TFIID plays a key role in transcription initiation of RNA polymerase II preinitiation complex assembly. TFIID is comprised of the TATA box binding protein (TBP) and 14 TBP-associated factors (TAFs). A second set of transcriptional regulatory multiprotein complexes containing TAFs has been described (called SAGA, TFTC, STAGA, and PCAF/GCN5). Using matrix-assisted laser desorption ionization mass spectrometry, we identified a novel TFTC subunit, human TAF9Like, encoded by a TAF9 paralogue gene. We show that TAF9Like is a subunit of TFIID, and thus, it will be called TAF9b. TFIID and TFTC complexes in which both TAF9 and TAF9b are present exist. In vitro and in vivo experiments indicate that the interactions between TAF9b and TAF6 or TAF9 and TAF6 histone fold pairs are similar. We observed a differential induction of TAF9 and TAF9b during apoptosis that, together with their different ability to stabilize p53, points to distinct requirements for the two proteins in gene regulation. Small interfering RNA (siRNA) knockdown of TAF9 and TAF9b revealed that both genes are essential for cell viability. Gene expression analysis of cells treated with either TAF9 or TAF9b siRNAs indicates that the two proteins regulate different sets of genes with only a small overlap. Taken together, these data demonstrate that TAF9 and TAF9b share some of their functions, but more importantly, they have distinct roles in the transcriptional regulatory process.Transcription initiation of protein-encoding genes by RNA polymerase II (Pol II) requires the transcription factor TFIID that is comprised of the TATA binding protein (TBP) and series of TBP-associated factors (TAFs) (1, 6, 57). In human HeLa cells, we showed that different human TFIID complexes containing or lacking TAF10 which exhibit functionally distinct properties exist (6,7,25). Cell type-specific TFIID complexes have been found to be composed of core TAFs and cell typespecific TAFs. TAF4b was found to be enriched in differentiated human B lymphocytes, and a unique TAF4b-containing TFIID was isolated from these cells (13). Moreover, during spermatogenesis, TAF7L-containing TFIID complexes have been found (48). Another set of human transcriptional regulatory multiprotein complexes containing TAFs are called TFTC, STAGA, or PCAF/GCN5 (6a, 36, 63). These complexes are functional homologues of the Saccharomyces cerevisiae SAGA complex, and all contain human homologues of the yeast histone acetyltransferase Gcn5 as well as a subset of SPT and ADA proteins, the 400-kDa TRRAP protein, and a number of TAFs (shared TAFs) also found in TFIID (36).TAF9 was first identified as a TFIID subunit from multiple organisms: human ( (44), and human TFTC-type complexes (10,36,67). Drosophila TAF9 has also been described in the Polycomb group complex and the e(y)2 protein-containing complex (17, 50).TAF9 was shown to interact directly with the tumor suppressor protein p53, the herpes simplex virus activator VP16, and the basal transcription factor TFIIB, and these interactions were suggested to be ...