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. Author manuscript; available in PMC: 2021 Sep 25.
Published in final edited form as: Nat Struct Mol Biol. 2021 Mar 25;28(4):337–346. doi: 10.1038/s41594-021-00572-y

Extended Data Fig. 6. Analysis of splice efficiency and splice site sequences of lncRNAs suppressed by ZC3H4-WDR82 in HeLa cells.

Extended Data Fig. 6

A) Splicing efficiency at WDR82-suppressed lncRNA junctions (n=3,717) (top panel) and at a randomly selected set of premRNA junctions (n=4,000) (bottom panel) in HeLa cells. A window of +/− 10 nucleotides centered on the 5’ splice sites was used to measure read counts in polyA RNA-seq data.

B) log2-transformed ratio of polyA RNA-seq reads in a 20 nt window centered on the 5’ splice sites of WDR82-suppressed lncRNA or of randomly selected set of mRNAs with at least one splice junction.

C) Analysis of 5’ (left) and 3’ (right) splice site strength (measured as MaxEnt scores) at WDR82-suppressed lncRNAs. Statistical significance was assessed using the two-tailed Wilcoxon rank sum test in correspondence of both the 5’ (p-value=1.2e-21) and the 3’ (p-value=2.6e-06) splice sites. ***=p-value <0.01. Nucleotide frequencies at splice sites are shown as sequence logos. Donor and acceptor splice sites are indicated as black triangles.

D) Effects of the depletion of WDR82-ZC3H4 on transcription of protein coding genes in HeLa cells. Expressed protein-coding genes (n=8,804) were divided into deciles based on their sensitivity to the depletion of WDR82 in 4sU-seq data, with the 10th decile including the most upregulated genes.

Log2-transformed RNA fold changes (polyA and 4sU RNA-seq data) and log2-transformed reads ratio across the first exon-intron junction, as annotated in GENCODE, are shown for the 10th, 5th and 1st deciles. Statistical significance was assessed using the two-tailed Wilcoxon rank sum test (pvalue = 2.0e-21). ***=p-value<0.01. Data were from n=3 independent experiments.

In the boxplots in panels B, C, D the median value for each group is shown with a horizontal black line. Boxes show values between the first and the third quartile. The lower and upper whisker show the smallest and the highest value, respectively. Outliers are not shown. The notches correspond to ~95% confidence interval for the median.