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. 2022 Apr 6;11:e76562. doi: 10.7554/eLife.76562

Figure 3. Clustering of 25 S rRNA modification profiles and percent change in modification frequency of mutant helicases Dbp3 and Prp43 and G-patch proteins Pxr1 and Sqs1.

(A) Barplots of the difference between wild-type modification frequency and dbp3ᐃ, prp43-cs, pxr1ᐃ, and sqs1ᐃ modification frequencies in 25 S yeast rRNA. Gray bars indicate the variance of wild type rRNA modification at each position and the black dotted lines represent the maximum variance observed at any site. (B) Hierarchical clustering of 25 S yeast rRNA modification profiles from wild type, dbp3ᐃ, prp43-cs, and pxr1ᐃ (1000 reads in each experiment). Each row is a full-length molecule, each column is a modified nucleotide and the color represents modification probability, see scale.

Figure 3.

Figure 3—figure supplement 1. Clustering of 18 S rRNA modification profiles and percent change in modification frequency upon mutation of helicases Dbp3 and Prp43 and G-patch proteins Pxr1 and Sqs1.

Figure 3—figure supplement 1.

(A) Barplots of the difference between wild-type modification frequency and dbp3ᐃ, prp43-cs, pxr1ᐃ, and sqs1ᐃ modification frequencies in 18 S yeast rRNA. Gray bars indicate the variance of wild type rRNA modification at each position and the black dotted lines represent the maximum variance. (B) Hierarchical clustering of 18 S yeast rRNA modification profiles from wild type, dbp3ᐃ, prp43-cs, and pxr1ᐃ (1000 reads in each experiment). Each row represents a full-length single read, each column represents a modified nucleotide and the scale represents the probability of being modified.
Figure 3—figure supplement 2. Clustering of 18 S rRNA modification profiles and percent change in modification frequency upon mutation of helicases Prp43 and Prp16, compared to wild type controls grown at 30 °C or shifted to 18 °C for 1 hr.

Figure 3—figure supplement 2.

(A) Barplots of the difference between 18 S yeast rRNA modification frequency of wild type cells grown at 30 °C and wild type, prp43-cs, and prp16-cs cells shifted to 18 °C for 1 hr. Gray bars indicate the variance of wild-type rRNA modification at each position and the black dotted lines represent the maximum variance. (B) Hierarchical clustering of 18 S yeast rRNA modification profiles from wild type 30 °C, wild type 18 °C, prp43-cs, and prp16-cs (1,000 reads in each experiment). Each row represents a full-length single read, each column represents a modified nucleotide and the scale represents the probability of being modified.
Figure 3—figure supplement 3. Clustering of 25 S rRNA modification profiles and percent change in modification frequency upon mutation of helicases Prp43 and Prp16, compared to wild-type controls grown at 30 °C or shifted to 18 °C for 1 hour.

Figure 3—figure supplement 3.

(A) Barplots of the difference between 25 S yeast rRNA modification frequency of wild-type cells grown at 30 °C and wild type, prp43-cs, and prp16-cs cells shifted to 18 °C for 1 hr. Gray bars indicate the variance of wild type rRNA modification at each position and the black dotted lines represent the maximum variance. (B) Hierarchical clustering of 18 S yeast rRNA modification profiles from wild type 30 °C, wild type 18 °C, prp43-cs, and prp16-cs (1000 reads in each experiment). Each row represents a full-length single read, each column represents a modified nucleotide and the scale represents the probability of being modified.
Figure 3—figure supplement 4. Clustering of underlying events to search for patterns of modification in the Dbp3 KO and Prp43 cold mutant.

Figure 3—figure supplement 4.

Hierarchical clustering of aligned standardized events from Dbp3 KO (A) and Prp43 cold mutant (B) covering the events from positions 1431–1455 (see Materials and methods). These positions cover the 3 2’O ribose methylations guided by the snoRNA U24 at positions 1437, 1449, and 1450.