title: Genome-wide structure and organization of eukaryotic pre-initiation complexes.
abstract: Transcription and regulation of genes originate from transcription pre-initiation complexes (PICs). Their structural and positional organization across eukaryotic genomes is unknown. Here we applied lambda exonuclease to chromatin immunoprecipitates (termed ChIP-exo) to examine the precise location of 6,045 PICs in Saccharomyces. PICs, including RNA polymerase II and protein complexes TFIIA, TFIIB, TFIID (or TBP), TFIIE, TFIIF, TFIIH and TFIIK were positioned within promoters and excluded from coding regions. Exonuclease patterns were in agreement 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 downstream +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 allow greater latitude in start-site selection. Our genomic localization of messenger RNA and non-coding RNA PICs reveals 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.
authors.affiliation: Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Ho Sung
authors.initials: HS
authors.lastname: Rhee
authors.forename: B Franklin
authors.initials: BF
authors.lastname: Pugh
mesh_terms: D004271:DNA, Fungal / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal / Q000235:genetics*; D016681:Genome, Fungal / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism; D011487:Protein Conformation; D012319:RNA Polymerase II / Q000737:chemistry / Q000378:metabolism*; D012331:RNA, Fungal / Q000235:genetics; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D016385:TATA Box / Q000235:genetics; D035165:Transcription Factors, General / Q000737:chemistry / Q000172:deficiency / Q000378:metabolism*; D024363:Transcription Initiation Site; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D004271:DNA, Fungal; D009707:Nucleosomes; D012331:RNA, Fungal; D012333:RNA, Messenger; D022661:RNA, Untranslated; D035165:Transcription Factors, General; D012319:RNA Polymerase II