JB Minireview—Functional Dynamics of the Nucleus Cracking the Enigmatic Linker Histone Code James S. Godde 1,2 and Kiyoe Ura 1, * 1 Division of Gene Therapy Science, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan; and 2 Department of Biology, Monmouth College, 700 East Broadway, Monmouth, IL 61462 USA Received November 16, 2007; accepted December 1, 2007; published online January 30, 2008 Recently, the existence of a ‘histone code’ has been proposed to explain the link between the covalent chemical modification of histone proteins and the epigenetic regulation of gene activity. Although the role of the four ‘core’ histones has been extensively studied, little is known about the involvement of the linker histone, histone H1 and its variants, in this code. For many years, few sites of chemical modification had been mapped in linker histones, but this has changed recently with the use of functional proteomic techniques, principally mass spectrometry, to characterize these modifications. The functionality of many of these sites, however, remains to be determined. Key words: epigenetic code, histone H1, histone modification, histone variant, linker histone. Abbreviations: bp, base pairs; CHO, Chinese Hamster Ovary; ES, embryonic stem; HPLC, High Performance Liquid Chromatography; Rb, retinoblastoma protein. For many years, almost every review of chromatin structure and function would begin with the nearly obligatory description of the four core histones: H2A, H2B, H3 and H4 and how these bind to one another to form a protein octamer, which then wraps about 200 bp of DNA around this molecular spool in order to form a nucleosome, the most basic unit of chromatin structure (for a historical perspective, see 1). Nucleosome structure was then described as being completed upon the binding of H1, the linker histone, which bound to the outside of the nucleosome, thereby sealing the two turns of DNA and serving as a prerequisite to the higher order folding of chromatin (1). In the last decade, however, this canon- ical view of the nucleosome has undergone a radical change. First, it is now understood that chromatin is much more dynamic than previously imagined and that the histones, particularly H1, exchange on and off of nucleosomes at some frequency (2). Secondly, it has been shown that histone H1 is not required for viability in a number of simple eukaryotes, as will be discussed in more detail, below (3). This final finding places some doubt on the traditional view of histone H1 playing such a fundamental role in chromatin structure. THE HISTONE CODE Around the time that the in vivo role of histone H1 began to be questioned, a hypothesis was put forth that covalent post-translational modifications of the histone N- and C-terminal ‘tails’ acted sequentially or in combination to form a ‘histone code’, which was read by regulatory proteins to affect cell processes such as transcription, replication and chromosome condensation during mitosis (4). All histones, including H1, have a tripartite structure, with a central globular domain surrounded by more extended tail domains which are very basic, rich in lysines and arginines (5). These tails are believed to be inherently flexible and largely unstruc- tured in solution (5). The N-terminal tail, especially, has many sites where covalent chemical modifications take place in the cell, namely acetylation, methylation, as well as phosphorylation (4). The histone code hypothesis built on a wealth of biochemical and genetic information that had been amassed over the years concerning the func- tionality of these, as well as other, modifications; it primarily focused on histones H3 and H4, for which most information existed, and mentioned the other three histones only in passing. A follow-up to this original paper, however, did mention two antagonistic roles that the covalent modification of histone H1 might play in the cell: the methylation of Lys 26 (K26) in the N-terminal tail was potentially linked to gene-silencing and the assembly of heterochromatin, while the ubiquitination of histone H1 at an unknown site seemed to correlate with trans- criptional stimulation (6). Progress on understanding the role that histone H1 plays in the histone code has been, until recently, quite slow. A recent review which dis- cussed the link between the histone code and the developmental process mentioned this sole site-specific modification, that of K26, compared with six sites in each of the H2 histones, eight in histone H4 and 16 in histone H3 (7). LINKER HISTONE VARIANTS Covalent chemical modification is not the only means of introducing variability among linker histones in the cell, histone H1 is also found to exist in a number of variants that differ in sequence and which are often differentially *To whom correspondence should be addressed. Tel: +81 6 6879 3901, Fax: +81 6 6879 3909, E-mail: kiyoeura@gts.med.osaka-u.ac.jp J. Biochem. 143, 287–293 (2008) doi:10.1093/jb/mvn013 Vol. 143, No. 3, 2008 287 ß 2008 The Japanese Biochemical Society.