Metasite analysis of nuclear exosome–targeted poly(A)⁺ RNA 3′-end cluster peaks reveals two distinct modes of NNS-dependent termination. (A) Pile-up analysis of PAT cluster peaks for all nuclear exosome–targeted PAT (xPAT) clusters (top) and WT PATs insensitive to the nuclear exosome (bottom). The PAT clusters are separated according to the absence (left) or presence (right) of DNase I–resistant sites (DRS) within 20 bp downstream from the cluster peak. As the pile-up is aligned with PAT cluster peaks at the zero-coordinate, overall PAT signal appears as a single sharp peak. (B) Motif enrichment upstream of xPATs relative to WT PATs. Sequences upstream of each peak were screened for the levels of motifs directing NNS-termination (Nab3p: CUUG, UCUU, UCUUG; Nrd1p: GUAG, UGUA), with reverse complements and the Hrp1p/Nab4p motif UAUAUA as controls. The y-axis represents the log₂ fold enrichment of each motif in the 250-bp region upstream of xPAT versus WT PAT cluster peaks.