Chromatin Flashcards
General Nucleosome structure (Number and type of subunits, how is DNA bound?)
H3-H4 tetramer + 2 H2A-H2B dimers
Octamer of histones
Nucleosomes are the fundamental subunits of chromatin.
Nucleosomes affect access to DNA.(Euchromatin/heterochromatin)
DNA is bound predominantly via hydrogen bonds between the phosphodiester backbone and lysine or arginine residues of histones.
Histone Chaperones
A group of proteins that bind histones and regulate nucleosome assembly. Required since under physiological salt concentrations histones bind non-specifically to naked DNA and do not form nucleosomes.
Histone Fold
The globular domain contains a structural motif called the “Histone Fold”.
The histone fold consists of 3 helices connected by 2 loops that confer a crescent-like shape on each histone.
Histone Dimerisation
The histone fold motifs form the basis of a dimerisation interface.
This allows histones to interact with each other in specific pairings (i.e. H3-H4 and H2A-H2B)
4 helix bundle interactions
(H3-H4)2 Tetramer:
The H3-H4 dimers interact with each other via 4-helix bundle to form a (H3-H4)2 tetramer
In Dimer/Tetramer Interface:
The H2A-H2B dimers are bound to the H3-H4 tetramer via another 4-helix bundle interaction to form the histone octamer
Histone Tails
Each histone also has N- and/or C-terminal highly flexible tails.
Tails contain many basic residues (lysine, arginine).
Play an important role in nucleosome dynamics and thus in gene expression.
“Nucleosomes protect DNA from nuclease digestion”
TRUE OR FALSE
TRUE
Nucleosome Positioning
Nucleosome positioning affects access to DNA.
Nucleosomes are positioned over transcribed genes.
ATP dependent chromatin remodelling enzymes act at different stages in the generation of chromatin at coding genes. Can cause sliding, ejection, insertion.
Targeting of ATP dependent remodelling enzymes occurs via accessory domains that can be in other subunits.
Histone Modifications
Histone tails protrude from the structure of the nucleosome and are subject to an assortment of posttranslational modifications.
Histone modifying enzymes are normally present inside cells as components of multi-protein complexes which may modulate their specificity.
A spectrum of enzymes direct modification of specific residues on different histones:
- Kinase: Add Phosphate
- Phosphatase: Remove Phosphate
- Histone acetyl transferase (HAT): Add Acetyl
- Histone Deacetylases (HDAC): Remove Acetyl
How do histone modifications exert their functions?
Histone modifications directly alter chromatin structure.
e.g. Acetylation results in the neutralization of some of the basic histone residues that may be involved in DNA binding resulting in a looser nucleosome structure.
Writer-reader model: A diverse range of protein folds specifically recognise histone modifications e.g. “Bromodomain” is the reader for HAT as a writer.
Modification of histones at different sites have distinct functions
DNA Methylation
Conversion of Cytosine –> Methyl Cytosine
Main role in silencing chromatin: Silence either the maternal or paternal allele, including the inactive X chromosome.
DNA methylation is reversible.
DNA methylation is an example of an EPIGENETIC modification.
Histone Variants
Canonical histones are produced in S phase.
However at some loci, nucleosomes contain specialised variants of the core histones instead of canonical histones.
Cell-Cell Epigenetics
Concept of “Cell Memory” or “Cellular Inheritance”
Involves “Establishment” and “Maintenance” of a transcriptional program.
Replication dependent propagation of an epigenetic mark.
Mechanisms that governs the inheritance of epigenetic marks are duplicated in S phase, such as:
- Histone handling at replication forks
- Histone modification maintenance: H3K27me3
- Maintenance DNA methylation
Histone Handling at Replication Forks
100% Old Histones -> 50% New and 50% Old Histones
3 Crucial steps: Disruption, Recyling, and Assembly
Disruption: FACT has key role in transcription: Nucleosome disruption ahead of RNA pol. and restores chromatin template behind.
Recycling: H3-H4: Tetramer > dimer, Additional factors must be involved to maintain the tetrameric state (chaperone).
Assembly: Chromatin assembly behind replisomes. New and old H3-H4 dimers are segregated into separate nucleosomes.
New and old H2A-H2B dimers can associate with both new or old H3.1-H4 tetramers
Histone Modification Maintenance
Histone posttranslational modification positional information is preserved through parental histone recycling.
Parental H3K27me3 domains are stable and inherited to daughter cells.
Restoration of histone posttranslational modification levels follows mark- and locus-specific kinetics.
