Recently we identified a novel human (h) multiprotein complex, called TATA-binding protein (TBP)-free TAF IIcontaining complex (TFTC), which is able to nucleate RNA polymerase II transcription and can mediate transcriptional activation. Here we demonstrate that TFTC, similar to other TBP-free TAF II complexes (yeast SAGA, hSTAGA, and hPCAF) contains the acetyltransferase hGCN5 and is able to acetylate histones in both a free and a nucleosomal context. The recently described TRRAP cofactor for oncogenic transcription factor pathways was also characterized as a TFTC subunit. Furthermore, we identified four other previously uncharacterized subunits of TFTC: hADA3, hTAF II 150, hSPT3, and hPAF65. Thus, the polypeptide composition of TFTC suggests that TFTC is recruited to chromatin templates by activators to acetylate histones and thus may potentiate initiation and activation of transcription.Initiation of transcription of protein-encoding genes by RNA polymerase II requires transcription factor TFIID that is comprised of the TATA-binding protein (TBP) 1 and series of TBPassociated factors (TAF II s) (1). TFIID directs preinitiation complex assembly on both TATA-containing and TATA-less promoters. Previously, we have shown that functionally distinct TFIID complexes composed of both common and specific TAF II s exist in human HeLa cells (for review, see Ref. 2).We have isolated and partially characterized a novel human (h) multiprotein complex, which contains neither TBP nor TBPlike factor but is composed of several TAF II s and a number of uncharacterized polypeptides (3). This novel complex, called TBP-free TAF II -containing complex (TFTC) is able to direct preinitiation complex formation and initiation of transcription on both TATA-containing and TATA-less promoters in in vitro transcription assays and can mediate transcriptional activation by .Following the discovery of the TFTC complex, TAF II s have also been described in different histone acetyltransferase (HAT) complexes: the yeast SPT-ADA-GCN5 acetyltransferase (SAGA) complex and the human PCAF-GCN5 and the human STAGA complexes (4 -6). Histone acetylation and deacetylation have been strongly linked to the regulation of transcription (7). Yeast (y) Gcn5 has HAT activity and is a transcriptional coactivator required for correct expression of various genes (8,9). Transcriptional activators, such as VP16 or GCN4, interact directly with the SAGA complex and direct nucleosomal acetylation to potentiate transcriptional activation (10). The yeast SAGA complex consists of yGcn5 and various Ada (Ada1, Ada2, and Ada3) and Spt (Spt3, Spt7, Spt8, and Spt20) proteins (11). In addition to these proteins the SAGA complex also contains a distinct set of yTAF II s (TAF II 90, TAF II 68, TAF II 60, TAF II 25, and TAF II 17/20) (4). To date two human homologues of the yGcn5 have been identified. The first human homologue of yGcn5 is hGCN5 (called hGCN5-L), which is highly homologous to yeast GCN5 but contains an extended amino-terminal domain (12, 13). Furthermore, in huma...