Eukaryotic cells are thought to contain a single TATA-binding protein
(TBP) that directs transcription by cellular RNA polymerases. Here we
report a cell type-specific TBP-related factor (TRF) that can form a s
table TRF/IIA/IIB TATA DNA complex and substitute for TBP in directing
RNA polymerase II transcription in vitro. Transfection studies reveal
that TRF can differentially mediate activation by some enhancer prote
ins but not others. Like TBP, TRF forms a stable complex containing mu
ltiple novel subunits, nTAFs. Antibody staining of embryos and polyten
e chromosomes reveals cell type-specific expression and gene-selective
properties consistent with the shaker/male sterile phenotype of trf m
utants. These findings suggest TRF is a homolog of TBP that functions
to direct tissue-and gene-specific transcription.