Linker DNA (Molecular Biology)

Linker DNA is the DNA connecting chromatosomes in chromatin. Its length can be taken to be the difference between the number of DNA base pairs in the nucleosome repeat unit and the 166 bp in the chromatosome. This varies from essentially "zero" in the yeast Saccharomyces cerevisiae and mammalian cortical neurons (which have a repeat length of ~166bp) to ~74bp in sea urchin sperm (repeat length ~240bp). Linker DNA is complexed with the basic C-terminal (1), and possibly N-terminal, tail of histone H1 and its variants; consequently, H1 is often designated as a "linker histone"). The details of the interaction are unclear, but it must be largely electrostatic (basic protein side chains interacting with DNA phosphate groups) and is important in promoting condensation of the linker DNA in the folding of the nucleosome filament into higher-order structure (see Chromatin). The linker is relatively accessible, compared with the DNA sequestered within the body of the nucleosome, and is preferentially cleaved by endonucleases, such as micrococcal nuclease (Staphylococcal nuclease), that are used to release nucleosomes (and oligomers thereof) from nuclear chromatin for biochemical and biophysical study. Transcription factor binding sites in the linker region, for example between positioned nucleosomes (see Chromatin), are likewise generally more accessible than those in DNA wrapped around the octamer. The repeat length, and hence linker length, can vary throughout the genome, as shown by Southern blotting using various probes of the "ladder" of DNA fragments extracted from a micrococcal nuclease digest of chromatin (2).

The nature of the path taken by linker DNA—whether bent or straight—is somewhat controversial, as are models for chromatin higher-order structure (see Chromatin) to which this feature is relevant. The solenoid and related models, in which the nucleosome filament is helically coiled with increasing ionic strength in vitro, require a bent linker to allow nucleosomes to pack together in space; other models invoke straight linkers. The models and evidence have been reviewed (3, 4). Electron microscopy suggests that the linkers may be straight in the extended nucleosome filament at low ionic strength, but linkers are not visible in the condensed structure and could well be bent. The roughly 10-nucleotide pattern of thymidine dimer formation observed for core DNA, and attributed to its curvature around the octamer, is absent for linker DNA, for which the pattern is relatively uniform (5); however, this should not be taken as definitive evidence for a straight linker rather than a differently curved linker, or a curved linker whose reactivity is altered by association with H1. Studies of the sedimentation properties of dinucleosomes, which become more compact with increasing ionic strength, are not readily compatible with a straight linker (6, 7). None of this evidence is absolutely conclusive, however, and definitive evidence from long polynucleosomes is badly needed. Analysis of all the available information on (average) nucleosome repeat lengths, long and short, has revealed that they are quantized, meaning that the linker DNA lengths are quantized (8). The values are related to each other by integral multiples of the helical twist of DNA (~9.5 to 10.5 bp/turn), suggesting that the basis for this is the requirement for definite protein-DNA and protein-protein interactions in a higher-order structure. Quantization would be expected for the solenoid model, but would also be compatible with the straight linker models.

Histone H1 is clearly a major factor in establishing a regular length of linker DNA in a reconstituted nucleosome array, and it presumably also plays this role in vivo. "Chromatin" reconstituted in vitro by mixing histones at high ionic strength (eg, 2 M NaCl) and then dialyzing to low ionic strength shows close packing of octamers, irrespective of the presence of H1, which has no effect because it is the last histone to bind in this procedure. Cell-free extracts from Xenopus eggs and oocytes and from Drosophila embryos will assemble plasmid DNA, irrespective of sequence, into "physiologically" spaced chromatin in an ATP-dependent fashion (see Chromatin), and the nucleosome spacing (and hence linker length) is increased by H1. Spacing may also have an electrostatic component, involving neutralization of charges on linker DNA (9), and this has been taken to suggest a connection (possibly the basis of quantization; see text above) between nucleosome spacing and the formation of higher-order structure, which is also ionic strength-dependent (10). A well-defined in vitro system starting with histones and DNA, and using polyglutamic acid, will also assemble "properly spaced" chromatin, in an H1-dependent, ATP-independent manner (11). In this case, formation of regular arrays is sensitive to (nucleosome positioning?) signals in the DNA.

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