Advanced Molecular Bio Exam 2 Epigenetics

polytene chromosomes

in drosophila salivary glands, divide without splitting into two cells, so you get multiple copies of the same gene stuck together

H4 tails

interact with the histones next to them setting up the next layer of DNA packaging

H3, H2A, H2B tails

poke through the minor groove, recruit nucleosome remodeling complexes

writer proteins 

place marks on histone tails 

reader proteins

recognize marks and recruit other proteins like DNA remodeling complexes that can shift and change histone orientation

eraser proteins

takes away marks from histones

acetylation mark 

weakens histone-DNA interactions and makes DNA less packaged 

methylation mark

activates or represses transcription

phosphorylation

influences histone structure and interactions

ubiquitination

regulates transcription and repair 

HAT writer

histone acetyl transferase

HD eraser

histone deacetylase

bromodomain protein

recruit’s chromatin remodeling proteins to open histones into euchromatin

chip seq analysis

chromosome immunoprecipitation sequencing, sonification breaks apart DNA, antibodies specific to particular histone modifications, PCR

barrier proteins

stop function of writers so they can only change packaging so far. keeps space between euchromatin and heterochromatin

tethering proteins 

nuclear lamina creates a matrix where DNA loops out from each side of the tether can have differing packaging states. 

gene regulation

tethering helps partition the genome into active and repressed compartments

maintaining chromatin structure

anchoring chromosomes so they can be folded into higher order looped structures

general rules of tethering—closer to the matrix 

less likely to contain genes and more likely to be packaged 

general rules of tethering—interior

tend to be less packaged and have a higher gene content

nucleosome repressor

binds to nucleosomes and prevents other writers and erasers from modifying proteins

strong modifying 

overpowers other modifying proteins to maintain a barrier 

dCTP methylation

initial methylation (de novo) DNMT3A DNMT3B, 2nd maintains it DNMT1

example of DCTP methylation

transcription factor binds to open chromosome until DNA gets methylated, TF no longer bind—Nucleosomes are repositioned and packaged

epigenetics agouti mouse example 

fat yellow mouse, skinny brown mouse, genetically identical but brown mouse is methylated and yellow mouse is unmethylated 

epigenetics Dutch hunger famine example

offspring of people who suffered during this time are more prone to obesity and diabetes

epigenetics bad vs good rat mom example

low maternal care—methylated, high anxiety and high cortisol

genetic imprinting 

genetically imprinted genes—-methylation patterns that depend on whether they came from mom or dad