Fig. 7: Delayed replication and instability.

Deletions of TL:8-2.7 (a–g) or TL:9-23, TL:9-24, or TL:9-30 (h–p). a, b, h AEI and ASRT in EB3_2 and GM12878 clones. The left Y-axis shows replication, and standard deviation (SD). Outliers in the standard deviation (SD) are highlighted in gray. The right Y-axis shows AEI. The X axis shows chromosome position (megabases). c FISH for TL:8-2.7 RNA (red, arrows) and chromosome 8 centromere DNA (green, arrowheads). d Quantification of RNA signals for TL:8-2.7 before and after deletion. Percent of nuclei with 0, 1, or 2 signals are shown. e Chromosome 8 showing the location of TL:8-2.7 (red dot). f Delayed replication following ASAR8-2.7 deletion. BrdU incorporation (green) and DNA FISH (CHR8 cen, purple) plus an ASAR8-2.7 Fosmid (red). g, m Quantification of BrdU incorporation following ASAR8-2.7 (g) or ASAR9-23, ASAR9-24, or ASAR9-30 (m) deletion. Box plots indicate mean (solid line), standard deviation (dotted line), 25th, 75th percentile (box), 5th and 95th percentile (whiskers) and individual cells (single points). P values were calculated using the Kruskal–Wallis test⁷⁸. i, j RNA-DNA FISH for TL:9-30 RNA (green, arrows) and TL:9-23 RNA (i) or TL:9-24 RNA (j) (red, arrows) and chromosome 9 centromere DNA (purple, arrowheads). k Sequencing traces of PCR products from DNA or cDNA (RNA) isolated from HTD114, and DNA from cell hybrids containing either CHR9A or CHR9B. l ASRT after deletion of ASAR9-23. Mitotic cell showing BrdU incorporation (green) and DNA FISH (CHR9 centromere; red). n–p DNA FISH using chromosome 9 paint (CHR9; red). m Deletions of ASAR9-23, ASAR9-24 or ASAR9-30 were from chromosome 9A (*CHR9A). n The bracket marks a chromosome bridge, and insets show longer exposures. o Micronucleus containing chromosome 9. p Mitotic cell containing a chromosome 9 fragment. Arrowheads mark intact chromosome 9 s. Scale bars are 10 µM (c, f, i–j, l, n–p), and 2.5 µM in insets in (f) and (l). q Percent cells containing rearrangements identified with chromosome paints. Deleted ASARs are indicated, and chromosomes 8 and 9 were scored in parental HTD114 cells. Source data are provided as a Source data file (d, g, m, q).