The yeast histone variant H2AZ (Htz1) is implicated in transcription activation, prevention of the ectopic spread of heterochromatin, and genome integrity. Our genome-wide localization analysis revealed that Htz1 is widely, but nonrandomly, distributed throughout the genome in an SWR1-dependent manner. We found that Htz1 is enriched in intergenic regions compared with coding regions. Its occupancy is inversely proportional to transcription rates and the enrichment of the RNA polymerase II under different growth conditions. However, Htz1 does not seem to directly regulate transcription repression genome-wide; instead, the presence of Htz1 under the inactivated condition is essential for optimal activation of a subset of genes. In addition, Htz1 is not generally responsible for nucleosome positioning, even at those promoters where Htz1 is highly enriched. Finally, using a biochemical approach, we demonstrate that incorporation of Htz1 into nucleosomes inhibits activities of histone modifiers associated with transcription, Dot1, Set2, and NuA4 and reduces the nucleosome mobilization driven by chromatin remodeling complexes. These lines of evidence collectively suggest that Htz1 may serve to mark quiescent promoters for proper activation.htz1 ͉ transcription ͉ nucleosome

The mammalian Tip49a and Tip49b proteins belong to an evolutionarily conserved family of AAA ؉ ATPases. In Saccharomyces cer- The related mammalian Tip49a and Tip49b proteins are members of a family of AAA ϩ (associated with various cellular activities) ATPases with roles in DNA repair, recombination, and transcriptional regulation (1, 2). In Saccharomyces cerevisiae, the Tip49a and Tip49b proteins (also known as Rvb1 and Rvb2) participate in chromatin remodeling as subunits of the multiprotein SWR1 and INO80 ATP-dependent chromatin remodeling complexes (3-5). The SWR1 complex remodels chromatin by catalyzing ATP-dependent replacement of H2A-H2B histone dimers in nucleosomes by dimers containing histone variant Htz1 (referred to as H2AZ in mammalian cells) (3). In addition to Tip49a and Tip49b, the SWR1 complex includes the SNF2 family helicase Swr1, actin-related proteins Arp4 and Arp6, YEATS domain family member Yaf9, bromodomain protein Bdf1, and additional proteins Swc3-Swc7, which are of unknown function (3-5).The INO80 complex catalyzes ATP-dependent sliding of nucleosomes along DNA and, based on genetic and other evidence, may be involved in the repair of DNA double strand breaks and in transcriptional regulation (6 -12). The INO80 complex includes Tip49a and Tip49b, the SNF2 family helicase Ino80, actin-related proteins Arp4, Arp5, and Arp8, YEATS domain family member Taf14, HMG (high mobility group) domain protein Nhp10, and six additional proteins designated Ies1-Ies6 (6, 13). Thus, the SWR1 and INO80 complexes share three proteins (Tip49a, Tip49b, and Arp4) and contain additional homologous components. In addition, each of the two complexes has a number of unique subunits.The orthologs of the Tip49a and Tip49b AAA ϩ ATPases also play roles in chromatin remodeling in higher eukaryotes. Tip49a and Tip49b are subunits of the mammalian and Drosophila melanogaster TRRAP-TIP60 histone acetyltransferase (HAT) 3 complexes (14 -17). In addition to Tip49a and Tip49b, the TRRAP-TIP60 complex includes ATM/ phosphatidylinositol 3-kinase family member TRRAP, the SNF2 family p400 or Domino helicase, actin-related protein Arp4, bromodomaincontaining protein BRD8, the enhancer of polycomb (EPC) and/or enhancer of polycomb-like (EPC-like) protein, inhibitor of growth 3 (ING3), DNA methyltransferase 1-associated protein (DMAP1), MRG15 and/or the related MRGX protein, the MRGBP protein, and TIP60, a HAT belonging to the MYST family. Characterization of the activities associated with the higher eukaryotic TRRAP-TIP60 complex revealed that it possesses HAT activity similar to that of the S. cerevisiae NuA4 HAT complex, which acetylates histones H2A and H4 (reviewed in Ref. 18). The human and D. melanogaster TRRAP-TIP60 complexes were found to play critical roles in double-stranded DNA break repair (16,17). Notably, the D. melanogaster TRRAP-TIP60 complex is capable of acetylating nucleosomal phospho-H2Av and replacing it with unmodified H2Av, indicating that in flies this single complex performs functions closely related t...

The Ada2a-containing (ATAC) complex is an essential Drosophila melanogaster histone acetyltransferase (HAT) complex that contains the transcriptional cofactors Gcn5 (KAT2), Ada3, Ada2a, Atac1 and Hcf. We have analyzed the complex by MudPIT (multidimensional protein identification technology) and found eight previously unidentified subunits. These include the WD40 repeat protein WDS, the PHD and HAT domain protein CG10414 (herein renamed Atac2/KAT14), the YEATS family member D12, the histone fold proteins CHRAC14 and NC2beta, CG30390, CG32343 (Atac3) and CG10238. The presence of CG10414 (Atac2) suggests that it acts as a second acetyltransferase enzyme in ATAC in addition to Gcn5. Indeed, recombinant Atac2 displays HAT activity in vitro with a preference for acetylating histone H4, and mutation of Atac2 abrogated H4 lysine 16 acetylation in D. melanogaster embryos. Furthermore, although ATAC does not show nucleosome-remodeling activity itself, it stimulates nucleosome sliding by the ISWI, SWI-SNF and RSC complexes.