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| Chromodomains |
interact with the methylated histone tails |
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mcs5109 Thu, 20 Nov 2008 06:59:35 GMT |
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| Bromodomains |
interact with the acetylated histone tails |
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mcs5109 Thu, 20 Nov 2008 06:59:35 GMT |
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| if no n-terminal tails... |
If no N-terminal tails, no 30 nm fiber!
Tails have to stabilize the 30 nm fibers by interacting with adjacent nucleosomes
Histone tails are modification targets influences ability to form the 30 nm fiber |
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mcs5109 Thu, 20 Nov 2008 06:34:07 GMT |
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| in vitro nucleosomal assembly |
-histones and DNA mixed in high salt (~1 M NaCl) and slowly reduce the salt concentration (~100 mM NaCl) |
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mcs5109 Wed, 19 Nov 2008 08:38:10 GMT |
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| histone chaperones |
-purified histones in DNA do nuthin'
-In vivo, histones are escorted by histone chaperones
-negatively charged proteins that form stable complexes with positively charged histones (H3·H4 tetramers and/or H2A·H2B dimer) |
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mcs5109 Wed, 19 Nov 2008 08:38:10 GMT |
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| H3·H4 Tetramers |
-Modifications in the old histones found in the new DNA recruit histone modification enzymes that add similar modifications to the adjacent nucleosomes
-important role in the inheritance of chromatin states |
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mcs5109 Wed, 19 Nov 2008 08:38:10 GMT |
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| When are histones compiled? |
-natent DNA strands are rapidly packaged into nucleosomes
-replication fork disassembles the nucleosomes into subassemblies (H3·H4 tetramers and H2A·H2B dimers)
-H2A and H2B dimers released into soluble pool and compete for H3H4 association |
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mcs5109 Thu, 20 Nov 2008 07:14:00 GMT |
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| Nucleosome Modification and Remodeling |
Modifications of N-terminal tails reduce the ability of nucleosomes to form repressive structures
Modifications recruit nucleosome remodeler
This allows formation of 10-nm chromatin fiber (for binding other proteins to nucleosomes)
Proteins bound on DNA recruits other modification factors to change chromatin structure |
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mcs5109 Wed, 19 Nov 2008 08:34:26 GMT |
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| Bromodomains and chromodomains |
chromodomains interact with the acetylated and methylated histone tails |
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mcs5109 Wed, 19 Nov 2008 08:34:26 GMT |
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| Acetylation and phosphorylation of N tail |
reduce the positive charges of the histone tails that decrease the affinity between histone tail and DNA |
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mcs5109 Wed, 19 Nov 2008 08:34:26 GMT |
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| Modification of the N-Terminal Tails of Histones |
-sites for post-translation modification
-codes that are read by proteins involved in gene expression
Lysine: acetylated or methylated
Arginine: methylated
Serine and Threonine: phosphorylated |
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mcs5109 Wed, 19 Nov 2008 08:30:17 GMT |
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| Methylation |
associated with both repressed and active chromatin |
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mcs5109 Wed, 19 Nov 2008 08:30:17 GMT |
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| Deacetylated nucleosomes |
are associated with transcriptionally-repressed chromatin |
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mcs5109 Wed, 19 Nov 2008 08:30:17 GMT |
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| Acetylated nucleosomes |
associated with regions of the chromosomes that are transcriptionally active |
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mcs5109 Wed, 19 Nov 2008 08:30:17 GMT |
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| DNA sequence-dependent Nucleosome Positioning |
-some DNA sequences that have high affinity for the nucleosome
A:T rich DNA: bends toward the minor groove which faces the histone octamer (next to octamer)
G:C rich DNA: bends away from the minor groove and faces away from the histone octamer (on outside of octomer) |
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mcs5109 Wed, 19 Nov 2008 08:27:52 GMT |
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| bind DNA binding proteins to interact w/ adjacent nucelosomes |
leading to position nucleosome at particular site |
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mcs5109 Wed, 19 Nov 2008 08:27:52 GMT |
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| bind 2 DNA binding proteins on sites <150bps away |
results in a nucleosome-free form |
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mcs5109 Wed, 19 Nov 2008 08:27:52 GMT |
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| Nucleosome Positioning |
-allows the DNA binding site opened for a regulatory protein binidng
-either DNA binding proteins or DNA sequence itself direct nucleosome positioning
-can have no nucleosome if too close
-some DNA binding proteins interact tightly with the adjacent nucleosomes |
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mcs5109 Wed, 19 Nov 2008 08:27:52 GMT |
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| nucleosome remodeling complexes |
stability of the histone octamer-DNA interaction is influenced by these large protein complexes
-multiple types
-use ATP to facilitate changes in nucleosome location or interaction with DNA (sliding, transfer and remodeling)
-contain different subunits which target to particular locations on the chromosomes |
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mcs5109 Wed, 19 Nov 2008 07:54:46 GMT |
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| Regulation of Chromatin Structure |
-histone octamer/DNA dynamic structure
-Spontaneous unwrapping of DNA from the nucleosome allows sequence-specific DNA-binding proteins to bind DNA
-center region of DNA in the core particle tightly associates with histone, which is less frequently accessible to the DNA binding protein |
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mcs5109 Wed, 19 Nov 2008 07:54:46 GMT |
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| CENP-A |
-extended N-terminal tail region
-may generate novel binding sites for other protein components of the kinetochore without altering the core structure of the nucleosome |
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mcs5109 Wed, 19 Nov 2008 07:43:49 GMT |
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| histone type info |
-core histones are the most conserved euk proteins
-but, several histone variants are found in eukaryotic cells
-form alternate nucleosomes to confer specialized functions
-ex: CENP-A |
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mcs5109 Wed, 19 Nov 2008 07:43:49 GMT |
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| 30 nm fiber is tethered to... |
...proteinaceous structure referred to as the nuclear scaffold |
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mcs5109 Wed, 19 Nov 2008 07:43:49 GMT |
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| zig zag model |
-requires the linker DNA to pass through the central axis of the fiber in a relatively straight form
-longer linker DNA favors this zig-zag model |
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mcs5109 Wed, 19 Nov 2008 07:32:23 GMT |
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| solenoid model |
-higher order helix
-contains approximately 6 nucleosomes per turn
-linker DNA is buried in the center of the super helix |
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mcs5109 Wed, 19 Nov 2008 07:32:23 GMT |
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| 30nm fibers |
-Binding of H1 stabilizes higher order chromatin structures
1. Solenoid model
2. Zig-zag model |
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mcs5109 Wed, 19 Nov 2008 07:32:23 GMT |
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| H1 binding angles |
-H1 binding produces a defined angle of DNA entry and exit from the nucleosome
-DNA takes on a zig-zag appearance
-if these angles are 20 degrees to dyad axis, nucleosomes would alternate on either side of a central region of linker DNA bound by H1 |
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mcs5109 Wed, 19 Nov 2008 07:32:23 GMT |
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| 14 |
# distinct sites of contact are observed between the histones and the nucleosomal DNA (minor groove) that DNA faces the histone octamer |
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mcs5109 Wed, 19 Nov 2008 07:23:10 GMT |
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| two H2A·H2B dimers |
each associate with approximately 30 bp of DNA on either side of the central 60 bp of DNA
-relatively short length of DNA bound |
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mcs5109 Wed, 19 Nov 2008 07:23:10 GMT |
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| H3·H4 tetramer |
-binds the middle and both ends of the DNA
-result in the DNA being bent |
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mcs5109 Wed, 19 Nov 2008 07:23:10 GMT |
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| exposed N-terminal tails |
-not required for the association of DNA with the histone octamer
-sites of extensive modifications
-alter the function of individual nucleosomes
-Stabilizes DNA Wrapping around the Octamer |
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mcs5109 Wed, 19 Nov 2008 07:23:10 GMT |
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| Greater than 20 percent of the residues in the histones are |
either Lys or Arg that contain positively charged side chains |
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mcs5109 Wed, 19 Nov 2008 07:10:33 GMT |
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| H1 |
-binds to the linker DNA
-unusual property of binding 2 distinct regions of the DNA duplex
1. to the linker DNA
2. to the middle of associated 147 bp
-binding increases the length of the DNA wrapped tightly around the histone octamer |
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mcs5109 Wed, 19 Nov 2008 07:24:56 GMT |
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| core histones |
H2A, H2B, H3 and H4
-contains N-terminal tail (not conserved)
-histone-fold domain (conserved) |
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mcs5109 Wed, 19 Nov 2008 07:10:33 GMT |
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| Eukaryotic cells contain five abundant histones |
H1, H2A, H2B, H3 and H4 |
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mcs5109 Wed, 19 Nov 2008 07:10:33 GMT |
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| 147 |
-Minimal nucleosome # base pairs of DNA
-plus histone is called the nucleosome core particle |
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mcs5109 Wed, 19 Nov 2008 07:07:22 GMT |
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| Micrococcal Nuclease |
-length of DNA associated with each nucleosome can be determined by using Micrococcal nuclease digestion assay
Minimal nucleosome includes 147bp of DNA plus histone is called the nucleosome core particle |
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mcs5109 Wed, 19 Nov 2008 07:07:22 GMT |
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| linker DNA |
-DNA between each nucleosome
-Each eukaryote has a characteristic average linker DNA length (not correlated to species complexity) |
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mcs5109 Wed, 19 Nov 2008 07:07:22 GMT |
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| nucleosome info |
-majority of euk DNA is packaged into nucleosomes
-core of 8 histone proteins
-DNA wrapped around histone
-core DNA (~147 bp) is wound 1.65 times around the outside of histone octamer |
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mcs5109 Wed, 19 Nov 2008 07:07:22 GMT |
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