BC 563 Chromatin

What is charge of histones

Mostly positive, except acidic patch

How do linker histones interact with DNA

moslty through arginines

What do most PTMs do

promote or inhibit action of proteins, except sometimes acetylation loosens histone

What do histone chaperones do

facilitate ATP independent histone folding, deposition and removal

What do chromatin remodeling enzymes do

use ATP to altern nucleosomes

What are 4 domains of histone remodelers

ISWI, CHD, SWI/SNF, INO80, all have lobe 1 and 2 with different additions

WHat is 10nm fiber

nucleosomes along DNA strand

How were 10nm fibers originally reconstituted in vitro

using DNA and recomb histones, with Nap1 and ISW2, but not uniformly phased nucleosomes

How are 10nm fibers formed now

Going from high salt to low salt using widom sequenced

WHat are limitations of widome sequences

Unusually bendable, unusually twistable, periodic and non random sequences

What are two methods to examine histone placement

MNase seq abnd restriction digest

How are nucleosomes positioned in eukarotes

nucloeosome depleted region before promoter, then nucleosome free region at promoteer, then very apparent nucleosome patterns for a few hundred base pairs

What does ISW1a do

sets spacing

WHat does Ino80 do

contributes to spacing, competes with isw1a

What contributes to NDRs

RSC< INO80, ISW2, poly dT and poly dA tracks

When do 10nm fibers form 30nm fibers

higher salt, analyzed by sedimentation velocity analytical ultracentifugation

WHat does linekr histone do to 30nM fibers

increases compaction, stabilizes 30nm folding at lower salt, n+5 disrupt compaction, n+10 compact tidily

What does 30nm fiber compaction require

histone tails, H4 interacts with acidic patch to help pack

What does acetlyation do to 30nm folding

disruots, d

What is structure of 30nm fiber

crisscrosses back and forth

How is chromatin organized in cell

DNA nucleosomes, loops, domains, Compartment A and B, territory

how does DNA exist in cells

in clutches, not 30nm fibers

10nm fiber and 30nm fiber similarities

Compaction driven by cation conc, requires H4 tail basic interacting with acidic patch, compaction transcriptionally repressive

What is RABL organization

centromeres cluster at spindle pole body/centrosome (helped with heterochromatin and nuclear membrane proteins)

what are LADs

lamina associated domains (b)

What are NADs

nuclear associated domains (B)

What are tads

topologically associated domains

What domains are active and inactive

Tads are active, nads and lads are inactive

What is SMC

structural maintinence of chromosomes help form loops

What is cohesin loaded by

NIPBL

What is cohesin unlodaded by

WAPL

What are megadomains

nested tads

WHat are ordinary domains

compartments

How does CTCF stop extrusion

n term interacts with stag 1 and 2

What do TADS do

function in far away enhancers, can enhance or repress

What else do TADs do

promote enhancer promoter contact inside loop, insulate against outside contacts

What are two types of heterochromatin

facultative and constitutive

What is facultative chromatin

can convert to euchromatin through acetylation or demethylation

what is constitutive chromatin 

not really active ever

how is constitiutive chromain mediated

HP1

how is facultative chromain mediated

Polycomb

what does HP1a do 

creates phase separated droplets and binds h3k9me

What happens during mitotic chromatin compaction

TADS and compartments are lost

When is cohesin removed in cells

during metaphase

what does condensin 1 do

scrunches things together

What does condensin II do

links things together

What does Ki 67 do

keeps chromosomes during mitossi by coating all in positive charge

When are TADS and compartments restored

during G1