Histone H4: Biological Overview | Evolutionary Homologs | Regulation | Developmental Biology | References

Gene name - Histone H4

Synonyms -

Cytological map position - 39D3-E2

Function - core histone

Keywords - chromatin component - histone

Symbol - His4

FlyBase ID:FBgn0001200

Genetic map position - 2-[54.6]

Classification - histone

Cellular location - nuclear

NCBI links: Precomputed BLAST | Entrez Gene

Chromatin is the DNA-protein complex that constitutes chromosomes. The major protein component of chromatin is the nucleosome octamer. One of the four proteins that comprise the nucleosome octamer is Histone H4. The special interest in Histone H4 derives from the fact that it is acetylated in several important processes, among them gene activation, chromatin assembly and histone displacement by protamines in spermatogenesis. Two of these processes are described below: gene activation and chromatin assembly. The evidence that Histone H4 acetylation is of fundamental biological importance is not confined to Drosophila, but has been gleaned from work with yeast, ciliates, flies, frogs and mammals. Histone acetylation is an evolutionarily conserved process, carrying out conserved biological functions.

Gene Activation: Histone acetylation plays a positive role in promoting access of transcription factors to nucleosomal DNA. The idea that acetylated histones are associated with transcriptionally active chromatin is more than three decades old. However, only in the last decade have experimental systems been sufficiently refined to provide convincing evidence. One such system is the 5s RNA gene of Xenopus. Whole histone octamers, consisting of (H2A/H2B/H3/H4)*2, prevent binding of transcription factor TFIIIA to the Xenopus 5s gene. Acetylation of the histones used to assemble the histone octamer onto the 5S RNA gene facilitates the association of TFIIIA with the gene. Removal of the N-terminal tails (the site of histone acetylation) from the core histones also facilitates the association of TFIIIA with nucleosomal templates. It is thought that histone tails have a major role in restricting transcriptional factor access to DNA and that their acetylation releases this restriction by directing dissociation of the tails from DNA or inducing a change in DNA configuration on the histone core to allow transcription factor binding (Lee, 1993).

Histone H4 isoforms can be found at four different lysine residues, acetylated in different combinations. When polytene chromsomes from Drosophila larva are examined with antisera specific for each of the four acetylated lysine residues, differently acetylated isoforms are found in distinct patterns of distribution. H4 molecules acetylated at lysines 5 and 8 are distributed in overlapping, but nonidentical islands throughout the euchromatic chromosome arms, suggesting that H4 acetylated at lysines 5 and 8 is associated with transcriptionally active genes. ß-Heterochromatin in the chromocenter is depleted in these isoforms, but relatively enriched in H4 acetylated at lysine 12. This suggests that H4 acetylated at lysine 12 is associated with transcriptionally silent ß-heterochromatin. H4 acetylated at lysine 16 is found at numerous sites along the transcriptionally hyperactive X chromosome in male larvae, but not in male autosomes or any chromosome in female cells.

The association of H4 acetylated at lysine 16 with male X chromosomes is intimately related to the process of dosage compensation. Males have only one X chromosome, compared with the two found in females. Were male X chromosomes to function at the same level of transcriptional activation as females, males would have only half the level of X chromosome coded gene products as females. The heightened activation of male X chromosomes is called dosage compensation (See Sex lethal). Dosage compensation is mediated by four loci, known as male-specific lethal genes (see also MSL-2). Histone H4 plays a role in dosage compensation. The specifically acetylated isoform of histone H4, H4Ac16, is detected predominantly on the male X chromosome. Two of the MSL proteins bind to the X chromosome in an identical pattern; the H4Ac16 pattern on the X is largely coincident with that of the MSL proteins. No H4HAc16 is found on X chromosomes in mutants of MSL genes. It has been suggested that acetylated Histone H4 plays a role in the heightened activation of the transcription of male X chromosomes (Bone, 1994).

Chromatin assembly: Control of gene accessability to transcription factors is not the only role of acetylation of H4 in the biology of the cell. Acetylation is involved in the process of histone assembly into nucleosomes. The cytoplasmic enzyme histone transacetylase B (HAT B) is involved in an evolutionarily conserved acetylation of newly synthesized Histone H4 on lysine 12 (Sobel, 1994 and 1995).

Hat B has been characterized from yeast, and it appears in the cytoplasm as a dimer consisting of two subunits, Hat1p and Hat2p. Hat1p is the histone transacetylase, while Hat2p is a member of an evolutionarily conserved family of p48 proteins. Members of the p48 family are histone escorts, accompanying newly synthesized histones from cytoplasm to nucleus. The p48 family members are conserved subfamily of WD-repeat proteins, possessing a motif involved in protein-protein interaction. p48 proteins are found in three contexts: associated with Hat B in the cytoplasm, associated with chromatin assembly factor (CAF-1) in the nucleus (Tyler, 1996 and Verreault, 1996), and associated with a histone deacetylase activity. It is likely that cytoplasmic H4 is acetylated by Hat B, carried to the nucleus by CAF-1 (See Nap1), where it is assembled into newly synthesized chromatin, and subsequently deacetylated in a process required for chromatin maturation. p48 family members act as histone escorts, accompanying the histones through the process of acetylation, assembly and deacetylation (Roth, 1996 and references).

A second histone transacetylase activity is found in the nucleus of yeast. GCN5p, a yeast protein involved in transcriptional activation, is homologous to tetrahymena HAT A, a nuclear histone acetyltransferase. Both the Tetrahymena protein and GCN5p possess histone acetyltransferase activity and a highly conserved bromodomain. p55 preferentially acetylates histone H3. The presence of a bromodomain in nuclear A-type histone acetyltransferases (but not in cytoplasmic B-type HATs), known to function in protein-protein interaction, suggests that HAT A is directed to chromatin through protein interaction to facilitate transcriptional activation (Brownell, 1996).

Thus histone acetylation plays biologically important roles in histone assembly, gene activation, and chromatin structure. The protein complexes responsible for orchestrating these funtions are only now being worked out. The payoff will be an understanding of the complex evolutionarily conserved machinery regulating chromatin dynamics and gene expression in living cells.


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 alternate directions. Three genes (H3, H2A and H1) are transcribed from one DNA strand, and two (H4 and H2B) from the other strand. The reassociation kinetics of this repeat unit indicates 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 are linked in species whose descendents subsequently diverged to give rise to Protosomia and Deuterostomia (Lifton, 1977).


Structural Domains

By searching the current protein sequence databases using sequences from human and chicken histones H1/H5, H2A, H2B, H3 and H4, a database was constructed of aligned histone protein sequences with statistically significant sequence similarity to the search sequence. In addition, a nucleotide sequence database of the corresponding coding regions for these proteins has been assembled. The region of each of the core histones containing the histone fold motif has been 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: see Histone fold motif (Baxevanis, 1996).

The histone octamer is a tripartite assembly in which two dimers (H2A-H2B) flank a centrally located tetramer (H3-H4)(H3-H4). The histone octamer appears either as a wedge or as a flat disc. The folded histone chains are elongated rather than globular and are assembled in a characteristic "handshake" motif; that is, rather than assembling like the globular domains of the alpha and beta chains of the hemoglobin dimer, which have small local contacts, the histone chains, by clasping each other, develop an extensive molecular contact interface. The four types of core histone chains have very low sequence homology but share the histone fold, a common motif of tertiary structure. This common motif consists of a long central helix flanked on either side by a loop segment and a shorter helix. This structure suggests a common evolutinary origin for the four core histones. Each histone fold appears to be the result of a tandem duplication that divides it into two similar and contiguous helix-strand helix (HSH) motifs.

The histone fold residues can be classified in one of four ways: surface, self, pair or interface. "Surface" residues are located on the sides of the dimer subunits facing the exterior of the fully assembled octamer and either are exposed to the solvent or interact with DNA. "Self" residues are involved in contacts within one chain. "Pair" residues contribute to the contacts used to establish histone dimers - i.e., between H3 and H4 or between H2A and H2B. "Interface" residues are involved in contacts between the histone dimers - i.e., at the H3-H3 interface or at the H2A-H2B dimer-(H3-H4)2 tetramer interfaces. The histone fold is engaged directly in the formation of the histone dimers and specifies the paired-element motifs that guide the docking of the DNA to the octamer. Since the HSH motif is seen twice per histone and is present in all four core histone classes, it emerges as the basis from which eight classes of successful variations on the original motif have evolved over time. It appears that evolution allows consideable variation in primary structure, but only to the extent that the pattern of the histone fold is preserved. The overall configuation of the fold within the octamer is strictly maintained through evolution by the requirement that three well-separated regions of the fold (docking pads) be spaced so as to interact with the three consecutive turns of the phosphate backbones of a tightly curved double helix (Arents, 1995).

The transcription factor TFIID is a multimeric protein complex containing the TATA box-binding polypeptide (TBP) and TBP-associated factors. The N-terminal regions of dTAFII62 and dTAFII42 have sequence similarities with histones H4 and H3. The histone-homologous regions of dTAFII62 and dTAFII42 form a heteromeric complex both in vitro and in a yeast two-hybrid system. Neither dTAFII62 nor dTAFII42 forms a homomeric complex, in agreement with a nucleosomal histone character. Moreover, circular dichroism measurements show that the heteromeric complex is dominated by alpha-helical secondary structure. These results strongly suggest the existence of a histone-like surface on TFIID (Nakatani, 1996).

A complex of two TFIID TATA box-binding protein-associated factors (TAFIIs) has been observed by X-ray crystallography. The amino-terminal portions of dTAFII42 and dTAFII62 from Drosophila adopt the canonical histone fold, consisting of two short alpha-helices flanking a long central alpha-helix. Like histones H3 and H4, dTAFII42 and dTAFII62 form an intimate heterodimer by extensive hydrophobic contacts between the paired molecules. In solution and in the crystalline state, the dTAFII42/dTAFII62 complex exists as a heterotetramer, resembling the (H3/H4)2 heterotetrameric core of the histone octamer, suggesting that TFIID contains a histone octamer-like substructure (Xie, 1996).

Using the yeast two-hybrid system, a human cDNA was isolated that encodes a protein (hp22) interacting with TATA box-binding factor TFIID subunit p80 containing similarity with histone H4. Sequence analysis showed that the open reading frame (ORF) specifies a 161-amino-acid (aa) polypeptide homologous to Drosophila TFIID subunit p22 (dp22). Comparison of the aa sequence of human TFIID subunit p22 (hp22) with that of dp22 reveals that p22 is composed of two distinct regions; the less conserved N-terminal (20% identity) and the highly conserved C-terminal (65% identity). Additionally, the C-terminal region was found to contain similarities with histones H2B and H3. Northern blot analysis shows mRNA corresponding to hp22 is expressed in all tissues examined (Choi, 1996).

Histone H4: Evolutionary Homologs | Regulation | Developmental Biology | References

date revised: 28 MAY 97  

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