Distribution of oligoadenylated 3′ ends along the reporter mRNA. (A) Distribution of 3′ ends of total sequence reads (red) and of oligoadenylated sequence reads (green) over the reporter mRNA sequence in the luciferase control. Green bars represent the last encoded nucleotide in the sequence read, i.e., the position to which the A tail is added. A hot spot consistently observed at nucleotides 392/393 is indicated with an arrow. Sequence representation ends at the “regular” poly(A) addition site at position 577. Numbering of the sequence is based on the transcription start site reported by the supplier of the pMT/V5 vector; note that the transcription start site identified by the cRT-PCR analysis is 3 nt downstream (Supplemental Table II). (B) The same type of data is displayed for the Mtr3 knockdown. (C) The same type of data is displayed for the Dcp2 knockdown. All data are taken from the experiment shown in Figure 2A,C. (D) Approximate extent of the mRNA sequence covered by the deep sequencing libraries. The numbers on the left indicate the first nucleotide of the second (nested) upstream primer, defining the upper end of the sequence. The lower end depended on the gel purification procedure and is thus less precisely defined, as indicated by the dotted lines.
