Histone H1

Pergamon PII: S1357-2725(97)00026-S

MOLECULES IN FOCUS

Histone Hl ALAN

P. WOLFFE

L&orator), of’ Molecular Embryology, National Institute qf’ Child He&h and Humurl Dcwlopmeut, NIH. Building 18T, Room 106, Bethesda, MD 20892-5431. U.S.A. Linker histones of which histone Hl is a representative are a diverse family of architectural proteins within the eukaryotic nucleus. These proteins have a variety of structures, but invariably contain a region enriched in lysine, serine, alanine and proline. All metazoan histone Hls also include a structured domain that binds to DNA through a helix-turn-helix motif. By binding to the linker DNA flanking the nucleosome core they contribute to the assembly of higher-order chromatin structures. Surprisingly, the use of “knockout” technology to eliminate histone Hl in isolated cells and Xenopus does not prevent the assembly of chromosomes or nuclei, however specific genes are activated or repressed indicative of targeted regulatory functions. A dual role for histone HI in chromatin structure and gene regulation might contribute to epigenetic phenomena in which heritable states of gene activity are maintained through mechanisms independent of gene sequence. This may have important implications for biotechnological and medical research. %‘I 1997 Elsevier Science Ltd. All rights reserved Keywords: Nucleosome Developmental control ht.

J. Biochcm.

Cdl

Bid.

Chromatin

Transcriptional

control

STRUCTURE

Eukaryotic DNA is wound up into nucleosomes through interaction with small basic proteins described as histones. Within each nucleosome, two molecules of each of the four core histones form an octamer around which is wrapped at least 146 bp of DNA. Between these nucleosome cores is a variable length of linker DNA that is bound by the linker histones such as histone Hl. The complex of a nucleosome core, linker DNA and histone Hl is known as a nucleosome. The core histones demonstrate remarkable sequence conservation through evolution, whereas the linker histones diverge significantly in sequence and structure. A variety of different molecules have been described as “histone Hl”. Members of this “histone Hl” protein family are best defined simply as abundant basic proteins that interact with linker DNA. 4 December

Translational

(1997) 29, 1463-1466

INTRODUCTION

Recewed

control

1996: accepted

5 February

1997. 1463

Metazoan histone HI has a three-domain structure: a central globular domain flanked by N- and C-terminal tail regions (Hartman V/ (I/., 1977). The globular domain has been proposed to bind to DNA where it enters and exits the nucleosome (see Fig. 1 left-hand panel. Staynov and Crane-Robinson, 1988). However, a recent crystal structure for the globular domain of a metazoan linker histone reveals unanticipated similarities to a family of eukaryotic transcription factors that have a “winged-helix” structure and that bind to DNA at a single site (Ramakrishnan et al., 1993; Clark et nl.. 199.1). This observation, coupled to nuclease protection and histone-DNA crosslinking experiments, has led to a new asymmetric model of the nucleosome (Hayes, 1996; Pruss et ~1.. 1996). In this model, the globular domain of the linker histone lies inside the turns of DNA in the nucleosome core, also making contact with the core histones (Fig. 2). It remains to be resolved

how frequently the two different nucleosomal structures that have been proposed are found within chromatin. The C-terminal tail region of histone HI is rich in lysine, serine, proline and alanine. This tail region binds to the linker DNA. neutralizing its charge and facilitating chromatin condensation. Numerous variants of histone HI exist, differing predominantly in the length and net charge of their C-terminal regions. In the protozoan T~~frtrl?!,l??crlu,the histone HI lacks a central globular domain entirely, consisting only of a 163 amino acid-long peptide with a very similar sequence to the C-terminal region of a metazoan linker histone. In contrast. within the S(r~c~hrr~on?,~~e.s cewrisirrc genome a gene exists encoding a linker Hl-like protein that has two globular “winged-helix” domains, separated by a lysine-. alanine- and proline-rich “tail” region only 42 amino acids in length (Wu et al., 1986; Landsman. 1996). The structure of metazoan linker histone genes falls into three classes encoding: (I) histone HI variants expressed in early development; (2) those expressed in normal somatic cells; and (3) differentiation-specific linker histone H 1 variants (Khochbin and Wolffe, 1994). The genes for histone Hl variants expressed in early development (such as the amphibian linker histone B4 or H lm) contain oocyteintrons; their promoters contain Nucleosome Globular

Higher-order structure

domain

Wad. axis

selective cis-acting elements such as the Y-box. Genes encoding somatic-specific variants 01 linker histone HI lack introns and show \‘er-4 similar promoter structures. containing ;I typical TATA box, CAAT box, G/C-rich sequence and a highly conserved histone-gene-specific HI box (S’AAGAAACACA3’). Genes for differentiation-specific histone HI variants (e.g. HI and H5) have promoter elements that diverge considerably, incorporating sequences that either are normally found in core histone gene promoters or in tissue-specific promoters (Khochbin and Wolffe, 1994).

Histone HI variants expressed in early amphibian and mammalian development are synthesized in the oocyte. generating stores of protein for use during early embryogenesis. Histone HI variants found in somatic cells are synthesized in the developing embryo from stores of masked maternal mRNA. These are laid down during oogenesis, but are only released for translation on fertilization (Khochbin and Wolffe, 1994). After early development is complete, the synthesis of somatic variant histone H 1 mRNA is coupled to DNA synthesis during the S phase. Two cis-acting elements contribute to S phase-specific H 1 gene transcription: the gene-specific HI box and the CCAAT box (Khochbin and Wolffee. 1994). Differentiation-specific histone HI variants respond to particular regulatory elements that monitor tissue type and developmental stage (Khochbin and Wolffe, 1994). For example, the gene for the histone Hl variant known as H5, found in chicken erythrocytes, is regulated by erythroidspecific transcription factors. Once histone H 1 is synthesized and assembled into chromatin through unknown molecular mechanisms, the protein appears to be very stable. This stability offers the possibility of histone HI and its variants imposing an epigenetic imprint on patterns of gene expression (see later). BIOLOGICAL

Nucleosomal Fig.

I.

Leti

panel:

the globular

domain

array

of histone

HI

(black

circle) is shown positioned symmetrically on the dyad axis of the nucleosomal DNA (Staynov and Crane-Robinson. 1988). Right panel: interactions between histone HI molecules help mediate the assembly of the nucleosomal array into the chromatin fibre (Thoma (‘I ol.. 1979).

FUNCTION

Histone Hl was. for a long time, thought to be essential for the assembly of nucleosomal arrays into the chromatin fiber (Fig. 1, right panel). This idea has now been shown to be an oversimplification. Strains of T~~trd~~wencr in which linker histone genes have been “knocked out” grow normally, however the size of their

Fig. 2. 97ir’ domain makes

contact

with

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d)‘NA superhelix

the Fams

the protein

within

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(ylow) histones.

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1.

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(ettey). In t&k asymnvctric &On; %LT g&&&r is &rapped (Pruss CI t/l.. 1996. courtesy of Dr E.

Alan

1466

P. WolH‘e

nuclei increases two-fold. Although DNA is less compacted in Hl-deficient chromatin, it is clear that linker histones are not essential either for the assembly of a nucleus or for cell survival (Shen et ul., 1995). Experiments using Xenopl*.v egg extracts support this conclusion. Immunological depletion of the early embryonic variants of histone Hl does not compromise the capacity of an egg extract to assemble chromosomes and nuclei. Instead of an essential role in chromatin packaging, histone Hl selectively regulates gene transcription. In Xenopus the somatic variant of histone H 1 selectively represses oocyte-type 5s ribosomal RNA genes. However, the expression of the vast majority of genes is unaffected by the inhibition of Hl protein accumulation (Patterton and Wolffe, 1996). In Tetrahymena, elimination of histone HI does not affect transcription by RNA polymerase I and III, nor is expression of most genes transcribed by RNA polymerase II changed. This demonstrates that histone Hl does not function as a general repressor of transcription in vivo. A specific role for Hl in transcription is shown by the activation and the repression of particular genes in the knockout strains (Shen and Gorovsky, 1996). Histone Hl might be required for the assembly of specific regulatory nucleoprotein complexes that either repress or activate transcription. POSSIBLE

MEDICAL AND APPLICATIONS

INDUSTRIAL

Epigenetic phenomena in which heritable states of gene activity are maintained through mechanisms largely independent of gene sequence have important implications for biotechnological and medical research. Certain human disease syndromes arise owing to the inheritance of parental specific patterns of gene activity that are largely independent of gene sequence. Comparable events compromise attempts to achieve successful gene therapy or to express transgenes in animals and plants. The molecular mechanisms that direct the differential expression of identical DNA sequences within the same cell and during development require changes to chromatin structure. Since histone

Hl modulates both chromatin structure and transcriptional activity, it has strong potential to contribute to epigenetic effects. Understanding the molecular mechanisms by which histone Hl exerts its functions might uncover new ways to manipulate gene expression. REFERENCES Clark K. L., Halay E. D.. Lai E. and Burley S. K. (1993) Co crystal structure of the HNF-3/fork head DNA recognition motif resembles histone H5. Nature 364, 412417. Hartman P. G., Chapman G. E., Moss T. and Bradbury E. M. (1977) Studies on the role and mode of operation of the very-lysine-rich histone Hl in eukaryotic chromatin: the three structural regions of the histone HI molecule. Eur. J. Biochem. 17, 45-51. Hayes J. J. (I 996) Site-directed cleavage of DNA by a linker histone-Fe(I1) EDTA coinugate: localization of a globular domain binding site within a nucleosome. Biochemktr~~ 35, I 193 I- 1 1937. Khochbin S. and Wolffe A. P. (1994) Developmentally regulated expression of linker-histone variants in vertebrates, Eur. J. Biochen7. 225, 501~510. Landsman D. (1996) Histone HI in Succhurom~~ce.s cereabiue: a double mystery solved. Trends Biochem. Sci. 21, 287-288.

Patterton D. and Wolffe A. P. (1996) Developmental roles for chromatin and chromosomal structure. Dee. Biol. 173, 2-13.

Pruss D., Bartholomew B., Persinger J., Hayes J., Arents G., Moudrianakis E. N. and Wolffe A. P. (1996) An asymmetric model for the nucleosome: a binding site for linker histones inside the DNA gyres. Science 274, 614-617. Ramakrishnan V., Finch J. T., Graziano V., Lee P. L. and Sweet R. M. (1993) Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature 362, 219-224. Shen X. and Gorovsky M. A. (1996) Linker histone HI regulates specific gene expression but not global transcription in nivo. Cell 86, 4755483. Shen X., Yu L., Weir J. W. and Gorovsky M. A. (1995) Linker histones are not essential and affect chromatin condensation in ciao. Cell 82, 47-56. Staynov D. Z. and Crane-Robinson C. (1988) Footprinting of linker histones H5 and Hl on the nucleosome. EMBO J. 7, 368553691. Thoma F., Keller T. and Klug A. (1979) Lnvolvement of histone Hl in the organization of the nucleosome and the salt dependent superstructures of chromatin. .I. Cel[. Biol. 83, 402427.

Wu M., Allis C. D., Richman R., Cook R. G. and Govorsky M. A. (1986) An intervening sequence in an unusual histone HI gene of Tetmhymena thermophilo. Proc. Nat1 Au/d. SC,;. l:.S.A 83, X674-8678.