A great deal of work has revealed, in structural detail, the components of the preinitiation complex (PIC) machinery required for initiation of mRNA gene transcription by RNA polymerase II (Pol II). However, less-well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining how rates of in vivo RNA synthesis are established. We used competition ChIP in budding yeast to obtain genome-scale estimates of the residence times for five general transcription factors (GTFs): TBP, TFIIA, TFIIB, TFIIE and TFIIF. While many GTF-chromatin interactions were short-lived (< 1 min), there were numerous interactions with residence times in the range of several minutes. Sets of genes with a shared function also shared similar patterns of GTF kinetic behavior. TFIIE, a GTF that enters the PIC late in the assembly process, had residence times correlated with RNA synthesis rates. The datasets and results reported here provide kinetic information for most of the Pol II-driven genes in this organism, offering a rich resource for exploring the mechanistic relationships between PIC assembly, gene regulation, and transcription. Synopsis: The RNA polymerase II transcription machinery is understood in structural detail, but much less is known about its assembly dynamics on promoter DNA in vivo. Measurements of genome-scale chromatin residence times of five key general transcription factors now allows exploration of mechanistic relationships between transcription complex assembly dynamics and RNA production. Competition-chromatin immunoprecipitation measures the genome-scale chromatin residence times of the general transcription factors TBP, TFIIA, TFIIB, TFIIE, and TFIIF in budding yeast. Many interactions were short-lived (<1 min), but interaction residence times in the several minutes range were also found for each factor. Genes with shared biological functions have promoters with shared chromatin-binding kinetic behavior. TFIIE, which binds late in the assembly process, had residence times that correlate with rates of RNA synthesis. Competition-ChIP experiments with TBP, TFIIA, TFIIB, TFIIE and TFIIF reveal the genome-wide chromatin binding dynamics of these general transcription factors in S. cerevisiae. [ABSTRACT FROM AUTHOR]