nucleosome - Nucleosome role in the Nucleus, Structure of the Core Particle

The basic unit into which the DNA is packed in the chromatin of eucaryotes. A nucleosome contains an octomer of proteins consisting of two copies each of histones H2A, H2B, H3, and H4, around which is wrapped two-and-a-half turns (146 base pairs) of DNA. Other proteins will be involved in the packing; these will vary according to whether the DNA is active or silent.

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.

Nucleosome role in the Nucleus

Nucleosomes appear to serve two major purposes within the cell nucleus. If the requirements of the cell change, enzymes known as remodeling factors can remove or change the position of the nucleosome to allow access.

Structure of the Core Particle

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

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. 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.

According to the crystal structure, the histone octamer likely interacts with the dsDNA around it roughly every 10 bp. 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. 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. Although nucleosomes tend to prefer some DNA sequences over others, they are capable of forming on just about any sequence. 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.

Structure and Purpose of the Histone Tails

The end of each histone protein contains a tail of amino acid residues of different lengths, characteristic of that histone. 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.

Higher Order Structure

Further compaction of chromatin into the cell nucleus is necessary, but is not yet well understood. The current understanding 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.

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.

Nucleosome Remodeling

Several enzymes (for example, RSC, SWI/SNF) have been observed to change the position of nucleosomes in vitro. 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.

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. The crystal structures of 11 such mutations have been described and it is possible that their structure may reveal information about how SWI/SNF provides access to genetic sequences initially sequestered through nucleosome wrapping.

Nucleosome Assembly in vitro

Nucleosomes can be assembled in vitro by either using purified native or recombinant histones or their various variant structures. A reaction consisting of the four core histones and a naked DNA template is first incubated at 4C at a 2M salt concentration. 183: 330 - 332 ^ McDonald D, "Milestone 9, (1973-1974) The nucleosome hypothesis: An alternative string theory", Nature Milestones: Gene Expression. http://www.nature.com/milestones/geneexpression/milestones/articles/milegene09.html ^ Kornberg, RD, "Chromatin structure: a repeating unit of histones and DNA", Science. 184: 868–871 ^ 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. ^ Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ, "Crystal Structure of the Nucleosome Core Particle at 2.8 Å Resolution", Nature. ^ Richmond TJ, Davey CA, "The structure of DNA in the nucleosome core", Nature. ^ 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. ^ 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; ^ Chakravarthy S, Park YJ, Chodaparambil J, Edayathumangalam RS, Luger K, "Structure and dynamic properties of nucleosome core particles", FEBS Letters. ^ 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. ^ 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. ^ 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);