Ch 8 Lecture (Chromatin) Flashcards
nucleosome
The basic structural subunit of chromatin, consisting of 200 bp of DNA and an octamer of histone proteins
Serves as the first level of chromatin organization
Packed 6X
histones
DNA binding proteins that are part of nucleosome structure
Histone tails
Flexible N- or C-terminal regions of the core histones that extend beyond the surface of the nucleosome
Are often extensively post-translationally modified
10 nm fiber
A fiber generated from the linear array of nucleosomes
30nm fiber
A coil of nucleosomes
40X packing
Basic level of organization in chromatin
Requires interactions of histone tails and linker histones
linker histones
A family of histones that are not components of the nucleosome core that bind nucleosomes and/or linker DNA
Histone H1
micrococcal nuclease
cleaves linker DNA and releases individual nucleosomes from chromatin
there is one nucleosome every
200 base pairs
what proteins are the octomer of core histone proteins
A pair of H2A, H2B, H3, and H4
Stable H32-H42 tetramer associates with two stable H2A-H2B dimers
histone proteins are
small, basic, and lysine and arginine rich
what histone proteins are highly conserved
H3 and H4
what histone proteins are not highly conserved
H2A and H2B
DNA is coiled around the histone how many times
1.6
Interdigitation of histone proteins is facilitated via the interaction of
histone folds
histone folds
Conserved structure of 3 -helices
Two short helices on end and one long helix in middle separated by loops
what facilitates heterodimer formation
loop to loop interactions
What binds to the middle 60bp and the entry/exit points of the DNA
H3-H4 tetramer
what stabilizes the DNA on the bottom of the nucleosome
H2A-H2B dimers
Association between DNA and the nucleosome is facilitated by
142 hydrogen bonds
intrinsic positioning
AT-rich regions position with minor groove towards octamer
GC-rich regions position with minor groove facing away from octamer
what on the histones help “lock” the DNA on the nucleosome
The N-terminal tails
Histone tails are distributed … around the nucleosome disc
evenly
histone tails
Each histone has a flexible N-terminal tail
H2A and H2B also have flexible C-terminal tails
Structures not well defined via molecular imaging
Conformation can be altered greatly by posttranslational modification
The tails (especially H4) interact with the H2A-H2B dimer of an adjacent nucleosome
linker histone
Help link neighboring nucleosomes into higher order chromatin structure
A set of closely related proteins that show variation between tissues and species
H1 histone
nucleosome+ linker histone =
chromatosome
H1 histone
Interacts with two distinct regions of DNA
Linker DNA at one end of nucleosome
Middle of nucleosome-bound DNA found at dyad axis
Produces a more defined angle of DNA entry and exit from nucleosome
Produces a zig-zag appearance of “beads on a string”
30nm fiber structure
Condensed zigzag structure
Facilitated by histone tail-to-tail interactions
Especially the H4 tail
Also requires the H1 histone
Linker DNA passes through the central axis of the fiber
All core histones except H4 are members of families of
histone variants
histone variants vary in
in their polypeptide chain length, amino acid sequence, and pattern of stable histone modifications
histone modifications
Covalent modifications to the amino acid side chains of histone proteins
variants often involve changes in
the histone tails
CenH3/CENP-A
Replaces H3 in nucleosomes of DNA regions associated with the kinetochore
H3.3
Expressed throughout the cell cycle
Some histone variants are primarily expressed only in the S phase
Available for assembly at regions of active transcription
“Replacement” histone
H2AX
Present in 10-15% of multicellular eukaryote nucleosomes
H2AX tails are a target of phosphorylation events associated with DNA damage, repair, and cell cycle arrest
Phosphorylated -H2AX is recognized by repair enzymes
histones are covalently modified by
Methylation
Acetylation
Phosphorylation
Ubiquitylation
ADP-ribosylation
histone modifications happen
Usually in tails
All reversible
May be transient or stable
acetylation
Neutralizes the positive charge of lysine
Releases histone tails from DNA
Increases accessibility of DNA to transcriptional machinery
Newly synthesized histones lose acetylation after incorporation into chromatin
methylation
Lysine or arginine
Can be mono-, di-, or tri-
Several types of trimethylated lysine modifications are important components of heterochromatin
phosphorylation
adding phosphates on serine or threonine
what is the memory effect
Modifications can remain long after transcription factors are gone
can be passed down to descendant cells
how are histone modifying enzymes recruited
by transcription factories
There are over … known coordinated sets of histone modifications in mammalian cells
15
what modifications turn gene expression on and are in highly accessible, open chromatin
H4K4me3 and H3K9ac
what modifications turn gene expression off and are found in heterochromatin
H3K9me3 and H3K27me3
After modification, histones and nucleosomes can be bound by
chromatin binding proteins
bromodomains recognize
acetylated lysines
chromodomains, PHD domains, and Tudor domains recognize
methylated residues
SANT domain recognizes
unstructured tails
ING PHD domain
Specifically recognizes H3K4me3
Also recognizes the 6 amino acids in the N-terminal tail of H3
reader protein complex
Nucleosome binding proteins that contain multiple binding domains that allow the protein to recognize a specific combination of histone modifications
Reader complexes may be attached to …that can make histone modifications
writer enzymes
reader-writer complexes
will bind a specific chromatin region and modify neighboring nucleosomes
reader write complexes work until
it meets a barrier insulator region
what complex can erase modifications
reader-eraser
Reader-writer complexes are involved in
heterochromatin spreading
