Open chromatin

Inactive and active chromatin domains can be defined at the molecular level by the presence (or absence) of specific histone modifications (or combinations of modifications), by the degree of chromatin compaction and the presence of chromatin associated proteins. Several earlier studies focusing on specific genes or loci showed that active chromatin is generally more accessible and enriched in acetylated forms of histones H3, H4, H2A [5] and histone H3 methylated at lysine 4 (H3/K4) [6]. H3/K4 di- and tri-methylation and H 3 acetylation correlate globally with open chromatin [7]. 

ChIP-Seq of histone modifications correlated with DNAse Seq of open chromatin in CD4 cells [8, 29]. 

Figure 7.6 Correiation of open chromatin IP (DNasel hypersensitivity data) with H3K4me3 enrichment. All H3K4me3 enriched regions (symbolized as gray bars) are aligned at the zero position and correlated with the open chromatin...

Results Two distinct peaks for the correlation of H3K4me3 enrichment and DNAse accessibility are obtained with a most frequent distance of 160 bp, indicatingthat open chromatin occurs with a specific distance of approximately 160 bp to regions with H 3 K4me3 methylation. Two peaks are obtainedbecause the measurement procedure of the open chromatin data and the histone modifications are not strand-specific. 

Closed chromatin trascriptional repression Open chromatin transcriptional activation... 

Acetylation of the lysine residues of histones H3 and H4 was one of the first modifications of chromatin to be described (Fig. 1) (14). It is associated with the establishment of an open chromatin state that is active transcriptionally. This modification contrasts with hypoacetylation, which is associated with a compacted chromatin structure that is inaccessible to transcription machinery. The majority of all lysine residues of the N-terminal tails of histones H3, H4, H2A, and H2B have the ability to be... 

Transcription factors are bound to the promoters of the rabl7 and rab28 gene in uninduced conditions in embryo, leaf and cell culture. These ABA inducible promoters are thus in an open chromatin structure and nucleosomes are probably absent or modified. The... 

Integration in open chromatin andlor near CpG islands... 

In conclusion, the results available suggest that the initial integration into open chromatin regions (such as those corresponding to the GC-richest isochores) is favoured even for a GC-poor provirus. Stability of integration and expression are, however, associated with an isopycnic localization. 

Alus GC-rich isochores more open chromatin + Stability... 

We also showed that the two subsets of bands investigated here not only have dirTeicni locations in the nucleus, but also correspond to different chromatin conformations, the H3 band DNA being remarkably more relaxed compared to the LI band DNA. This is understandable if we consider the special properties of H3 isochores compared to 1,1 isochores. In fact, the more open chromatin of the 113 band DNA corresponds to the highest concentration of genes and to the highest level of transcriptional activity. This... 

Figure 7,27. A carioon showing that the cemromeric proximal regions of chromosomes tend to be present in compact chromatin structures at the periphery of the imerphase nucleus (blue blocks), whereas the distal regions are in an open chromatin structure (red filaments) in the tenter of the nucleus. Only two chromosomes ate depicted. In this simplified drawing entire chromosome arms arc represented as completely open. More realistically, the open chromatin loops should concern a number of regions from each chromosome arm.

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