Researchers Focus on Histone Code

Histones, the proteins around which DNA coils to form chromatin, are moving toward the forefront of epigenetic research (see also, "The Meaning of Epigenetics"). A recently floated hypothesis states that the highly modifiable amino termini, or tails, of these proteins could carry their own combinatorial codes or signatures to help control phenotype, and that parts of this code may be heritable. Histones are perhaps more intimately linked with DNA than any other protein. Transcriptional regulation, recombination, repair, and replication--basically anything that happens to the DNA--must happen within the context of its packaging. That alone lends importance to the field. Leukemia therapeutics based on inhibition of histone modifiers have already made it to the clinic.1 And in light of this new "histone code" hypothesis, researchers are quick to tout further possibilities in human development, fertility, and other types of cancer. Shelley L. Berger, associate professor of molecular genetics at the Wistar Institute, University of Pennsylvania, says, "I think it's going to be really critical in human biology. It's not just some dry academic pursuit." Though first voiced in 1993 by Bryan Turner, professor of experimental genetics, University of Birmingham Medical School, Birmingham, U.K.,2 the histone code hypothesis was formally named last year by C. David Allis, Byrd professor of biochemistry and molecular genetics, University of Virginia Medical School, and his postdoc, Brian Strahl.3 Before the new hypothesis, the reigning theory had stated that modifications like acetylation and phosphorylation alter the electrostatic charge of histone tails, thereby loosening their grip on the DNA. While not excluding old assumptions, the new hypothesis states that specific modifications, like acetylation, phosphorylation, or methylation, to specific amino acid residues on histone tails facilitate processes by forming combinatorial codes that other proteins read. According to Allis, modification patterns might form a sort of landing pad upon which specialized regulatory proteins dock. Birth of this notion came from observations that the same modification could bring about different regulatory outcomes depending on where it appears on the histone tails. A case in point, says Allis, are the recent indications that the distinct methyl marks occurring only a few amino acids away from each other are associated with transcriptionally active euchromatin or unexpressed heterochromatin. "It has such a wonderfully split personality that it really makes you think about a code," Allis says. Though intentionally vague, the hypothesis finds support in recent Science articles.4-5 Berger and her lab found that in budding yeast, a certain phosphorylation event on the histone H3 tail is required for acetylation at a different amino acid on the same tail. Further, the kinase that phosphorylates at one promoter sequence does not necessarily phosphorylate at others.4 Berger says, "The very clear establishment of that pattern leads to support for the idea that there is a code, a histone code, and that the modifications vary at different places in the genome and are doing very specific things to regulate transcription." For the past five years--basically since the first histone acetyltransferase and histone deacetylases were found,1 acetylation has been a hot research topic. Now, say Allis and others, methylation is coming into its own. Because methyl groups are relatively stable and there is yet no known histone demethylase to remove the marks, histone methylation, which can activate or silence a gene, is believed to pass its signature on to daughter cells. In a nontransient form of histone modification, it's possible, says Turner, "to maintain a particular gene expression pattern--either on or off--over a long period." Berger explains, "The methyl transferase enzymes actually have domains... that recognize the methylated histone. Why would you need that? Well, it would allow you to provide a heritable mark." Allis points out that methylation at one amino acid coincides quite thoroughly with X inactivation in sex determination and the phenomenon of gene imprinting. Shiv Grewal, assistant professor of molecular biology and genetics at Cold Spring Harbor Laboratory, showed that differential sites of histone H3 methylation mark active and inactive regions of the chromosomes in fission yeast to establish a specific histone code.5 In inactive heterochromatic regions, histone H3 tails were specifically methylated at lysine 9, and in the adjacent active region, the tails were methylated at lysine 4 only a few amino acids away. Specific DNA sequences stand in between different chromatin neighborhoods. When Grewal's lab mutated the boundaries, the methlyation pattern associated with heterochromatin spread past them, silencing formerly expressed genes. "You have implications," Grewal says, "not only at the molecular level, but at a cellular level ... and all the way up to population biology." Yet with four different histone proteins, each with between 10 and 30 amino acid residues on their N-termini, along with numerous other types of histone modifications like ubiquitination and ADP-ribosylation, researchers are just beginning to unravel this mystery. For now, the limitations lie in the technique. Chromatin Immunoprecipitation (ChIP) is really the only tool researchers have for examining these ideas, says Turner. "Advances in this area are going to depend on advances in the chromatin immunoprecipitation approach," he says. And, while leaders in the field will continue to be those who are best equipped to produce the antibodies, new technologies could aid in moving the field forward. Grewal notes that some are moving toward amalgamating the advances in ChIP with advances in microarray technology, "So we have what we call, 'ChIP on a chip." He believes that in 10 years, scientists will have a clearer picture of the kind of epigenetic map the histone code could make up. But don't wait for a Rosetta stone, Turner cautions. This will not be static like the genetic code, he says, but something that is context-dependent--meaning different things in different situations. "I think the potential is enormous," Turner says. The genome, relatively small in size, is just the starting point. "What matters is how you use it." Brendan A. Maher can be contacted at bmaher@the-scientist.com. References 1. E. Russo, "Hot Papers in acetylation," and "Hot papers in deacetylation," The Scientist, 13[5]:13, March 1, 1999. 2. B.M. Turner, "Decoding the nucleosome," Cell, 75[1]:5-8, 1993. 3. B.D. Strahl and C.D. Allis, "The language of covalent histone modifications," Nature, 403:41-5, Jan. 6, 2000. 4. W. Lo et al., "Snf1--A histone kinase that works in concert with the histone acetyltransferase Gcn5 to regulate transcription," Science, 293:1142-6, Aug. 10, 2001. 5. K. Noma et al., "Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries," Science, 293:1150-55, Aug. 10, 2001.

Researchers Focus on Histone Code

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