Nucleosome

Nucleosomes are the fundamental repeating units of eukaryotic chromatin, ^[1] with the exception of mature sperm. Animals Plants fungi, and Protists are eukaryotes (juːˈkærɪɒt or -oʊt Organisms whose cells are organized into complex Chromatin is the complex basis of DNA and protein that makes up Chromosomes It is found inside the nuclei of eukaryotic cells, and within the ^[2] They are the smallest structural unit of eukaryotic DNA packaging, fundamental to the structure of the chromosome(s) inside the cell nucleus and can play a role in controlling gene expression. Animals Plants fungi, and Protists are eukaryotes (juːˈkærɪɒt or -oʊt Organisms whose cells are organized into complex Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known A chromosome is an organized structure of DNA and Protein that is found in cells. In Cell biology, the nucleus (pl nuclei; from Latin la ''nucleus'' or la ''nuculeus'' "little nut" or kernel is a membrane-enclosed Gene expression is the process by which inheritable information from a Gene, such as the DNA sequence, is made into a functional Gene product, such They are made up of about 146 base pairs of DNA and four pairs of proteins called histones, and resemble "beads on a string of DNA" when observed with an electron microscope (a 10nm fiber). Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl In Biology, histones are the chief Protein components of Chromatin. An electron microscope is a type of Microscope that uses Electrons to illuminate a specimen and create an enlarged image The nucleosome hypothesis proposed by Don and Ada Olins^[3] and Roger Kornberg^[4][5] in 1974, was a paradigm shift for understanding eukaryotic gene expression. Roger David Kornberg (born) is an American Biochemist and Professor of Structural biology at Stanford University School of Medicine The proteins that make up the nucleosome are called histones. In Biology, histones are the chief Protein components of Chromatin. Histones H2A, H2B, H3 and H4 form the core of the nucleosome, around which the DNA is wrapped, while histone H1 sits on the base of the nucleosome at the junction between nucleosome DNA and linker DNA, extending along the DNA into the linker region.

Various roles in the nucleus

Besides providing a scaffold for compaction of DNA in the nucleus, nucleosomes are also important for the regulation of transcription, and define the boundaries of euchromatin and heterochromatin. Euchromatin is a lightly packed form of Chromatin that is rich in Gene concentration and is often (but not always under active transcription. Heterochromatin is a tightly packed form of DNA Its major characteristic is that transcription is limited During initiation of transcription, nucleosomes can prevent RNA polymerase from unnecessarily accessing the promoter regions of genes which are not needed by the cell. RNA polymerase ( RNAP or RNApol) is an Enzyme that produces RNA. In Biology, a promoter is a region of DNA that facilitates the transcription of a particular Gene. When the requirements of the cell change, chromatin remodeling factors can alter the position of the nucleosomes to allow access.

Nucleosomes are also chromatin boundary markers and carry epigenetically inherited information in the form of N-terminal modifications of their core histones. The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or In Biology, histones are the chief Protein components of Chromatin.

Structure of the core particle

The crystal structure of the nucleosome core particle consisting of H2A , H2B , H3 and H4 .

The crystal structure of the nucleosome has currently been determined with a resolution better than 2. In Mineralogy and Crystallography, a crystal structure is a unique arrangement of Atoms in a Crystal. 0 Å,^[6] but most of the important features were known by 1997 with the publication of its structure at a resolution of 2. 8 Å. ^[7]

The nucleosome repeats, with some variations and exceptions, roughly every 200 base pairs (bp) throughout eukaryotic chromatin. In Molecular biology, two Nucleotides on opposite complementary DNA or RNA strands that are connected via Hydrogen bonds are called The nucleosome core particle shown in the figure consists of about 146 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 a "relaxed" double-helical segment of DNA, the two strands twist around the helical axis once every 10 In Biology, histones are the chief Protein components of Chromatin. A histone octamer is an Octamer of the Histones found at the center of a Nucleosome core particle. 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) shares a very similar structural motif consisting of three alpha helices separated by loops. Histone H2A is one of the 5 main Histone Proteins involved in the structure of Chromatin in eukaryotic cells Histone H2B is one of the 5 main Histone Proteins involved in the structure of Chromatin in Eukaryotic cells Histone H3 is one of the five main Histone Proteins involved in the structure of Chromatin in Eukaryotic cells Featuring a main globular domain Histone H4 is one of the 5 main Histone Proteins involved in the structure of Chromatin in eukaryotic cells A common motif in the Secondary structure of Proteins the alpha helix (α-helix is a right-handed coiled conformation resembling a spring, in which 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. A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen 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. ^[8]

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. ^[9] 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 purpose of the tails are not totally clear at present, but they appear to contribute to the stability of the nucleosome^[10] 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. ^[11] See: chromatin. Chromatin is the complex basis of DNA and protein that makes up Chromosomes It is found inside the nuclei of eukaryotic cells, and within the

Higher order structure

The current chromatin compaction model.

Further compaction of chromatin into the cell nucleus is necessary, but is not yet well understood. The current understanding^[12] 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. ^[13] 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. Histone H1 is one of the 5 main Histone Proteins involved in the structure of Chromatin in eukaryotic cells 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. Euchromatin is a lightly packed form of Chromatin that is rich in Gene concentration and is often (but not always under active transcription. Further compaction leads to transcriptionally inactive heterochromatin. Heterochromatin is a tightly packed form of DNA Its major characteristic is that transcription is limited

Nucleosome remodeling

Several enzymes (for example, RSC, SWI/SNF) have been observed to change the position of nucleosomes in vitro. RSC is a 15- Subunit complex with the capacity to remodel the structure of Chromatin. SWI/SNF (SWItch/Sucrose NonFermentable is a Yeast Nucleosome remodeling complex composed of several proteins - products of the SWI and SNF genes ( /,,) as well ^[14] 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. This remodeling also involves histone acetyltransferases (HATs). Histone acetyltransferases (HAT are Enzymes that acetylate conserved Lysine Amino acids on Histone proteins by transferring an These enzymes add acetyl groups onto the basic amino acids in histone tails, which reduces the positive charge on the histone and weakens its binding to the DNA (which is negatively charged). In Organic chemistry, acetyl (ethanoyl is a Functional group, the Acyl of Acetic acid, with Chemical formula - C[[Oxygen This process can be reversed by histone deacetylases (HDACs), which remove the acetyl groups and cause the chromatin to recondense into the heterochromatin structure. Histone deacetylases (HDAC ( EC number 351 are a class of Enzymes that remove Acetyl groups from an ε-N-acetyl Lysine Amino acid

Sin (Swi/Snf independent) mutations

It is well known that the production of SWI/SNF, a nucleosome remodeling enzyme complex, is essential for the survival of yeast. SWI/SNF (SWItch/Sucrose NonFermentable is a Yeast Nucleosome remodeling complex composed of several proteins - products of the SWI and SNF genes ( /,,) as well ^[15] 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^[16] 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

Diagram of nucleosome assembly.

Nucleosomes can be assembled in vitro by either using purified native or recombinant histones or their variant structures. ^{[17] [18]} One standard technique of loading the DNA around the histones involves the use of salt dialysis. In Medicine, dialysis (from Greek "dialusis" meaning dissolution "dia" meaning through and "lusis" meaning loosening is primarily A reaction consisting of the histone octamers and a naked DNA template can be incubated together at a salt concentration of 2 M. By steadily decreasing the salt concentration, the DNA will equilibrate to a position where it is wrapped around the histone octamers, forming nucleosomes.

See also

• Protamine

References

External links

• The nucleosome - The building blocks of chromosomes (dutch)
• Nucleosomes in Proteopedia