The Human Initiator Is a Distinct and Abundant Element That Is Precisely Positioned in Focused Core Promoters

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 7,678 focused transcription start sites revealed 40% with a perfect match to the Inr and 16% with a single mismatch outside of the CA+1 core. 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. Transcription Start Site (TSS) mapping with two 5'GRO-seq experiments (including or excluding an RNA fragmentation step) using MCF-7 cells