Nrd1 and Nab3 can terminate transcription of long transcripts by binding to 3′ UTRs. (A, B) Nrd1 and Nab3 preferentially bind transcripts approximately ≤1 kb. The histogram in (A) shows the length distribution (including UTRs) of transcripts bound by Nrd1 and Nab3 in the 3′ UTR. Only transcripts where cross-linked motifs mapped to the 3′ UTR were selected. The bracket indicates the percentage of transcripts longer than 782 nucleotides. The boxplot in (B) shows a comparison of the length distribution of the transcripts in (A) with the length distribution of all non-intronic protein coding genes in yeast. The P-value was calculated using a two-sample Kolmogorov-Smirnov test and indicates the likelihood that the two samples originate from the same continuous distribution. (C, D) UCSC genome browser images of YTA7 region. ‘Selected intervals’ indicate genomic regions with a read coverage FDR ≤0.01 used for pyMotif analyses. The Pol II serine phosphorylation ChIP data were obtained from . See the legend to Figure 5 for more details. Chromosomal positions of RT-PCR products are indicated below the YTA7 gene. The Nab3 and Nrd1 motifs in the approximately 100 bp region downstream of YTA7 are indicated in cyan and red, respectively. (E). Quantitative-RT-PCR results for YTA7 coding sequence (exon) and downstream region. Error bars indicate standard deviations.