Chromatin composition
How many base pairs are wrapped by an octamer?
(Extra 100 points: how many bp does tetramer vs h2a/h2b bind)
147, 90, 30
What technique was used starting in 1955 to see chromatin structure?
Metaphase spread
Using only octamers, DNA, and solution components (i.e. no other proteins), how can you reconstitute chromatin?
salt dialysis
Is chromatin liquid or solid on the mesoscale?
solid
Why is the Hi-C diagonal so intense
self-self contact (autocorrelation)
What are the canonical histones and how are they organized?
(H3/H4)2 and 2x(H2A/H2B)
STORM takes advantage of what intrinsic property of fluorophores?
photoblinking
What nuclease is commonly used to map nucleosome sites?
Mnase
What two components are typically present at TAD boundaries?
CTCF and cohesin
How are adjacent digested regions coupled in Hi-C?
DNA Ligase
What is the histone variant involved in binding centromeres?
CENP-A
What is the most commonly used technique to measure dynamic distance changes?
single-molecule FRET
What is a 601 sequence?
A nucleosome positioning sequence
what is the diameter of a single chromatin fiber?
10 nm
GRO-seq, CHIP-seq for histone marks, etc.
helix-loop-helix-loop-helix
What are two methods that use force feedback to measure nucleosome composition
AFM and Optical tweezers
What component of the an in vitro solution can you change to modify histone stability?
salt
About how big are typical chromatin domains?
~200 nm and/or ~200 kb
What do "corner peaks" on TAD triangles represent?
extra 100 pts: which type of organism are these most apparent in?
chromatin loops; mammals
Name the 4 most common histone tail modifications
acetylation, methylatoin, phosphorylation, ubiquitination
The diffraction limit prohibits us from resolving structures closer than ____ nm. Superresolution can bring us as low as __ nm.
250, 10
What two enzymes are most used to achieve well-positioned nucleosomes
nap1 and isw1a (will also accept chaperone and remodeler)
What's the structural difference between heterochromatin and euchromatin?
...
Hi-C contact frequency is built by sequencing hits. How is ORCA contact frequency built?
by spatial proximity (<150 nm)