Fig. 1: Characterisation of centromere and pericentromere transcripts.

a Upper, middle and bottom plots: the number of cenRNA reads; cen- and noncoding pericenRNA reads; cen-, noncoding pericen-, and coding pericenRNA reads (as mean read counts), respectively, deriving from all sixteen chromosomes and tallied from three independent experiments (n = 3), are plotted against the sequences from which they derived. The CEN core regions are indicated by a grey column. The full lines represent the read pairs deriving from the upper strand, the dashed lines those deriving from the lower strand. Orange lines: RIO1-AID cells treated with a mock for 1 h (n = 3), blue lines: RIO1-AID cells treated with 500 µM auxin for 1 h (n = 3). The left and right plots comprise 500 bp and 100 bp of the periCEN regions surrounding the CEN core sequences, respectively. b Left plot: length-based distribution of the cenRNA reads deriving from all chromosomes. Right plot: length-based distribution of all noncoding pericenRNA reads deriving from all chromosomes. The cen- and noncoding pericenRNA reads identified in RIO1-AID cells treated with a mock (tallied from three replicate experiments, n = 3) are indicated in orange and pink, respectively. The cen- and noncoding pericenRNA reads identified in RIO1-AID cells (tallied from three replicate experiments, n = 3) treated with auxin are shown in dark and light blue, respectively. c Violin plot of the length-based distribution of cenRNA reads (classified by short or long) and of noncoding pericenRNA reads in RIO1-AID cells treated with a mock or auxin (three replicate experiments, n = 3). d Distribution of cenRNA reads that contain the entire CEN core sequence (“CEN”) or that terminate in a specific CEN element (CDEI, CDEII, CDEIII) in RIO1-AID cells treated with a mock (encircled in orange) or auxin (encircled in blue) (three experimental replicates, n = 3). The filled and open slices indicate the percentage of reads deriving from the upper and lower strand, respectively. e Distribution of the start sites of cen- and noncoding pericenRNA reads in RIO1-AID cells treated with a mock (left plot) or auxin (right plot). Full and dashed lines: read start sites localising on the upper and lower strand, respectively (three experimental replicates, n = 3).