Effects of ICOP knockdowns (KDs) on DNA excision. (A) mRNA expression levels in fragments per kilobase per million mapped reads (FPKM) compared between ICOPa and ICOPb KDs for transcripts early in development (40% old MAC fragmentation) or asynchronous (asyn.) cultures (*) in which new MACs were observed in 20% of cells but the majority of the cells were in early development. ICOPa/b indicates cosilencing of ICOPa and ICOPb. (B) Survival of recovered postautogamous KD cells followed for several vegetative divisions. Alive (pink): four divisions per day; sick (red): fewer than three divisions per day; dead (cayenne): no cells. (C) Retention of mating type, 51A2591 and 51A6649 IESs. ISWI1-KD: positive control. Retained IESs (IES+) result in a larger amplicon. (D) Genome-wide IES retention scores (IRS) across ∼45,000 IESs in different KDs. (E) Correlation of IRSs among KDs. Diagonal indicates IRS distributions of individual KDs; below diagonal, correlation graphs of pairwise comparisons; above diagonal, corresponding Pearson correlation coefficients; red lines, ordinary least-square (OLS) regression; orange lines, LOWESS; and gray lines, orthogonal distance regression (ODR).
