A histone octamer is the eight protein complex found at the center of a nucleosome core particle. It consists of two copies of each of the four core histone proteins (H2A, H2B, H3 and H4). The octamer assembles when a tetramer, containing two copies of both H3 and H4, complexes with two H2A/H2B dimers. The histone octamer can be assembled either in vivo, as the nucleosome core particle where the presence of DNA and the physiological salt concentrations allow it or without DNA under high salt concentrations. These histones of the histone octamer all contain N-terminal tails that emanate from their central histone folds, and core domains with the C-terminals. The tails comprise up to 20% of each histone and can be modified to alter the expression of the surrounding DNA. Additionally, the histone octamer interacts with the surrounding DNA through 14 points along the minor groove. These interactions, as well as hydrogen bonds and salt bridges, keep the DNA and histone octamer loosely associated and ultimately allow the two to re-position or separate entirely.
Post-translational modifications of histone were first identified and listed as having potential regulatory role on the synthesis of RNA in 1964.1 Since then over the couple of decades chromatin theory began to evolve. Chromatin subunit models as well as a notion of nucleosome were established in 1973 and 1974, respectively.2 Richmond et al. has been able to elucidate a crystal structure of histone octamer with DNA wrapped up around it at a resolution of 7 ˚A in 1984.3 Histone octamer structure was revisited 7 years later and 3.1 ˚A resolution was reached for octamer crystal at a high salt concentration but without a DNA around it. Each peptide of a histone has an element of helix-loop helix and therefore named histone fold.4 Furthermore the details of protein-protein and protein-DNA interactions were fine tuned by X-ray crystallography studies at 2.8 and 1.9 ˚A in the 2000s.
Core histones are four proteins called H2A, H2B, H3 and H4 and they are all found in equal parts in the cell. All four of the core histone amino acid sequences contain between 20 to 24% of lysine and arginine and the size or the protein ranges between 11400 and 15400 Daltons making them relatively small yet highly positively charged proteins.5 High content of positively charged amino acids allow them to closely associate with negatively charged DNA. In solution, histone-fold domain of core histones pair tightly to form interlocked crescent shaped quasi symmetric heterodimers, the histone-only intermediates. Each histone fold domain is composed of 3 α-helix regions that are separated by disordered loops. Histone fold domain is responsible for formation of hear-to-tail heterodimers of two histones: H2A-H2B and H3-H4. However, H3 and H4 histones first form a heterodimer and then in turn the heterodimer dimerizes to form a tetramer H32-H42.6 The heterodimer formation is based on the interaction of hydrophobic amino acid residue interactions from two proteins.6
Quasi symmetry allows heterodimer to be superimposed on itself by 180 degree rotation around this symmetry axis. As a result of the rotation, two ends of histones involved in DNA binding of the crescent shape H3-H4 are equivalent, yet they organize different stretches of DNA. H2A-H2B dimer also folds similarly. H32-H42 tetramer is wrapped with DNA around it as a first step of nucleosome formation. Then two H2A-H2B dimers are connected to the DNA- H32-H42 complex to form a nucleosome.7
Each of the four core histones besides their histone-fold domain also contain flexible, therefore unstructured extensions called histone “tails”.8 Treatment of nucleosomes with protease trypsin indicates that after histone tails are removed DNA is able to stay tightly bound to the nucleosome.5 Histone tails are subject to a wide array of modifications which includes phosphorylation, acetylation, and methylation of serine, lysine and arginine residues.
The nucleosome core particle is the most basic form of DNA compaction in eukaryotes. Nucleosomes consist of a histone octamer surrounded by 147 base pairs wrapped in a superhelical manner.9 In addition to compacting the DNA, the histone octamer plays a key role in the transcription of the DNA surrounding it. The histone core and nucleosomal DNA primarily interact through two methods. First, they interact whenever the minor groove of the DNA faces the histone core. Studies have found that the histones interact more favorably with A:T enriched than G:C enriched regions in the minor grooves.5 Second, the histones’ N terminal tails can be modified in several ways—most commonly acetylation, phosphorylation, or methylation—to limit or increase their transcription. The interactions between the histone octamer and DNA, however, are not permanent. The two can be separated quite easily and often are during replication and transcription. Specific remodeling proteins are constantly altering the chromatin structure by breaking the bonds of the nucleosome.
Histones are composed of mostly positively charged amino acid residues such as Lysine and Arginine. The positive charges allow them to closely associate with the negatively charged DNA through electrostatic interactions. Neutralizing the charges in the DNA allows it to become more tightly packed.
Moreover, the histone octamer interacts with nucleosomal DNA at fourteen distinct sites. These sites are the fourteen instances when the minor groove of the DNA is facing the histone core. At these sites, hydrogen bonds serve as the binding force at two separate locations—the oxygen in the phosphodiester bond of the DNA backbone surrounding the minor groove and the A:T rich bases of the minor groove. Together these sites have a total of about 40 hydrogen bonds, most of which are from the backbone interactions.5
The histone tails also play a significant role for the DNA of the nucleosome. Each histone has an N-terminal tail that protrudes from the histone core. These flexible units direct DNA wrapping in a left-handed manner around the histone octamer. Once the DNA is bound the tails continue to interact with the DNA. The parts of the tail closest to the DNA hydrogen bond and strengthen the DNA’s association with the octamer; the parts of the tail furthest away from the DNA, however, work in a very different manner. Cellular enzymes modify the tips of the distal sections of the tail to influence the accessibility of the DNA. The tails have also been implicated in the stabilization of 30-nm fibers.
In all, these associations protect the nucleosomal DNA from the external environment but also lower their accessibility to cellular replication and transcriptional machinery.
In order to access the nucelosomal DNA, the bonds between it and the histone octamer must be broken. This change takes place periodically in the cell as specific regions are transcribed, and it happens genome-wide during replication. Remodeling proteins work in three distinct ways: they can slide the DNA along the surface of the octamer, replace the one histone dimer with a variant, or remove the histone octamer entirely. No matter the method, in order to modify the nucleosomes, the remodeling complexes require energy from ATP hydrolysis to drive their actions.
Of the three techniques, sliding is the most common and least extreme. The basic premise of the technique is to free up a region of DNA that the histone octamer would normally tightly bind. While the technique is not well defined, the most prominent hypothesis is that the sliding is done in an “inchworm” fashion.5 In this method, using ATP as an energy source, the translocase domain of the nucleosome-remodeling complex detaches a small region of DNA from the histone octamer. This “wave” of DNA, spontaneously breaking and remaking the hydrogen bonds as it goes, then propagates down the nucleosomal DNA until it reaches the last binding site of with the histone octamer. Once the wave reaches the end of the histone octamer the excess that was once at the edge is extended into the region of linker DNA. In total, one round of this method moves the histone octamer several base pairs in a particular direction—away the direction the “wave” propagated.
Numerous reports show a link between age-related diseases, birth defects, and several types of cancer with disruption of certain histone post translational modifications. Studies have identified that N- and C-terminal tails are main targets for acetylation, methylation, ubiquitination and phosphorylation.10 New evidence is pointing to several modifications within the histone core. Research is turning towards deciphering the role of these histone core modifications at the histone-DNA interface in the chromatin. p300 and CBP possess histone acetyltransferase activity. p300 and CBP are the most promiscuous histone acetyltransferase enzymes acetylating all four core histones on multiple residues.11 Lysine 18 and Lysine 27 on H3 were the only histone acetylation sites reduced upon CBP and p300 depletion in mouse embryonic fibroblasts.12 Also, CBP and p300 knockout mice have an open neural tube defect and therefore die before birth. p300−/− embryos exhibit defective development of the heart. CBP+/− mice display growth retardation, craniofacial abnormalities, hematological malignancies, which are not observed in mice with p300+/−.13 Mutations of both p300 have been reported in human tumors such as colorectal, gastric, breast, ovarian, lung, and pancreatic carcinomas. Also, activation or localization of two histone acetyltransferases can be oncogenic.
- Allfrey, VG; Mirsky, AE (1964 May 1). "Structural Modifications of Histones and their Possible Role in the Regulation of RNA Synthesis.". Science (New York, N.Y.) 144 (3618): 559. PMID 17836360.
- Burgoyne, Hewish (1973). "Chromatin sub-structure.The digestion of chromatin DNA at regularly spaced sites by a nuclear deoxyribonuclease". Biochem. Biophys. Res. Commun. 52: :504–510.
- Klug; Richmond (1984). "Structure of the nucleosome core particle at 7 ˚A resolution". Nature 311: 532–537.
- Arents; Burlingame (1991). "The nucleosomal core histone octamer at 3.1 ˚A resolution: a tripartite protein assembly and a left-handed superhelix". PNAS 88: 10148–52.
- School, James D. Watson, Cold Spring Harbor Laboratory, Tania A. Baker, Massachusetts Institute of Technology, Stephen P. Bell, Massachusetts Institute of Technology, Alexander Gann, Cold Spring Harbor Laboratory, Michael Levine, University of California, Berkeley, Richard Losik, Harvard University ; with Stephen C. Harrison, Harvard Medical. Molecular biology of the gene (Seventh edition. ed.). Boston: Benjamin-Cummings Publishing Company. p. 241. ISBN 0321762436.
- Luger, Karolin (April 2003). "Structure and dynamic behavior of nucleosomes". Current Opinion in Genetics & Development 13 (2): 127–135. doi:10.1016/S0959-437X(03)00026-1.
- D’Arcy, Sheena; Martin, Kyle W.; Panchenko, Tanya; Chen, Xu; Bergeron, Serge; Stargell, Laurie A.; Black, Ben E.; Luger, Karolin (September 2013). "Chaperone Nap1 Shields Histone Surfaces Used in a Nucleosome and Can Put H2A-H2B in an Unconventional Tetrameric Form". Molecular Cell 51 (5): 662–677. doi:10.1016/j.molcel.2013.07.015.
- Harshman, S. W.; Young, N. L.; Parthun, M. R.; Freitas, M. A. (14 August 2013). "H1 histones: current perspectives and challenges". Nucleic Acids Research. doi:10.1093/nar/gkt700.
- Andrews, Andrew J.; Luger, Karolin (9 June 2011). "Nucleosome Structure(s) and Stability: Variations on a Theme". Annual Review of Biophysics 40 (1): 100. doi:10.1146/annurev-biophys-042910-155329.
- Jenuwein, T; Allis, CD (2001 Aug 10). "Translating the histone code". Science (New York, N.Y.) 293 (5532): 1074–80. PMID 11498575.
- Schiltz, RL; Mizzen, CA; Vassilev, A; Cook, RG; Allis, CD; Nakatani, Y (1999 Jan 15). "Overlapping but distinct patterns of histone acetylation by the human coactivators p300 and PCAF within nucleosomal substrates.". The Journal of biological chemistry 274 (3): 1189–92. PMID 9880483.
- Jin, Q; Yu, LR; Wang, L; Zhang, Z; Kasper, LH; Lee, JE; Wang, C; Brindle, PK; Dent, SY; Ge, K (2011 Jan 19). "Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation.". The EMBO journal 30 (2): 249–62. PMID 21131905.
- Yao, TP; Oh, SP; Fuchs, M; Zhou, ND; Ch'ng, LE; Newsome, D; Bronson, RT; Li, E; Livingston, DM; Eckner, R (1998 May 1). "Gene dosage-dependent embryonic development and proliferation defects in mice lacking the transcriptional integrator p300.". Cell 93 (3): 361–72. PMID 9590171.