Figure 2

RACE sequencing reveals a distribution of 3′ termini for MRP RNA. a The majority of HEK293T cellular MRP RNA 3′ ends are genomically encoded (black pie slice), with a modest portion of these containing oligo(A)_n additions to these genomically encoded ends (range of n=1-10, light blue slice). In contrast, while nearly three quarters of the reads from in vitro transcribed MRP (ivt-MRP) are the exact target sequence (grey slice), the remaining reads consist of single nucleotide additions to this designed end (+A in blue; +C in green; +G in yellow; +U in red). Both cellular and ivt-MRP displayed a small portion of other simple sequences shown as white slices (i.e. …CUCC, …CUGC, and see Figure 3). Total trimmed reads = 1,497,440 (cellular) and 906,145 (ivt). b Reads from endogenous MRP terminate at specific nucleotides in the flanking RMRP gene with non-random abundances (black bars) and distinct probabilities of oligo(A) addition (light blue caps). As an example, the relative frequency of different numbers (n) of A’s found on one of the genomically encoded termini is illustrated in the inset. The major genomically encoded end is not observed on ivt-MRP (lower panel), nor is there appreciable propensity for oligo(A) addition. Although a single A is sometimes added to the designed terminus, C and G are added with similar frequency.