Chromatin active

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). 

Some of this differential expression is achieved by having different regions of chromatin available for transcription in cells from various tissues. For example, the DNA containing the P-globin gene cluster is in active chromatin in the reticulocyte but in inactive chromatin in muscle cells. All the factors involved in the determination of active chromatin have not been elucidated. The presence of nucleosomes and of complexes of histones and DNA (see Chapter 36) certainly provides a barrier against the ready association of transcription fac-... 

The cis-acting elements that decrease or repress the expression of specific genes have also been identified. Because fewet of these elements have been smdied, it is not possible to fotmulate genetalizations about their mechanism of action—though again, as for gene activation, chromatin level covalent modifications of histones and other proteins by (repressor)-recruited multisubunit corepressors have been imphcated. 

Ahmad K, Henikoff S (2002) The histone variant H3.3 marks active chromatin by repUcation-independent nucleosome assembly. Mol Cell 9 1191—1200... 

Kumar A, Brown DT, Leno GH (2004) DNA intercalators differentially affect chromatin structure and DNA repUcation in Xenopus egg extract. Anticancer Drugs 15(6) 633—639 Kuo MT (1981) Preferential damage of active chromatin by bleomycin. Cancer Res 41(6) 2439—2443 Kuo MT, Sarny TS (1978) Effects of neocarzinostatin on mammalian nuclei release of nucleosomes. Biochim Biophys Acta 518(1) 186—190... 

One possible function for H3.3 and some of the other replacement variants is to maintain the integrity of chromatin structure by replacing histones that are damaged or lost during normal cellular metabolism. Ahmad and Henikoff [104] suggested that replication independent incorporation of H3.3 could provide a mechanism to switch patterns of histone modification by removing H3 molecules that may be irreversibly modified by methylation. They also suggested that H3.3 could serve as a mark of transcriptionally active chromatin. One complication for... 

H3 replacement variants are also present in plants [108] and Tetrahymena [109]. Phylogenetic analyses indicates that these H3 replacement variants arose independently of animal H3.3 [109]. Like H3.3, the plant H3 replacement variant also appears to be preferentially deposited into transcriptionally active chromatin [110]. The H3 replacement variant in Tetrahymena, hv2, is found only in the transcriptionally active macronucleus [49]. In contrast to H3.3, the amino acid differences between hv2 and the replication dependent H3 of Tetrahymena do not appear to be essential for replication independent incorporation into chromatin [111]. In this case constitutive expression appears to be the dominant factor that can drive replication independent deposition of hv2 or an H3 variant that is normally replication dependent. This difference between hv2 and H3.3 is not necessarily surprising because hv2 appears to have arisen independently of H3.3 and does not have the structural features characteristic of H3.3 [109]. 

Messenger RNAs for H2A.Bbd have been detected in human testis, fibroblasts and lymphocytes [77], but little is known about the amount of H2A.Bbd protein in these or other human cell types or about its presence in other species. The distribution of H2A.Bbd in chromatin was examined by expressing epitope-tagged or GFP-tagged H2A.Bbd in cultured cells. These studies revealed a striking deficiency of H2A.Bbd in the inactive X chromosome, leading to its name which stands for Histone H2A Barr-body deficient [77]. The distribution of H2A.Bbd overlapped extensively with that of H4 acetylated on lysine 12, suggesting that H2A.Bbd may preferentially associate with transcriptionally active chromatin. 

Chromatin fractionation approaches including ChIP assays have provided evidence for and against uH2A and uH2B being associated with transcriptionally active chromatin [270,281-285]. Most evidence supports uH2A being associated... 

The association between a histone tail modification and a particular functional state of chromatin, came with the demonstration that transcriptionally active chromatin fractions were enriched in acetylated histones, firstly by biochemical co-fractionationation ([8,9] and references therein) and then by Chromatin ImmunoPrecipitation, ChIP [10]. Subsequently, regions of transcriptionally silent constitutive and facultative heterochromatin, were shown, by immunofluorescence microscopy, to be under-acetylated [11,12]. This supported the idea that acetylation of the histone tails, with the associated loss of positive charge and reduction in DNA-binding constant, somehow caused chromatin to become more open (or less condensed ) and thereby more conducive to transcription. While this is likely to be an important contributory factor, it has now become clear that the... 

Boffa, L.C., Walker, J., Chen, T.A., Sterner, R., Mariani, M.R., and Allfrey, V.G. (1990) Factors effecting nucleosome structure in transcriptionally active chromatin. Histone acetylation, nascent RNA and inhibitors of RNA synthesis. Eur. J. Biochem. 194, 811-823. 

Hebbes, T., Thorne, A.W., and Crane-Robinson, C. (1988) A direct link between core histone acetylation and transcriptionally active chromatin. EMBO J. 7, 1395-1403. 

Finally, targeted active demethylation has been put forward as an explanation for the unmethylated state of CpG islands (Fig. 3e). In this model, features of active chromatin structure (e.g., histone hyperacetylation) cause active demethylation of associated sequences [43,44]. Based on a broad analysis of existing data, Szyf... 

Fig. 7. The model proposed by Szyf to explain the unmethylated status of active genes (for references and further details see Section 5.1). a) Inhibition of acetylation of the tails of core histones prevents active demethyiation. (b) When histone tails are acetylated, as in transcriptionally active chromatin regions, the demethyiase binding to the regions is enhanced, and the DNA is actively demethylated.

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