Linker histones chromatin compaction

The genetic information of eukaryotic cells is propagated in the form of chromosomal DNA. Besides the nucleic acid component, chromosomes contain architectural proteins as stoichiometric components, which are involved in the protective compaction of the fragile DNA double strands. Together, the DNA and proteins form a nucleoprotein structure called chromatin. The fundamental repeating unit of chromatin is the nucleosome core particle. It consists of about 147 base pairs of DNA wrapped around a histone octamer of a (H3/H4)2 tetramer and two (H2A-H2B) heterodimers. One molecule of the linker histone HI (or H5) binds the linker DNA region between two nucleosome core particles (Bates and Thomas 1981). 

Bednar, J., Horowitz, R.A., Grigoryev, S.A., Carruthers, L.M., Hansen, J.C., Koster, A.J., and Woodcock, C.L. (1998) Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc. Natl. Acad. Sci. USA 95, 14173-14178. 

A second model for HMGN action is that it counteracts chromatin compaction by linker histones. The ability of HMGN proteins to unfold SV40 minichromosomes and stimulate transcription from them is dependent on the presence of linker histones, and the data is consistent with HMGN counteracting the repressive... 

Since linker histones are involved in compacting the chromatin fiber, it was of interest to see whether the methylation-mediated chromatin compaction could be explained by a higher affinity of linker histones for methylated DNA. The literature on this point is highly controversial some reports demonstrated strong preference of linker histones for methylated DNA [168,169] whereas others found that linker histone binding was indifferent to the methylation status of the DNA [164,170,171]. 

The possible structural involvement of linker histones in the methylation-mediated chromatin condensation has been recently addressed by using the Atomic Force Microscope [175]. This extensive study combined in vivo and in vitro approaches to demonstrate that DNA methylation could cause chromatin compaction only in co-operation with linker histone binding. Finally, it may be... 

In eukaryotic cells, DNA is packaged into a highly compacted and condensed nucleoprotein structure called chromatin. Biochemical studies and electron microscopy indicated that DNA in eukaryotic chromatin is folded as regular units, each of which contains 146 base pairs of DNA and a core of histone proteins. Structurally, DNA makes approximately 1.8 turns around a central histone octamer that consists of two molecules of each of the four core histones H2A, H2B, H3, and H4. The combination of a histone core and associated DNA makes up the nucleosome. Nucleo-somes are linked by 20-100 base pairs (bp) of linker DNA, so as to form a beadlike nucleosomal array. In conjunction with the linker histone, Hl,... 

The same parameters were obtained by AFM imaging of chromatin fibers reconstituted in vitro with unmethylated and methylated DNA when reconstitution was performed in the absence of linker histone. After addition of H1 histone to chromatin fiber reconstituted around methylated DNA, the degree of compaction observed was different and was very close to that observed in vivo after induction ofDNA hypermethylation. The values obtained were 0.46 for the control vs. 0.70 for the hypermethylated chromatin fibers from the in vivo experiments and 0.48 for the control vs. 0.67 for the methylated HI-containing reconstituted ones. This leads to the conclusion that HI histone is required for DNA-methylation dependent compaction of chromatin structure. ... 

Kaiymov MA, Tomschik M, Leuba SH et al. DNA methylation-dependent chromatin fiber compaction in vivo and in vitro Requirement for linker histone. FASEB J 2001 15 2631-2641. 

Mg (but not Na" ") results in a structure that is equivalent to the 30-nm compact fiber in the extent of condensation [49]. Finally, the independent and critical function of core histone N-termini in chromatin condensation was demonstrated by showing that nucleosomal filaments reconstituted from core histones lacking their N-terminal domains are unable to condense into folded structures upon an increase of Mg " ", despite the presence of properly bound histone H5 ([50,51], see also Ref. [52] for the discussion of the special role of H3 and H4 tails). Thus, the presence of HI is not a sine-qua-non condition for salt-induced chromatin folding, which can proceed in Hi s absence and is an intrinsic property of filaments consisting of spaced core particles. A key question is how many of the features of the native 30-nm compact fiber are due to the presence of histone HI From the available data it seems that HI may influence the intrinsic folding pathway of the chromatin filament by stabilizing a single ordered conformation. This property can have much to do with the cooperativity of HI interactions within chromatin but also with the way HI is bound to the nucleosome and with the efifect it exerts on the path of linker DNA. 

Nucleosomes are connected to one another by linker DNA of variable length and the linker-binding histone HI protein (Fig. 1) (7). These long arrays of nucleosomes spontaneously condense to form helical arrays of nucleosomes, termed the 30-nm fiber after its apparent diameter (Fig. 1) (8). Additional condensation and compaction of chromatin occur through intemucleosomal interactions. One important internucleosomal interaction required for chromatin fiber formation is the interaction of a highly acidic patch of histone H2A with the histone H4 tail (8). Ultimately, these internucleosomal interactions form interphase chromatin with an unknown architecture (Fig. 1) (9). 

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