Transcriptional activation within a permissive domain frequently correlates with additional, targeted acetylation of histones at promoter nucleosomes (Brown et al., 2000; Forsberg and Bresnick, 2001), although notable exceptions exist (Deckert and Struhl, 2001). With the availability of more diagnostic reagents and more sophisticated analyses, the old idea (Turner, 1993) that what matters are patterns of acetylation at specific lysines within the histone N-termini, rather than simple charge neutralization by non-specific modification, receives convincing confirmation (Vogelauer et al., 2000; Deckert and Struhl, 2001). However, the exact requirements are not at all transparent. Whereas in some instances targeted acetylation of histone H3 is found in conjunction with broader acetylation of histone H4 (Schübeler et al., 2000; Vignali et al., 2000), these observations cannot be generalized (Litt et al., 2001).
Given the importance of HATs as co-activators of transcription and the frequent association of repression with HDACs, transcriptional regulation must involve targeting of these enzymes to specific sites. Localized histone acetylation is observed in promoter and enhancer elements, but can also be found enriched at boundary or insulator elements of chromosome domains and other DNase I hypersensitive sites in nuclei (Litt et al., 2001), supporting the idea that histone acetylation facilitates protein–DNA interactions within chromatin in general. Many cases in which activating transcription factors recruit HAT-containing co-activators to specific promoters have now been documented (Brown et al., 2000). Yeast HAT complexes can associate with the transactivation domains of activators like VP16, Gcn4, Gal4 and Hap4 (Utley et al., 1998), although this may require an adapter protein. For example, the yeast SAGA and NuA4 complexes, which contain the HATs Gcn5 and Esa1, respectively, are recruited via the shared subunit Tra1 (Brown et al., 2001). The human homolog of Tra1, TRRAP, is also implicated in recruiting HAT complexes, in this case to transcription complexes containing c-myc (McMahon et al., 2000; Bouchard et al., 2001; Frank et al., 2001) and E2F (Lang et al., 2001). Although some basic principles are emerging, our present understanding of HAT involvement in gene activation remains dominated by inherent complexities. Activator–co-activator selectivity is inferred from the fact that different activators induce different acetylation patterns in vivo (Deckert and Struhl, 2001). For example, the recruitment of SAGA by VP16 leads to local H3 acetylation near the promoter, while targeting of NuA4 by the same protein results in broad acetylation of H4 over a domain of >3 kb (Vignali et al., 2000). The targeting of diverse HAT complexes via sequence-specific DNA-binding proteins leads to stimulation of transcription from chromatin templates in vitro (Ikeda et al., 1999; Kundu et al., 2000) and in yeast (Bhaumik and Green, 2001; Larschan and Winston, 2001). Although the HAT subunits of co-activator complexes are currently the center of interest, large HAT complexes like SAGA contain other functions as well. This is illustrated by the observation that SAGA has been found to be an essential co-activator for Gal4-activated transcription in vivo, but this activation function relied mainly on the SAGA components Spt3 and Spt20 and less on the HAT subunit Gcn5 (Bhaumik and Green, 2001; Larschan and Winston, 2001).
Whereas tethering of HATs to defined sites via activators explains local hyperacetylation, it is less obvious how the acetylation of large domains is achieved. Potential mechanisms include the recruitment of HATs to distinct ‘entry sites’ from which they ‘spread’ throughout a domain (Kelley and Kuroda, 2000), possibly by attachment to a tracking protein such as RNA polymerase II (Wittschieben et al., 1999). Alternatively, the residence of a particular chromosomal domain within an acetylation-competent nuclear compartment may ensure relatively uniform modification (Schübeler et al., 2000). If acetylation itself were to generate high-affinity binding sites for HATs, propagation schemes could be envisaged (Gu et al., 2000; Forsberg and Bresnick, 2001).