Genome-wide structure and organization of eukaryotic pre-initiation complexes

The structural and positional organization of transcription pre-initiation complexes (PICs) across eukaryotic genomes is unknown. We employed ChIP-exo to precisely examine ~6,000 PICs in Saccharomyces. PICs, including RNA polymerase II and general factors TFIIA, -B, -D/TBP, -E, -F, -H, and -K were positioned within promoters and excluded from coding regions. Exonuclease patterns agreed with crystallographic models of the PIC, and were sufficiently precise to identify TATA-like elements at so-called TATA-less promoters. These PICs and their transcription start sites were positionally constrained at TFIID-engaged +1 nucleosomes. At TATA box-containing promoters, which are depleted of TFIID, a +1 nucleosome was positioned to be in competition with the PIC, which may afford greater latitude in start site selection. Our genomic localization of mRNA and noncoding RNA PICs reveal that two PICs, in inverted orientation, may occupy the flanking borders of nucleosome-free regions. Their unambiguous detection may help distinguish bona-fide genes from transcriptional noise.