Nucleosome

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Nucleosomes are the fundamental repeating subunits of all eukaryotic chromatin (except when packaged in sperm). They package DNA into chromosomes inside the cell nucleus and control gene expression. They are made up of DNA and four pairs of proteins called histones, and resemble "beads on a string of DNA" when observed with an electron microscope. The nucleosome hypothesis proposed by Don and Ada Olins ^[1] and Roger Kornberg^{[2] [3]} in 1974, was a paradigm shift for understanding eukaryotic gene expression.

[edit] Nucleosome role in the Nucleus

Nucleosomes appear to serve two major purposes within the cell nucleus. First, they provide the lowest level of compaction which is required to fit dsDNA (on the order of meters) into the cell nucleus. Secondly, they are important in the regulation of transcription by preventing RNA polymerase from unnecessarily accessing the promoter regions of genes which are not needed by the cell. If the requirements of the cell change, enzymes known as remodeling factors can remove or change the position of the nucleosome to allow access. Nucleosomes also appear to be major carriers of epigenetically inherited information.

[edit] Structure of the Core Particle

The crystal structure of the nucleosome core particle at 2.8 Å resolution.

The histone-DNA contacts of the H3-H4 tetramer (a) are very similar to those found on the H2A/H2B dimers (b).

The crystal structure of the nucleosome has currently been determined with a resolution better than 2.0 Å^[4], but most of the important features were known by 1997 with the publication of its structure at a resolution of 2.8 Å^[5].

The nucleosome repeats, with some variations and exceptions, roughly every 200 bp throughout eukaryotic chromatin. The nucleosome core particle shown in the figure consists of about 145 bp of dsDNA wrapped in 1.65 left-handed superhelical turns around four identical pairs of proteins individually known as histones and collectively known as the histone octamer. The remaining 50 bp of the repeating unit consists of "linker DNA", dsDNA which separates the core particles.

Each of the four histones (H2A, H2B, H3, and H4) share a very similar structural motif consisting of three alpha helices separated by loops. In solution, histones form pairs with identical copies of themselves and are referred to as dimers or histone-fold pairs. In the case of the H3 and H4 histones, they assemble further into tetramers, an association of two H3-H4 dimers, whereby buried charged groups of the same alpha helix on both of the H3 histones hydrogen bond to each other. The assembly of a nucleosome core particle occurs first by the attachment of the H3-H4 tetramer onto the dsDNA with the later association of two separate H2A-H2B dimers, a process that is likely to occur in a cooperative manner (i.e. both H2A-H2B dimers assemble onto the tetramer at once).

According to the crystal structure, the histone octamer likely interacts with the dsDNA around it roughly every 10 bp. Each of the four histone dimers contain three regions of interaction with the dsDNA. The central interaction site for each dimer is formed by an alpha helix from each histone in the pair pointing at a single phosphate group on the dsDNA to which they hydrogen bond. At positions 10 bp away on either side, a loop from both histones in the pair converge to hydrogen bond to other single phosphate groups. See the figure on the right for a visual representation. Two other interactions (for a total of 14) occur through the interaction of histone tails from each of the H3 histones. These interactions occur at the entry and exit points of the dsDNA wrapping around the nucleosome and help to clamp these regions onto the core particle.

Analysis of the structure of dsDNA wrapped around the histone octamer suggests that it is predominantly B-form, although more tightly constrained than free DNA due to its interaction with the octamer. Curvature into the superhelix comes primarily when either the minor or the major groove faces the octamer and therefore occurs in spurts of roughly 5 bp. Major groove bending around the octamer occurs smoothly. Minor groove bending is facilitated by arginine side chains inserted into the groove and occurs smoothly around the H3-H4 tetramer, but is kinked around the H2A/H2B dimer regions. The DNA is most tightly constrained in regions where it interacts with the double loop structures of the histone dimers mentioned above, which implies that there is more variability in how the DNA interacts with the double alpha helix structures of the histone dimers in order to accommodate the binding of different sequences. ^[6]

Many proteins bind only to specific DNA sequences. Although nucleosomes tend to prefer some DNA sequences over others, they are capable of forming on just about any sequence. It has been shown that water molecules roughly double the number of histone-DNA interactions by acting as intermediates between atoms which would otherwise be too far apart to Hydrogen bond.^[7] It is the flexibility in the formation of these water-mediated interactions which allows for the histone octamer to wrap a very wide variety of DNA sequences.

[edit] Structure and Purpose of the Histone Tails

Location of the histone tails. Dark regions indicate residues which interact with wrapped DNA. The dashed line indicates regions which are not well structured when crystallized. Acetylation sites are indicated by arrows. Ubiquitination sites are marked with "U".

The end of each histone protein contains a tail of amino acid residues of different lengths, characteristic of that histone. The purpose of the tails are not totally clear at present, but they appear to contribute to the stability of the nucleosome^[8] as well as serve as docking sites for other proteins. The structure of the tails can be altered slightly by other enzymes in the nucleus and may play a significant role in the generation of higher order chromatin structure.^[9]

[edit] Higher Order Structure

Structure of the tetranucleosome, as observed by Schalch et al..

The current chromatin compaction model.

Further compaction of chromatin into the cell nucleus is necessary, but is not yet well understood. The current understanding^[10] is that repeating nucleosomes with intervening "linker" DNA form a 10-nm-fiber, known descriptively as "beads on a string", and have a packing ratio of ~6, compared to "free" DNA (per nm length). A chain of nucleosomes can be arranged in a 30 nm fiber, a compacted structure (thought to be a helical solenoid, a zigzag ribbon structure, a superbead, or having no regular structure) with a packing ratio of ~40. A crystal structure of a tetranucleosome has been presented and used to build up a proposed structure of the 30 nm fiber.^[11] The result yields strong evidence in support of the two-start helix model, in which nucleosomes are assembled in a zigzag ribbon that twists or supercoils. The H1 histone stabilizes the 30 nm fiber. Beyond this the structure of chromatin is poorly understood, but it is classically suggested that the 30 nm fiber is arranged into loops along a central protein scaffold to form transcriptionally active euchromatin. Further compaction leads to transcriptionally inactive heterochromatin.

The proteins that make up the nucleosome are called histones. Histones H2A, H2B, H3 and H4 are part of the nucleosome while histone H1 is involved the linker DNA between the two nucleosomes.

[edit] Nucleosome Remodeling

Several enzymes (for example, RSC, SWI/SNF) have been observed to change the position of nucleosomes in vitro.^[12] Their purpose is to expose genetic information held within the nucleosome core particle when it is required by the cell. It has been suggested that remodeled nucleosomes not only have altered positions on the DNA template but have stable or semi-stable altered structures as well. These altered states may be necessary for transcription to occur.

[edit] Sin (Swi/Snf Independent) Mutations

It is well known that the production of SWI/SNF, a nucleosome remodeling enzyme, is essential for the survival of yeast.^[13] However, this limitation can be overcome through various single-residue mutations of either the H3 or the H4 histone. The crystal structures of 11 such mutations have been described^[14] and it is possible that their structure may reveal information about how SWI/SNF provides access to genetic sequences initially sequestered through nucleosome wrapping.

[edit] Nucleosome Assembly in vitro

Diagram of nucleosome assembly.

Nucleosomes can be assembled in vitro by either using purified native or recombinant histones or their various variant structures.^[15] The standard technique of using salt dialysis relies upon the fact that H3-H4 tetramer associates with the DNA at higher salt concentrations than the H2A/H2B dimers. A reaction consisting of the four core histones and a naked DNA template is first incubated at 4C at a 2M salt concentration. This concentration is steadily reduced by exchanging buffer manually, or by pumping a low salt buffer into the reaction while pumping out the reaction mixture at the same rate. As the salt concentration decreases, free tetramer in solution begin to associate with the DNA template. As the salt concentration decreases even further, the H2A/H2B dimers associate with the tetramer on the template.

[edit] References

1. ^ Olins AL and Olins DE, "Spheroid Chromatin Units (nu Bodies)", Science (1974); 183: 330 - 332
2. ^ McDonald D, "Milestone 9, (1973-1974) The nucleosome hypothesis: An alternative string theory", Nature Milestones: Gene Expression. (2005) Dec 1; http://www.nature.com/milestones/geneexpression/milestones/articles/milegene09.html
3. ^ Kornberg, RD, "Chromatin structure: a repeating unit of histones and DNA", Science. (1974); 184: 868–871
4. ^ Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, "Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution.", Journal of Molecular Biology. 2002 Jun 21; 319 (5): 1097-1113.
5. ^ Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ, "Crystal Structure of the Nucleosome Core Particle at 2.8 Å Resolution", Nature. 1997 Sep 18; 389 (6648): 251-60.
6. ^ Richmond TJ, Davey CA, "The structure of DNA in the nucleosome core", Nature. (2003) May 8; 423 (6936): 145-150.
7. ^ Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, "Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution.", Journal of Molecular Biology. 2002 Jun 21; 319 (5): 1097-1113.
8. ^ Brower-Toland B, Wacker DA, Fulbright RM, Lis JT, Kraus WL, Wang MD, "Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes", Journal of Molecular Biology (2005) Feb 11; 346 (1): 135-146
9. ^ Luger K, Richmond TJ, "The histone tails of the nucleosome.", Current Opinion in Genetics and Development. (1998) Apr; 8 (2): 140-6.
10. ^ Chakravarthy S, Park YJ, Chodaparambil J, Edayathumangalam RS, Luger K, "Structure and dynamic properties of nucleosome core particles", FEBS Letters. (2005) Feb 7; 579 (4): 895-898.
11. ^ Schalch T, Duda S, Sargent DF, Richmond TJ, "X-ray structure of a tetranucleosome and its implications for the chromatin fibre", Nature. (2005) Jul 7; 436: 138-141.
12. ^ Lia G, Praly E, Ferreira H, Stockdale C, Tse-Dinh YC, Dunlap D, Croquette V, Bensimon D, Owen-Hughes T, "Direct Observation of DNA Distortion by the RSC Complex", Molecular Cell (2006) Feb 3; 21 (3): 417-425.
13. ^ Kruger W, Peterson CL, Sil A, Coburn C, Arents G, Moudrianakis EN, Herkowitz I, "Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription, Genes Development. (1995) Nov 15; 9 (22): 2770-2779.
14. ^ Muthurajan UM, Bao Y, Forsberg LF, Edayathumangalam RS, Dyer PN, White CL, Luger K, "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions", EMBO Journal. (2004) Jan 28; 23 (2): 260-271.
15. ^ Dyer PN, Edayathumangalam RS, White CL, Bao Y, Chakravarthy S, Muthurajan UM, Luger K, "Reconstitution of nucleosome core particles from recombinant histones and DNA", Methods in Enzymology (2004); 375: 23-44

• Luger K, "Dynamic Nucleosomes", Chromosome Research. 2006; 14 (1): 5-16.