Extended Data Fig. 6: Summary of the transcriptional yield of reincorporated MN chromosomes in all generation 2 families.

Each bar plot shows the transcriptional yield of both homologues of the MN chromosome (filled for the MN homologue that is annotated below each plot; open for the intact homologue) in the MN daughters (two on the left) and one or both MN nieces (on the right) in a family. Families are grouped based on the status of MN nuclear envelope integrity (left: NE disruption during generation 1 interphase; right: intact NE) and the segregation pattern of MN chromosomes (top, 2:2; bottom 1:3). Nine families (NE disruption: F12, F24, F34, F37, F154, F155, F281, F34; intact NE: F25) without MN nieces are shown separately from the remaining families with MN nieces. MN chromosomes with near normal transcriptional yield are shown in green: Under a 2:2 segregation, the MN haplotype displays a transcriptional ratio of 1:0 between the MN daughters and normal (monosomic) transcription in the MN nieces; under a 1:3 segregation, the MN haplotype displays a transcriptional ratio of 2:1 between the MN daughters and complete transcriptional loss in the MN nieces. (See Extended Data Fig. 2a for the segregation patterns.) MN chromosomes with significantly reduced transcription are shown in magenta. For these chromosomes, the MN haplotype shows a statistically significant lower transcription than normal transcription (monosomic transcription under 2:2 segregation and disomic transcription under 1:3 segregation, two-sided z-test). In families F24, F205, F259, and F37, we identified transcription of the MN haplotype in both daughter cells that is consistent with chromosome fragmentation; we combined the transcriptional yield in both MN daughters in these samples to assess the normality of transcription of reincorporated MN chromosomes. All MN chromosomes with deficient transcription are associated with NE disruption. The summary bar charts of normal and deficient transcription in 2:2 segregation samples and 1:3 segregation samples only include MNs with the predicted patterns of transcriptional imbalance. Deviations from the predicted patterns are explained below. In family F233 and F261, the presence of an extra copy of the Chr.12A homologue in all family members indicates a pre-existing duplication of Chr.12A that is a frequent alteration in RPE-1 cells. In family F12, we inferred the MN chromosome to be the active X (the transcription yield of the inactive X is not shown) that also contains a duplicated 10q segment. In seven families (F236, F231, F25, F189, F238, F281, F34), we inferred that the MNs contain only a chromosome arm; in family F238, we inferred the 1p arm was reincorporated into one MN daughter and the 1q arm was persistent in a MN niece cell based on live-cell imaging. We note that for MN chromosomes that underwent 1:3 segregations, the normality of transcription is assessed by comparing the level of MN haplotype-specific transcription to the level of total transcription of normal disomies (2). The proportional gain of transcription of duplicated homologue (2) is verified using observations from 18 spontaneous trisomies.