A novel synthesis and detection method for cap-associated adenosine modifications in mouse mRNA

Kruse, Susanne; Zhong, Silin; Bodi, Zsuzsanna; Button, James; Alcocer, Marcos J. C.; Hayes, Christopher J.; Fray, Rupert

Core promoters of Pol II transcribed genes may be focused, directing transcription initiation at a single site or cluster of adjacent sites, or they may be dispersed and have multiple start sites over a region of 50-100 nucleotides 6 . In case of focused promoters the transcription start sites are contained within and around the Inr (YYANWYY), where the A is the principal start site and surrounding nucleotides are utilised to varying degrees 6 . Recent high-throughput sequencing from full length mRNAs, suggests that purine instead of A may be a better representation of the Inr consensus. However, most core promoters have several closely arrayed transcription start sites with different initiation rates rather than initiating at a single nucleotide 32 . Thus, most genes will give rise to a population of mRNAs that differ in their starting nucleotides. For example the Prm2 message initiates predominantly at the central A of the Inr as well as a second A 3 nucleotides upstream, whereas, Apoa1 strongly initiates at the A of the Inr but also uses surrounding U, G, C and sites at a significant level (Supplementary Figure S2 online) and (Fig. 4B) .