Higher Order Chromatin and Epigenetics Flashcards
Cohesins
Proteins that hold sister chromatids together
Condensins
Proteins that help in DNA packing
30 nm fiber
More tightly packed than 10 nm fiber
Made up of wound-up 10 nm fiber
Attached to nuclear scaffold
10 nm fiber
More loosely packed than 30 nm fiber
“Beads on a string”
Bead- nucleosome
String- linker DNA
Nucleosome
DNA wound around histone core
DNA packing and expression of genes
More tightly packed, less expressed (transcriptional machinery can’t access DNA)
Histone octamer
8 proteins, 2 of each subunit (H2A, H2B, H3, H4)
Amino acids that make up histone tails
Lysine and arginine: basic amino acids-positively charged
Histone tail interactions
Tails interact with each other
Tails physically block transcriptional machinery
H1 histone
Non-core histone
Recruited to 10 nm fiber, causing nucleosome to condense into 30 nm fiber, so that the histone tails can interact
2 forms of 30 nm fiber
Solenoid (helical structure, short linker DNA)
Zigzag (more accessible form, longer linker DNA)
What influences whether the 30 nm fiber will form a solenoid or a zigzag
Level of expression of genes
Length of linker DNA
Area of chromosome
3 ways to change interaction of histones with DNA
Change nucleosome positioning
Nucleosome remodeling
Histone tail modification
Activators and nucleosome positioning
Activators can block histones from being able to bind to DNA
Repressors and nucleosome positioning
Repressors can recruit histones
Fluidity of macromolecules
Proteins don’t just sit on DNA- may unbind and re-bind
Areas of DNA that histones make contact with
Minor groove
Usually makes contact with A:T-rich regions (A:T-rich regions are flexible)
More C’s and G’s in regions that are highly expressed (general rule)
Nuclease-sensitivity assay
Active genes have HS (hyper-sensitive to endonucleases) sites where linker DNA is
- Treat DNA with DNase
- Remove proteins (histones)
- Gel electrophoresis, followed by southern blot to probe for DNA
- If nucleosome is present, large fragment will result; if no nucleosome is present, small fragments will result
Transcriptional access to nucleosome-associated DNA
DNA that is closer to the outside of a nucleosome is easier to access- little bits of DNA become unwound
SWI/SNF
Protein complex that facilitates chromatin remodeling
3 subdomains: torsion subdomain (top half of “pincher”), ATPase subdomain (makes “pincher” work), tracking subdomain (bottom half of “pincher”)
3 ways that SWI/SNF facilitates chromatin remodeling
Sliding DNA along histones
Ejection: getting rid of histone
Dimer exchange: exchanging parts of histone octamer
Sliding bulge model
SWI/SNF complex is on top of DNA wrapped around nucleosome
“Pinchers” (torsion subdomain and tracking subdomain) of SWI/SNF complex come together, pulling DNA around nucleosome
Bulge of DNA is present- not stable conformation
DNA ratchets through the tracking subdomain
Bulge moves around histone
Torsion subdomain resets and binds new DNA
3 ways to modify histone tails
Phosphorylation
Methylation
Acetylation
Phosphorylation of histone tails
Adds negative charge to histone tails- DNA is repulsed, causing it to no longer bind histone
Acts as flag for other proteins
