BIOLOGICAL OVERVIEW

In eukaryotic cells, the combination of DNA with numerous proteins known as chromatin organizes what would otherwise be a tangled DNA helix. In the absence of linker histones, chromatin forms a 10nm thick nucleosome-containing chromatin fiber, the first order of DNA - protein packing. The linker histone H1, serves to stabilize a higher order 30 nm diameter chromatin fiber that is fundamental to the structural organization of chromosomes. The linker histone binds to each nucleosome, and by self affinity, links these nucleosomes together resulting in the 30 nm chromatin fiber. Modulation of linker histone binding is thought to be an additionally important element in the ordering of chromatin structure accompaning activation and inactivation of gene transcription.

The first order of chromatin compaction consists of 146 bp of DNA wound in two superhelical turns around a core histone octamer consisting of two molecules each of histones H2A, H2B, H3 and H4. The core histones, constituting the nucleosome, interact with DNA to form the 10 nm thick chromatin fiber. A single Histone H1 polypeptide interacts with an additional 20 bp of DNA as it enters and leaves the nucleosomal core.

Just where does linker histones bind to the nucleosomal core? The traditional model for H1 binding to nucleosomes cores posits that the globular domain of the linker histone binds to the outward facing DNA, at the site where DNA enters and leaves the core nucleosome structure. In this model, linker histones span the entering and exiting DNA, holding the DNA in place. Linker histones exposed on the surface of nucleosomes are then free to self associate, resulting in the higher order 30 nm chromatin fiber (Thomas 1992 and citations).

More recently it has become clear that linker histone might actually nestle inside the coils of the DNA that wrap around core histones, and that linker histone is not found symmetrically associated with entering and exiting DNA but is displaced by approximately 60 nucleotides from the center (dyad axis) of the nucleosome bound DNA (Pruss, 1996 and Hayes, 1996). Crystal structure analysis has shown that each linker histone consists of a globular 'winged-helix" central domain flanked by basic NH2- and COOH-terminal tail domains (Ramakrishnan, 1993). If linker histone-DNA interactions were analogous to those of the winged helix transcription factor HNF-3-DNA - that is, if linker histone were to bind within the major groove of DNA - then the globular domain would not be centered at the nucleosomal dyad (the earlier hypothesis), because at that place the major groove of the nucleosomal DNA faces the histone octamer, and only the minor groove faces out and is available for additional interaction.

The newer idea of an asymmetic nucleosome described above might impart a directionality to the folding of the chromatin fiber, consistent with a polar head-to-tail arrangement of linker histone molecules. The orientation of the winged-helix domain would favor interaction of the basic COOH-terminal tail of the linker histone with linker DNA (the DNA between nucleosomes), facilitating chromatin compaction. The binding of the winged-helix domain in the major groove would account for sequence selectivity of nucleosome position and the restriction of nucleosome mobility that is dependent on linker histones. Removal of histone H1 as seen on transcriptional activation of inducible promoters would remove a major positional signal for chromatin organization; the resulting mobility of histone octamers with respect to DNA sequence could greatly facilitate transcriptional activation (Pruss, 1996 and references).

Histone H1 is absent from Drosophila embryos early in development, but appears during midblastula transition, at a time when zygotic messenger RNA synthesis becomes activated. The high mobility group protein HMG-D, present at high levels prior to midblastula transition declines in prevalence relative to H1 concentration. It is thought that this change in relative protein concentrations is an important factor in activation of zygotic transcription. More information about this important interaction is found at the HMG-D site.

GENE STRUCTURE

The plasmid cDm500 consists of a 4.8-kb sequence of genes coding for five histone genes, H1, H3, H4, H2a, and H2b repeated in tandem 1.8 times. The five genes are consecutively oriented on alternate strands, and thus each successive gene is transcribed in the alternate direction. Three genes (H3, H2A and H1) are therefore transcribed from one DNA strand, and two (H4 and H2B) from the other strand. The reassociation kinetics of this repeat unit indicate that its sequence is repeated approximately 100 times per haploid genome. Virtually all copies of the DNA sequence are located in the region 39DE of salivary gland polytene chromosomes, a region that appears to span most of the 12 chromomeres associated with 39DE. In several species of sea urchin these five genes are likewise tandemly repeated, but all the genes are transcribed in the same direction. The finding that both sea urchin and the fly contain all five genes arranged in such a way, leads to the belief that the five histone genes were linked in species whose descendents subsequently diverged to give rise to Protosomia and Deuterostomia (Lifton, 1977).

PROTEIN STRUCTURE

Amino Acids - 255 (Murphy, 1986)

Structural Domains

By searching the current protein sequence databases using sequences from human and chicken histones H1/H5, H2A, H2B, H3 and H4, a new database has been constructed consisting of aligned histone protein sequences with statistically significant sequence similarity to the search sequence. A nucleotide sequence database of the corresponding coding regions for these proteins has also been assembled. The region of each of the core histones containing the histone fold motif is identified in the protein alignments. The database contains >1300 protein and nucleotide sequences. All sequences and alignments in this database are available through the World Wide Web at Histone fold motif This should be checked online (Baxevanis, 1996).

date revised: 1 April 98

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