Fig. 4

Comparison of the telomeric chromatin-associated TERRA between HeLa1.3 and ALT U2-OS cell lines. a Bar graph of FPKM of the telomerase RNA component (TERC) in telomerase-maintained telomeres (HeLa1.3) and ALT telomeres (U2-OS). b Pie charts show the percentage of telomere repeat sequence reads including TERRA/ARRET in the input and TH59-DB pull-down fractions from HeLa1.3 and U2-OS. Upper part and lower part show experiment 1 and experiment 2, respectively. c A browser view of chromatin-associated TERRA transcripts at a subtelomeric region downstream transcription start site (TSS) coding TelBam3.4 sequence using Integrative Genomic Viewer (IGV) in HeLa1.3 or U2-OS. The numbers on the left side in tracks indicate the read counts in RNA-seq. Telomere region in TelBam3.4 that was defined previously (Nergadze 2009, Usui 2015). Borderlines (vertical dotted black lines) are shown between pre-telomere, telomeric repeat-poor, and -rich regions based on TTAGGG repeat density. d Scatter plots of read per kilobase with normalized count per million (RPKM) in U2-OS cells versus that of HeLa1.3 cells for each RNA from two independent PI-PRICh experiments. RNA that is transcribed from the subtelomeric region of TelBam3.4 is highlighted in red