DNA Is Associated With Two Major Groups Biology Essay

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In eukaryotic cells, DNA is associated with two major groups of proteins, the histones and non-histones. Histone proteins package DNA into a size and structure that can be easily fitted into the cell nucleus. Histones are small basic proteins and consist of five major types, H1, H2A, H2B, H3 and H4. [1] DNA is assembled into the nucleosome, the basic unit of chromatin, which are composed of 145-147 base pairs of DNA wrapped around an octameric containing two H2A-H2B dimmers and an H3-H4 tetramer. [11,30] While HI linker histone, links the two nucleosomes [14] and stabilizes the assembly of the octameric core into higher-order structures characteristics of chromatin [11] that allow further rounds of compaction and condensation to occur. [30] There are also histone variants which perform specialized functions. Chromatin structure also consists of other proteins such as high-mobility group (HMG). [30] Chromatin can exist in 2 forms; euchromatin (where the fibres are loosely packed and only become visible in mitosis/meiosis after chromosome condensation) or heterochromatin (where the fibres are densely and tightly packed and can be distinguished in interphase and even metaphase). [1] High content of lysine and arginine residues, which accounts for 20-30% of the amino acids in histones, results in the strong basic charge of histones. [1] Histones are bound to DNA through electrostatic interactions between positive charges of histones and the negatively charged phosphate group on the surface of the DNA helix. [1] Histones can bind both to themselves and DNA and can form a higher-order chromatin structure with additional histone-DNA and histone-histone contacts with other nucleosomes. [18,57]

Chromatin structure is highly dynamic and is regulated by numerous remodeling enzymes. Nuclear processes such as transcription, replication, recombinant and DNA repair [12] that require access to DNA, such as gene transcription and DNA replication and repair is blocked by the highly condensed chromatin. [57] Thus making the regulatory region of nucleosome structure and DNA-histone interactions regions unavailable for the binding of the transcriptional machinery and other factors involved in activation. [33] In response to change the state of chromatin, certain enzymes and protein complexes work by numerous mechanisms, with resultant effects on gene expression. [33]

Nuclear activities, such as replication, chromatin assembly and transcription have been long associated with post-translational histone modifications. [11] There are two main purposes of histone modifications. One of which is to "provide or remove recruitment signals for non-histone proteins involved in transcriptional activation and silencing". [9] And the second purpose is to change with the physical interactions between histones and DNA by modifying the chromatin structure. [9]

Histone chaperone proteins are associated with chromatin remodeling activities and can reversibly remove and replace histone variants within chromatin, as well as control the assembly/disassembly of nucleosomes during DNA transcription and replication. [57,63] For example, NAP-1 (nucleosome assembly protein 1) can remove H2A-HAB dimers from chromatin and their transient removal can affect fundamental nuclear processes especially transcription. [64]

ATP-dependent nucleosome-remodeling factors protein complexes that are involved in a range of nuclear processes, such as transcription, replication and DNA repair and can regulate chromatin structure at the nucleosomal level by altering histone-DNA interactions. [65] An example include the SWI/SNF complex which expsose or mask DNA by utilize the energy of ATP hydrolysis to remove or reposition nucleosomes. [57]

Histones are subjected to reversible DNA post-translational modifications such as methylation, acetylation, phosphorylation, sumoylation, ubiquitylation and ADP-ribosylation which are catalysed by nuclear enzymes. [12] Most of these modifications take place at the lysine and arginine rich terminal segments that protrude from the main globular domain. [1] The modifications eliminate one positive charge for each addition and reduce the strength of the electrostatic attraction of histones to DNA. [1] The histone tails have an essential role in mediating nucleosomal histone-histone interaction and chromatin folding; therefore their modifications are likely have influences on gene expression by altering chromatin accessibility and other DNA-related activities. [30,66] Recent studies have shown correlation of site-specific combinations of histone modifications and particular biological functions. [66] For example, acetylation of H3K18 is possibly associated with transcriptional activation, DNA replication and repair, whereas methyaltion of H3K27 by specific enzymes is likely to be associated with transcriptional silencing. [66] Studies on the post-translational modification of histones have given rise to the concept of "histone code" [30] where the various modifications within the histone tails combine to produce very specific effects on the chromatin structure and send exquisitely-tuned signals to histone- and DNA-binding proteins. [57]

Polyubiquitination, another post-translational modification, modulates protein function by inducing proteasome-dependent degradation by targeting the side-chain of lysine residue. [14] Studies have demonstrated that protein acetylation can also affect protein stability because there is an active competition between acetylation and ubiquitination for the same lysine residues. [14]

Acetylation (574 words)

Cellular mechanisms, including nucleosome assembly, gene regulation, DNA replication, cell division and compaction of DNA, are correlated to the various histone modifications. [1] Histone acetylation is the most extensively studied post-translation histone modification. In the past decade, a number of studies have been carried out over the years to identify enzymes which are responsible for the specific site of histone acetylation and the importance of acetylation role in the regulation of gene expression. Acetylation of the histone tail can have multiple effects, such as alteration of histone-histone interaction, histone-regulatory protein interactions and also weakens the histone-DNA contact. [14,18] This can lead to an open chromatin structure, which facilitates the process of transcription. [18]

Histone acetylation is a reversible process. Histone acetylation refers to the transfer of an acetyl moiety from acetyl coenzyme A (Ac-CoA) to the ε-amino group of a specific lysine residues located at the highly basic N-terminal domains of core histones. [54] Its steady state is maintained by the balance between two classes of enzymes with opposing effects, which are histone acetyltransferases (HATs) and histone deacetylases (HDACs).

Histones are held in chromatin by electrostatic interactions and during nucleosome assembly histones are temporarily acetylated before being added to DNA and then deacetylated when assembly is completed. [1] This temporary acetylation may reduce the electrostatic attraction between the histones and DNA and this would permit precise control of nucleosome assembly. [1] Acetylation disrupts the internucleosomal link, leading to a more open conformation of nucleosomes which enhances accessibility to DNA by enzymes (e.g. regulatory protein and transcription factors) catalyzing RNA transcription. [1]

HATs and HDACs are recruited to chromatin through interactions with DNA binding-transcription factors rather than binding directly to DNA, which add flexibility to the control of gene expression or through their ability to recognize epigenetic marks in promoter regions. [12,53] HATs function as transcriptional coactivator and HDACs as corepressor. [12] Lysine acetylation can destabilizes nucleosome structure or arrangement and give other nuclear factors such as transcription complex more access to a genetic locus when HATs neutralizes the positive charge of histone tails by transferring acetyl group of ε amino terminal of lysine residue, which potentially weakens the histone-DNA or nucleosome-nucleosome interactions. [33] By contrast, HDACs change activated nucleosomes to their inactivated or repressed state causing chromatin condensation. [12]

Chromatin accessibility is influenced by recruitment of multicomponent-protein complexes through protein domain, which are embedded in chromatin-associated proteins to recognize modified histone residues. [30] For example, acetylated lysine residues are recognized by bromodomain, a domain which is conserved by many chromatin-modulating proteins, such as GCN5, which also have intrinsic HAT activity. [30] By contrast, chromodomain, a domain shared by many chromatin structure regulators such as heterochromatin protein 1 (HP-1) proteins, are recognized by methylated lysine residues. [30]

Histone proteins and their domains differ in their degree of conservation and specific pattern of core histone acetylation has been observed. [54] Histone H3 acetylation is primarily associated with transcription and histone H4 acetylation is associated with transcription and chromatin assembly. [67] In histone H2A, about two positions are acetylated and several lysine residues in the N-terminal is reported to remain non-acetylated, even in the hyperacetylated chromatin state. [54] In histone H2B, seven to eleven positions are available for acetylation, however only four or five positions can be acetylated. In H3 histone, there are only four or five acetylation positions and acetylation occurs in all four of the lysine residues of the N-terminal domain of histone H4. [54]