4 is a TF - and need GCN5 to work (GCN4 uses GCN5 to open up chromatin so you have better access)
What do you need with an activator?
A repressor - it changes chromatin configuration by getting rid of acetylases, blocking activation
What are histone deacetylation complexes?
Used for transcriptional repressors to act
Removes acetyl groups on histone tails, giving rise to condensation of chromatin around DNA sequence
What are pioneer transcription factors?
DNA binding transcriptional activators that function by interacting with DNA via sequences exposed on the outside of the DNA
Have two HATs
- Recruit enzymes that alter the configuration of neighbouring histone tails, opening chromatin to permit association with TFa
What are epigenetics marks?
DNA marks read by specific proteins - then used to modify histones in proximity thougoh mSin3 recruitment
Histone marks can nucleate histone methyltransferase to repress gene activity across genetic region - often heritable marks
What do epigenetic readers do?
They ensure epigenetic marks are properly inherited by daughter cells
