Week 8 - Tues Flashcards
What is ChIP sequencing
Chromatin Immuno Precipitaton sequencing
-Tells where DNA targets specific protein of interest
-Can also be used to check for histone acetylation
What is RNA seq
Measures expression levels across genome
What is Epigenetics
Modifies chromatin by histone proteins or DNA by methylation to make long term changes in DNA expression
Bisulfite sequencing
Genomic technique to find positions where Cs have been methylated
True or false: Epigenetic modifications change the sequence of the DNA
False
-it does not change the sequence of DNA
Which form is inactive because transcription machinery cannot access DNA (heterochromatin or euchromatin)
Heterochromatin
Which form is active and accessible to transcription
(heterochromatin or euchromatin)
Euchromatin
What controls heterochromatin or euchromatin formation
How tightly DNA is stuck to histones
What are HATS (histone acetyl transferases)
Adds acetyl group
What are HDAC (histone deacetylases)
Remove acetyl group
Which increases transcription HATS or HDAC and why?
HATS because it makes tail (-) and since DNA is (-) it will repel and be loose allowing for TF to bind
Which decreases transcription HATS or HDAC and why?
HDACS because it makes tail (+) and since DNA is (-) it will attract and be tight preventing TF to bind
What is methylation
Methylation of Cs in CpG islands represses expression of adjacent genes
Methylation is used as a marker for what and how does it affect formation?
Methylation recruits HDACs which makes heterochromatin formation
What will hypermethylation do increase or decrease expression?
Decrease expression because it recruits HDACs
What is bisulfite sequencing
Used to locate methylated cytosines in genome
-Converts C to U
Does unmethylated cytosines turn a C into a U?
Yes, C turns into a U
Does methylated cytosines turn C into a U?
No it stays a C
How are the Us in bisultfite sequencing
read as Ts
How is labor divided in development?
- Regional specification –> sets up unique areas within embryo
- Differentiation –> process of cells becoming more specialized
What are the 3 types of stem cell potencies?
- Totipotent
- Pluripotent
- Multipotent
Which stem cell can differentiate to the most specific type of cell?
Multipotent cells can differentiate into specific cells
de-differentiation
reversing differentiation to produce induced stem cells
Spatial variation in environmental determinants is responsible for initiating
Regional specification
Gradients do what
set the stage for threshold induction of gene expression
