Figure 3.
Nucleosome positioning is associated with intron splicing efficiency. (A) Relative distribution of different classes of introns. Introns are grouped based on their length (3n or non-3n) and whether their retention causes a premature termination codon making them sensitive to the nonsense-mediated decay (NMD) mechanism (NMD-sensitive) or not (NMD-insensitive). Within each group, introns are classified based on the distance to the closest nucleosome center as in Figure 2G. P-values are calculated using the χ2 test, and only the significant ones are indicated. (B) Intron repartition according to the categories defined in Figure 2F as a function of their relative position within a gene. Introns are grouped based on their NMD sensitivity. Bin size = 20%. A barplot representation with relative P-values is displayed in Supplemental Figure S3A. (C) The retention rate of introns in WT (dashed lines) and in NMD-depleted (NMDKD; solid lines) cells as a function of their relative position within a gene. Introns are grouped as in panel B. Error bars represent the SEM. P-values calculated using Mann–Whitney U test, and adjusted with a false-discovery rate (5%), are displayed in Supplemental Figure S3B. Bin size = 20%. (D) The retention rate of introns in WT (dashed lines) and in NMDKD (solid lines) cells as a function of gene expression levels. Error bars represent the SEM. Colors and groups are as in panel B. P-values calculated using Mann–Whitney U test, and adjusted with a false-discovery rate (5%), are displayed in Supplemental Figure S3C. (E) Relative characterization of introns, within the same categories as in panel B, based on the strength of splicing acceptor and donor sites. P-values are calculated using the χ2 test and adjusted with a false-discovery rate (5%). Tests were run between introns belonging to the same positional group or between introns belonging to the same NMD group. P-value in all the plots: (*) <0.05, (**) <10−2, (***) <10−3, (****) <10−4, (*****) <10−5, and (******) <10−6.