The elongator complex is a major component of the RNA polymerase II (RNAPII) holoenzyme responsible for transcriptional elongation in yeast. Here we identify Elp3, the 60-kilodalton subunit of elongator/RNAPII holoenzyme, as a highly conserved histone acetyltransferase (HAT) capable of acetylating core histones in vitro. In vivo, ELP3 gene deletion confers typical elp phenotypes such as slow growth adaptation, slow gene activation, and temperature sensitivity. These results suggest a role for a novel, tightly RNAPII-associated HAT in transcription of DNA packaged in chromatin.

Most current knowledge about DNA polymerase zeta (pol ζ) comes from studies of the enzyme in the budding yeast Saccharomyces cerevisiae, where pol ζ consists of a complex of the catalytic subunit Rev3 with Rev7, which associates with Rev1. Most spontaneous and induced mutagenesis in yeast is dependent on these gene products, and yeast pol ζ can mediate translesion DNA synthesis past some adducts in DNA templates. Study of the homologous gene products in higher eukaryotes is in a relatively early stage, but additional functions for the eukaryotic proteins are already apparent. Suppression of vertebrate REV3L function not only reduces induced point mutagenesis but also causes larger-scale genome instability by raising the frequency of spontaneous chromosome translocations. Disruption of Rev3L function is tolerated in Drosophila, Arabidopsis, and in vertebrate cell lines under some conditions, but is incompatible with mouse embryonic development. Functions for REV3L and REV7(MAD2B) in higher eukaryotes have been suggested not only in translesion DNA synthesis but also in some forms of homologous recombination, repair of interstrand DNA crosslinks, somatic hypermutation of immunoglobulin genes and cell-cycle control. This review discusses recent developments in these areas.

Elp3 and Gcn5 are histone acetyltransferases (HATs) that function in transcription as subunits of Elongator and SAGA/ADA, respectively. Here we show that mutations that impair the in vitro HAT activity of Elp3 confer typical elp phenotypes such as temperature sensitivity. Combining an elp3Delta mutation with histone H3 or H4 tail mutations confers lethality or sickness, supporting a role for Elongator in chromatin remodelling in vivo. gcn5Deltaelp3Delta double mutants display a number of severe phenotypes, and similar phenotypes result from combining the elp mutation with mutation in a gene encoding a SAGA-specific, but not an ADA-specific subunit, indicating that Elongator functionally overlaps with SAGA. Because concomitant active site alterations in Elp3 and Gcn5 are sufficient to confer severe phenotypes, the redundancy must be specifically related to the HAT activity of these complexes. In support of this conclusion, gcn5Deltaelp3Delta phenotypes are suppressed by concomitant mutation of the HDA1 and HOS2 histone deacetylases. Our results demonstrate functional redundancy among transcription-associated HAT and deacetylase activities, and indicate the importance of a fine-tuned acetylation-deacetylation balance during transcription in vivo.

The DDB protein complex, comprising the subunits DDB1 and DDB2, binds tightly to UV light-irradiated DNA. Mutations in DDB2 are responsible for xeroderma pigmentosum group E, a disorder with defects in nucleotide excision repair of DNA. Both subunits are also components of a complex involved in ubiquitin-mediated proteolysis. Cellular defects in DDB2 disable repair of the major UV radiation photoproduct in DNA, a cyclobutane pyrimidine dimer, but no significant direct binding of DDB to this photoproduct in DNA has ever been demonstrated. Thus, it has been uncertain how DDB could play a specific role in DNA repair of such damage. We investigated DDB function using highly purified proteins. Co-purified DDB1-DDB2 or DDB reconstituted with individual DDB1 and DDB2 subunits binds to damaged DNA as a ternary complex. We found that DDB can indeed recognize a cyclobutane pyrimidine dimer in DNA with an affinity (K a app ) 6-fold higher than that of nondamaged DNA. The DDB1-DDB2 complex also bound with high specificity to a UV radiation-induced (6-4) photoproduct and to an apurinic site in DNA. Unexpectedly, DDB also bound avidly to DNA containing a 2-or 3-bp mismatch (and does not bind well to DNA containing larger mismatches). These data indicate that DDB does not detect lesions per se. It instead recognizes other structural features of damaged DNA, acting as a sensor that probes DNA for a subset of conformational changes. Lesions recognized may include those arising when translesion polymerases such as POLH incorporate bases across from DNA lesions caused by UV radiation.The human disorder xeroderma pigmentosum (XP) 2 has been intensely studied because of the striking phenotypes of sunlight sensitivity, predisposition to skin cancer, and an association with defects in DNA repair. Seven of the eight complementation groups of the disorder (designated XP-A through XP-G) have defects in nucleotide excision repair (NER) of damaged DNA (1). An eighth group, XP-V, is defective in DNA POLH (pol ) (2), which can bypass the major photoproduct caused by UV radiation in DNA, the cis-syn cyclobutane pyrimidine dimer (CPD). The clinical and cellular characteristics of XP group E are similar to those of the other XP complementation groups but are generally milder. The overall level of NER as measured by unscheduled DNA synthesis in XP-E cells is 50 -80% of normal cells. The gene defective in the XP-E group is DDB2. The 48-kDa DDB2 protein, together with the 127-kDa DDB1 protein (3-5), constitute the DNA damage binding factor known as DDB or UV-DDB (6). The DDB subunits are also found in a protein complex that includes components of a cullinbased ubiquitin ligase as well as the COP9 signalosome (7). The function and physiological substrates of this complex are presently unclear (8).Despite the ability of the DDB protein to bind UV light-irradiated DNA, the specific role of DDB in NER is uncertain. One difficulty in determining the function is that NER can be reconstituted with purified components and damaged naked DNA in the absence ...

A group of recent publications contribute new insights concerning the role of the DNA damage-binding protein complex (DDB) in DNA repair. Mutations in the 48kDa DDB2 subunit are now found in all confirmed cases of xeroderma pigmentosum complementation group E. Several studies have reported a connection between the 127kDa DDB1 subunit and proteins involved in ubiquitin-mediated proteolysis. One such multiprotein complex containing DDB1 and DDB2 is closely related to a complex containing DDB1 and the Cockayne syndrome group A (CSA) protein. There is accumulating evidence for several levels of cellular regulation of DDB, including translocation to the nucleus, proteolytic degradation of DDB2 protein, and transcriptional induction of DDB2 mRNA. Although the mechanism is not yet known, it appears that DDB assists in nucleotide excision repair in chromatin.

Heterochromatin formation in yeast involves deacetylation of histones, but the precise relationship between acetylation and the association of proteins such as Sir3, Sir4, and the histone deacetylase Sir2 with chromatin is still unclear. Here we show that Sir3 protein spreads to subtelomeric DNA in cells lacking the transcription-related histone acetyltransferases GCN5 and ELP3. Spreading correlates with hypoacetylation of lysines in the histone H3 tail and results in deacetylation of lysine 16 in histone H4. De-repression of genes situated very close to the ends of the chromosomes in gcn5 elp3 suggests that Sir3 spreads into subtelomeric DNA from the tip of the telomere. Interestingly, growth defects caused by gcn5 elp3 mutation can be suppressed by SIR deletion, suggesting that Sir proteins become detrimental for growth when chromatin is severely hypoacetylated. C ore histones are subject to a variety of covalent modifications, and enzymes responsible for these modifications have been intensely studied over the past few years. However, in contrast to our basic knowledge of these enzymes and their capabilities, only little is known about the molecular effects of changes in histone modification in vivo. For example, it is unclear whether histone hypoacetylation in itself is inhibitory to transcription or whether it merely enables downstream processor proteins, such as transcriptional repressors, to associate with chromatin and decrease the efficiency of the transcription process. Likewise, whether histone hypoacetylation is a prerequisite for, or a result of, heterochromatin formation is also not entirely clear.Heterochromatin in complex eukaryotes such as fruit flies and mammals is condensed, stains darkly cytologically, and has the ability to silence nearby genes epigenetically (1, 2). Budding yeast also has chromosomal regions with many of the features of heterochromatin: the silent mating (HM) loci and chromatin domains adjacent to telomere ends. The chromatin in these regions is condensed, late replicating, and associated in foci that localize to the nuclear periphery (1, 3, 4). Yeast heterochromatin is also hypoacetylated on all four core histones relative to that packaging active genes (5-7).The products of the SIR genes are important factors for the establishment and maintenance of yeast heterochromatin. SIR2, SIR3, and SIR4 are important for silencing both at telomeres and at the silent mating loci, whereas SIR1 is only required for the establishment of silencing at the silent mating loci. Other components with important roles in silencing include DNAinteracting factors such as Rap1, Abf1, the origin recognition complex (ORC), and histones H3 and H4 (4). A large number of pairwise interactions between these components have been reported. For example, Sir3 and Sir4 interact with each other, as well as with Rap1 and the amino-terminal tails of histones H3 and H4 (8, 9). Sir4 also interacts directly with Sir2 (10, 11). Such results have given rise to models for heterochromatin formation at telomeres in whi...

The molecular architecture of six-subunit yeast holoElongator complex was investigated by the use of immunoprecipitation, two-hybrid interaction mapping, and in vitro studies of binary interactions between individual subunits. Surprisingly, Elp2 is dispensable for the integrity of the holo-Elongator complex, and a purified five-subunit elp2⌬ Elongator complex retains histone acetyltransferase activity in vitro. These results indicate that the WD40 repeats in Elp2 are required neither for subunit-subunit interactions within Elongator nor for Elongator interaction with histones during catalysis. Elp2 and Elp4 were largely dispensable for the association of Elongator with nascent RNA transcript in vivo. In contrast, Elongator-RNA interaction requires the Elp3 protein. Together, these data shed light on the structure-function relationship of the Elongator complex.

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