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 +1 BW 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 +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.Supplemental material is available for this article.Received November 14, 2016; revised version accepted December 19, 2016. The multifarious signals that lead to the initiation of transcription ultimately converge at the core promoter, which is sometimes referred to as the gateway to transcription (for reviews, see Smale and Kadonaga 2003;Goodrich and Tjian 2010;Kadonaga 2012;Danino et al. 2015). The core promoter is the stretch of DNA-which typically is from about −40 to +40 nucleotides (nt) relative to the +1 transcription start site (TSS)-that directs the initiation of transcription. Core promoters are diverse in terms of their composition and function, and their activities are driven by the presence or absence of DNA sequence motifs such as the TATA box, initiator (Inr), TFIIB recognition elements (BRE u and BRE d ), polypyrimidine initiator (TCT), motif ten element (MTE), and downstream core promoter element (DPE). There are no universal core promoter motifs. Specific core promoter elements can be important for enhancer-promoter specificity (for example, see Butler and Kadonaga 2001; Juven-Gershon et al. 2008) as well as the regulation of gene networks (for example, see Juven-Gershon et al. 2008;Parry et al. 2010;Duttke et al. 2014;Wang et al. 2014).The long-term goal of this study is to gain a more specific understanding of the human core promoter. It has been estimated, for instance, that <25% of human core promoters contain the well-known TATA box or a TATA-like sequence (Gershenzon and Ioshikhes 2005;Carninci et al. 2006;Yang et al. 2007). In fact, it appears that the Inr is the most common core promoter element in humans. For example, ∼48%-49% of human promoters were found to have a sequence in the TSS region (from −5 to +6 relative to the +1 TSS) that is related to the 8-nt "cap signal" (i.e., Inr) position-weight matrix (based on 502 eukaryotic promoters) (Bucher 1990;Gershenzon and Ioshikhes 2005). In addition, it has been found that ∼46% of human promoters contain the YYA +1 NWYY Inr consensus within −80 to +80 nt relative to the TSS (Yang et al. 2007). These observations were interesting, but the precise sequence, abundance, and positioning of the human Inr remained to be determined.The Inr is an extensively studied core promoter element. The presence of a distinct sequence motif that encompasses the TSS was initially described by Corden et al. (1980), and the function of this sequence, w...

Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture

“…We defined these regions as the "core", since they contain core promoter element-like motifs such as the Initiator element (Inr) and the TATA box. Inr is highly enriched at PRO-cap identified TSSs (Ngoc et al 2017) (Supplementary Fig. 5) and diQTL alleles associated with a shift in directionality towards stronger expression of the strand where the diQTL is located have stronger matches to the motif (Fig.…”

“…This alternate allele is also associated with increased eRNA transcription, which is concordant with the change in the TF binding sequence in the central region. Conversely, the non-reference allele of rs8050061 diQTL disrupts a match to the canonical Initiator element (Inr) (Ngoc et al 2017), coinciding with decreased transcription from the affected strand ( Fig. 4B).…”

“…Measuring the effect of diQTL SNPs on Initiator elements. Initiator (Inr) element likelihood is calculated using published human Inr frequency matrix (Ngoc et al 2017) by taking the natural exponent of the PWM scores. First, we selected diQTL SNPs within 5 base pairs (bp) from the defined nascent transcription start sites (nTSSs) of tTREs.…”

Promoter analysis and prediction in the human genome using sequence-based deep learning models

“…The high fidelity of the RNA polymerase II (pol II) transcription system is necessary for precise spatiotemporal regulation of endogenous protein expression and essential to proper development and homeostasis in eukaryotes. Among the key cis-regulatory modules for RNA pol IImediated transcription is the core promoter, which is typically situated within a DNA segment spanning from -40 bp to +40 bp relative to the transcription start site (TSS) at position +1 (Kadonaga, 2012;Danino et al, 2015;Vo Ngoc et al, 2017a). This stretch of DNA serves as a platform on which RNA pol II and a number of auxiliary factors assemble into the transcription machinery, which is capable of integrating a range of intrinsic and extrinsic signals, to ultimately determine the proper initiation of transcription (Lodish et al, 2000;Butler and Kadonaga, 2002;Morris et al, 2004;Juven-Gershon et al, 2008;Kadonaga, 2012;Roy and Singer, 2015;Zabidi et al, 2015;Vo Ngoc et al, 2017b).…”

Finding the start site: redefining the human initiator element

“…The importance of the sequence at individual positions in the BBCABW consensus Inr sequence was tested using in vitro transcription assays (Vo ngoc et al 2017). Two native core promoters that each contained a consensus Inr were used, and single-point mutations were made at each position from −3 to +3 that took the sequence away from consensus.…”