Chromatin Fiber

Chromatin Fiber

Genetic information is written in the sequence of nucleotides, or bases, in the DNA double helix of chromosomes, whose lengths in human cells achieve a total of approximately two meters. Chromosomes are coated with histone proteins, which assemble the DNA into compact chromatin fibers that enable condensation of this extraordinary length into the tiny volume of the nucleus. In addition to allowing DNA to be packaged into the compact structure of chromosomes, chromatin is involved in the regulation of gene expression and other genomic functions such as DNA repair and replication, and organization of nuclear architecture. The intimate relationship between the bases of DNA and the histone proteins forming a complex constitutes the chromatin molecule.

A significant part of the chromatin fiber is made of DNA and nucleosome structures, which are built of histone proteins, around which the DNA is coiled. In addition to that, the fiber contains significant quantities of non-histone chromatin proteins, which exhibit high diversity, and it is generally accepted that they confer specific features to the chromatin in a particular cellular environment. Moreover, both histones and DNA are post-translationally modified, which is generally understood as imparting another layer of information — the epigenetic information — in addition to that encoded in the genome.

DNA Components

The primary component of chromatin is DNA, a polymer consisting of strands of nucleotides linked together by covalent bonds. Each nucleotide in DNA consists of one of four nitrogenous bases attached to a molecule of deoxyribose sugar, which in turn is linked to a phosphate group. The nitrogenous bases are responsible for the information stored within DNA. Each strand of DNA contains a sequence of bases, which form a code that specifies the amino acid sequence of proteins; DNA also contains codes that regulate protein synthesis. Each nucleotide in one strand of DNA is linked by base-pairing hydrogen bonds to a nucleotide in the other strand. Units of DNA found within the nucleus are organized into structures called chromosomes. While DNA is present in an uncondensed state during interphase, being coiled around proteins and forming a complex called chromatin, the cell's genetic information cannot be accessed by proteins. DNA condenses during mitosis to form the characteristic chromosome structure.

Nuclear DNA is a double-stranded helical polyanionic structure whose conformation is dictated by the local chemical environment. The existence of multiple long strands causes steric crowding and drives the formation of a condensed structure. This negative charge creates special electrostatic binding conditions that allow for association with positively charged protein components in chromatin. A feature of DNA that should be emphasized is the rigid long-range structure and the unique primary sequence of base pairs. Its unique primary structure creates the potential for specific base-pair binding of proteins at specific sites along the DNA molecule.

Histone:

Histones are small basic proteins that contain approximately 100-150 amino acid residues with a high density of positively charged residues. Histones are basic proteins with a high content of positively-charged amino acid residues, whose binding to the predominantly negatively-charged phosphate backbone of DNA favors the electrostatic interactions to form the basic building unit of chromatin fibers. Histones are classified into five distinct families: H1, H2A, H2B, H3, and H4. The first family, linker histones, is clearly involved in the stabilization of the nucleosome chain; while the other four are the core histones, responsible for the main structuring of the nucleosomes. Core histones are organized into structural units comprising two copies of each type of core histone. Linker histones and core histones interact electrostatically, and through hydrogen bonds, both with the negative charge of the phosphates in the DNA and with each other. The nucleosomes consist of two molecules of H2A, H2B, H3, and H4, around which the magazine constituents of a DNA strand are coiled. The histones and DNA in their initial nucleosome structure, plus non-histone proteins- as linker proteins, topoisomerases, chromatin remodeling complexes, or other enzymes regulating histone post-translational modifications and also, more rarely, RNA molecules-are what generally compose the chromatin fibers.

Non-histone:

Non-histone proteins constitute a heterogeneous family of proteins that encompass high-mobility group proteins, histone-like proteins, transcription factors, RNA polymerases, RNA processing proteins, and polymerase complexes, and segregate chromatin in distinctive regulatory domains. Some non-histone proteins are stable components of DNA domains endowed with structural function, and only some of them dynamically associate with chromatin during specific functions; within those specific functions, they act in close collaboration with other proteins. Non-histone proteins are understood to be involved in three main functions attributable to chromatin: DNA packaging, DNA replication and repair, and gene regulation.

Organization of Chromatin Fiber:

During all the active phases of the cell cycle, within which the genetic information is read, transcribed and replicated, eukaryotic DNA is not naked, but closely associated with the histones to uniformly organized chromatin. During the biological activity of the organism, chromatin is thought to have different dynamic and functional states that participate in the control of the transcriptional process and in the expression of a series of specific genes. However, with the exception of some short regions that need to be kept open and accessible for structural and functional purposes, eukaryotic DNA is a long polymer that is always associated to histone proteins in the form of nucleoprotein fibers. This was experimentally demonstrated by using a centrifugation protocol sensitive to the chromatin solubility, at different ionic strength and in the presence of specific denaturing reagents, that were able to separate insoluble aggregated chromatin fibers with predominant high-order structure and soluble nucleoplasmic chromatin with predominantly lower order structures, that can still be considered "primitive" DNA-protein complexes.

Within one nucleosome, the DNA strand wraps around a core particle that is formed by 8 histone proteins, 2 copies of the H2A-H2B dimers and a central tetramer formed by the H3 and H4 histone proteins. The nucleosomal DNA linker is formed by different lengths of DNA that separates the core histones, and it is kept bent and together with a specific aspect ratio by the histone H1. Nucleosomes are joined together in a higher-order structure by linker histone proteins that interact with adjacent core particles in a solenoidal or zig-zag organization of the nucleosomes in an array. Histone H1 and other proteins that were recently identified take care of stabilize this structure, keeping together DNA segments that are bent around the adjacent nucleosome core.

ecause of their fundamental role in the packing of eukaryotic DNA, nucleosomes have been extensively studied since they were first described. Early studies revealed some of their three-dimensional attributes, including a disc shape with a diameter of 10–12 nm, thickness of 5–6 nm, organization as beads-on-a-string chromatin fibers, and formation of a 146-base-pair meat on a proteinaceous core of eights histones molecules arranged as an octamer of two each of H2A, H2B, H3, and H4. These are all hallmarks of what was subsequently described as the structure of the nucleosome core particle, which contains the histone octamer and the 146 bp of DNA that wrap around the octamer. Two additional histone proteins, H1 and H5, bind to the linker DNA in either direction, forming a bridge with the nucleosome on either side, connecting the core nucleosome particles in an overall solenoid-like structure. Other features of nucleosomes include their periodic positioning along eukaryotic DNA, their interaction with nonhistone proteins some of which could be responsible for those sites of protein-core granule transition for DNA transcription at active loci.

In more recent studies, the remarkable stability of the nucleosome core particle was also directly related to major allostery of some of its components and to energetically favorable and unfavorable DNA and histone sequences allowing or disallowing nucleosome formation, respectively. However, while nucleosome core packing occurs at the onset of DNA replication, transcription, double-strand repair, junk DNA packing, DNA replication or recovery checkpoints, and daughter or uncleaved chromatin and other chromatin transitions, the entire possible repertoire enables and disables nucleosomal formation and packing, each resulting in specific changes in chromatin structure and function. Nucleosome dynamics and stability along the entire eukaryotic DNA requires a systematic and exhaustive study of all gene loci. It is what would accomplish the stated goals of the large projects announced in recent years.