Euchromatin and Heterochromatin

Chromatin may be crudely divided into two types, euchromatin and het-erochromatin . In general, euchromatin comprises transcriptionally active 

Selected DNA modifications caused by enzymatic (5-methyl and 5-hydroxymethylcytosine) and chemical (i.e. damaging) methylation (1-meA, 1-meG, 3-meT, 3-meC). Enzymes capable of catalysing deme-thylation of 5-meC have not yet been discovered. DNMT = DNA methyltransferase SAM = S -adenosylmethionine. 

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Grunstein M, Hecht A, Eisher-Adams G, Wan J, Mann RK, Strahl-Bolsinger S, Laroche T, and Gasser S (1995) The regulation of euchromatin and heterochromatin by histones in yeast. J Cell Sci Suppl 19 29-36... 

The structural differences between euchromatin and heterochromatin are coor-dinately regulated by reversible covalent modification of the DNA or histones. 

Figure 5.5 Schematic showing euchromatin and heterochromatin, illustrating the accessibility to transcription machinery (transcription factors and RNA polymerases) as a result of different histone and DNA modifications. H3K4 methylation and lysine (hyper)acetylation are generally associated with euchromatin formation, while H3K9, H3K27 and H4K20 methylation, together with lysine hypoacetylation and DNA 5-meC methylation, are characteristic of heterochromatin.

In addition to the role for the nucleosome-nucleosome interactions, the histone tails are known as the region that undergoes post-transcriptional modifications, such as acetylation, phosphorylation, and methylation (Fig. Ic) (Peterson and Laniel, 2004). These modifications trigger the formation of euchromatin (acetylation), heterochromatin (methylation), or metaphase chromosome (phosphorylation). The details of these modifications will be described in chapters 8-11. 

Other Metal-Peptide and -Protein Interactions.—The determination of protein-bound trace elements in biological material by neutron activation analysis has been described Zn, Hg, Cu, and Se were accurately detected in human liver samples, provided that most of the element concerned was protein bound. An interaction of mercury with a protein or a protein-DNA complex has been invoked to explain the partitioning of the metal in euchromatin over heterochromatin (from mouse liver nuclei) by a 10 1 ratio. " Bovine retinas, isolated rod outer segments and emul-phogene extracts of rod outer segments have been shown to contain appreciable amounts of Zn ", Ca and the zinc levels being light sensitive. 

In addition to elevated AdoMet levels, trypanosomes treated with DFMO in vivo experience a six-fold increase in the activity of protein methylase II but not I or III (55). Protein methylase II specifically methylates carboxyl groups of aspartate and glutamate residues. In mammalian cells, histone methylation may be involved in the condensation of euchromatin to heterochromatin prior to mitosis (56-58), and may therefore have a role in gene expression. Aspartate- and glutamate-rich histones have also been characterized from both T. b. brucei and Crithidia fasciculata making these likely substrates for protein methylase II activity (59,60). 

DNA and RNA serve as the genetic material for prokaryotic and eukaryotic cells, for viruses, and for plasmids, each of which stores it in a different arrangement or location. In prokaryotes, DNA is not separated from the rest of the cellular contents. In eukaryotes, however, DNA is located in the nucleus, where it is separated from the rest of the cell by the nuclear envelope (see Fig. 10.20). Eukaryotic DNA is bound to proteins, forming a complex called chromatin. During interphase (when cells are not dividing), some of the chromatin is diffuse (euchromatin) and some is dense (heterochromatin), but no distinct structures can be observed. However, before mitosis (when cells divide), the DNA is replicated, resulting in two identical chromosomes called sister chromatids. During metaphase (a period in mitosis), these condense into discrete, visible chromosomes. 

Transcriptionally inactive chromatin is densely packed during interphase as observed by electron microscopic smdies and is referred to as heterochro-matin transcriptionally active chromatin stains less densely and is referred to as euchromatin. Generally, euchromatin is repficated earfier than heterochromatin in the mammafian cell cycle (see below). 

Acetylation of the histone tails correlates with the activities of genes (Kimura et al., 2005). However, the detailed analyses of the acetylation on the individual lysine residue have revealed that the relationship between the acetylation and the chromatin-compaction is not simple. There are 1-6 lysine residues in each histone subunit, that could be acetylated the Lys of H2A, Lys, Lys, Lys, and Lys ° ofH2B, Lys , Lys , Lys, Lys, Lys, andLys of H3, and Lys, Lys, Lys, and Lys of H4. In mammal, more than ten HATs (7/istone Acetyl Transferases) have been identified, each of which acetylates a specific lysine residue. Acetylation frequently occurs in euchromatin regions, and some in heterochromatin regions. For example, the acetylation of Lys of H4 leads to a telomeric silencing (Kelly et al., 2000). In Drosophila, Lys of H4 is acetylated specifically in the... 

Meneghini MD, Wu M, Madhani HD (2003) Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112 725-736 Mermoud JE, Costanzi C, Pehrson JR, Brockdorff N (1999) Histone macroH2A1.2 relocates to the inactive X chromosome after initiation and propagation of X-inactivation. J Cell Biol 147 1399-1408... 

Htzl H2Av H2A.Z Various functions in different organisms in euchromatin (transcription, boundary function, repression) maintenance or heterochromatin (subtelomeric, pericentric, and other) RD/RI... 

Euchromatin generally corresponds to looped 30-nm fibers. Heterochromatin is more highly condensed. Figure 1-1-14 shows an electron micrograph of an interphase nucleus containing euchromatin, heterochromatin, and a nucleolus. The nudeolus is a nuclear region spedalized for ribosome assembly (discussed in Chapter 3). 

In the nuclei of eukaryotes (see p. 196), DNA is closely associated with proteins and RNA. These nucleoprotein complexes, with a DNA proportion of approximately one-third, are known as chromatin. It is only during cell division (see p. 394) that chromatin condenses into chromosomes that are visible under light microscopy. During interphase, most of the chromatin is loose, and in these conditions a morphological distinction can be made between tightly packed heterochromatin and the less dense euchromatin. Euchro-matin is the site of active transcription. 

Two states can be distinguished in chromatin heterochromatin and euchromatin. The two states describe for every cell type a characteristic difference in degree of condensation and transcription activity of DNA. Genes located in the condensed heterochromatin can not be transcribed, whereby genes located in euchromatin are accessible for transcription. 

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