title: The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters.
abstract: DNA sequence signals in the core promoter, such as the initiator (Inr), direct transcription initiation by RNA polymerase II. Here we show that the human Inr has the consensus of BBCA+1BW at focused promoters in which transcription initiates at a single site or a narrow cluster of sites. The analysis of 7678 focused transcription start sites revealed 40% with a perfect match to the Inr and 16% with a single mismatch outside of the CA+1core. TATA-like sequences are underrepresented in Inr promoters. This consensus is a key component of the DNA sequence rules that specify transcription initiation in humans.
authors.affiliation: Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA.
authors.forename: Long
authors.initials: L
authors.lastname: Vo Ngoc
authors.affiliation: Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA.
authors.forename: California Jack
authors.initials: CJ
authors.lastname: Cassidy
authors.affiliation: Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA.
authors.forename: Cassidy Yunjing
authors.initials: CY
authors.lastname: Huang
authors.affiliation: Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA.
authors.forename: Sascha H C
authors.initials: SH
authors.lastname: Duttke
authors.affiliation: Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA.
authors.forename: James T
authors.initials: JT
authors.lastname: Kadonaga
mesh_terms: D017124:Conserved Sequence / Q000235:genetics; D004252:DNA Mutational Analysis; D006801:Humans; D061986:MCF-7 Cells; D009154:Mutation; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D016385:TATA Box / Q000235:genetics; D024363:Transcription Initiation Site
keywords: RNA polymerase II; core promoter; focused transcription; initiator; transcription start site