Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4

Characteristics of 17p telomere intra-chromosomal fusions sequenced from MRC5^HPVE6E7 cells undergoing telomere-driven crisis or HCT116 cells undergoing 17p TALEN-induced DNA damage and repair. (A) Cartoon representation of a head-to-head intra-chromosomal fusion between two 17p chromatid telomeres (one striped and one blocked color) identified using discordant and soft-clipped read pairs generated by Illumina HiSeq 2000 paired-end sequencing of fusion amplicons from 17p TALEN-transfected HCT116 cells. Asymmetric subtelomeric distributions of sequencing reads mapping 17p intra-chromosomal fusions in t48 HCT116 WT (B) and crisis-stage MRC5^HPVE6E7 cells (C). The top panel of each series displays the read frequency distribution and individual read pair linkages along the 17p subtelomere visualized using IGV software (Farré et al. 2015) (centromere to telomere orientation illustrated left to right). The 17p TALEN cleavage site 3024 bp telomeric of the 17p6 fusion primer is indicated with an arrow. Two conspicuous frequency peaks in the HCT116 sample map the long (>2 kb) and short (<1 kb) 17p chromatids that comprise the characteristic asymmetric intra-chromosomal fusions observed for all HCT116 samples. Asymmetry in the MRC5^HPVE6E7 intra-chromosomal fusions results almost exclusively from the fusion of one chromatid containing telomere repeats (IGV peak ≥3050 bp from 17p6) and one resected into 17p subtelomeric sequence. The central panel contains a frequency plot (with 100-bp binning) of full-length unclipped (white) and soft-clipped (black) discordant read pairs used to map precise individual fusion junction positions (lower panel) along the 17p subtelomere.