Figure 1. SE associates with intronless genes in a transcription dependent manner.
(A) Venn diagram showing the overlap of SE ChIP-seq targets in three independent biological replicates. (B) Visualization of SE ChIP-seq data in WT and se-1. Tracks showing counts of sequencing reads mapped to the depicted genomic loci. (C) Validation of SE targets by ChIP-qPCR using SE-specific antibodies in WT and se-1 mutants. Quantification of enriched DNA fragments was performed by qPCR. Error bars indicate the range of two independent biological experiments. (D) Annotation of the 1012 SE-ChIP targets sites. Peaks are categorized in six distinct classes: promoter-transcription start site (promoter-TSS), transcription start site (TSS), 5’-UTR, exon, intron, 3’-UTR. Y-axis denote the number SE peaks within each category. (E) Analysis of SE enrichment at selected targets by ChIP-qPCR in the presence and absence of the transcriptional inhibitor cordycepin. Error bars indicate mean ± SEM of three independent biological replicates. (F) Analysis of SE enrichment at SE target loci in WT, se-1 and cbp20 mutants by ChIP-qPCR. Error bars indicate mean ± SEM of three independent biological replicates. (G) Analysis of CBP20 enrichment at SE target loci in WT and se-3 mutants by ChIP-qPCR using a CBP20-specific antibody. Rabbit IgG served as a background control. Error bars indicate mean ± SEM of three biological replicates. (H) Classification of SE target genes and non-targets based on intron number. A Fisher’s exact test was performed to access whether differences between SE targets and non-targets were significant. *p<0.05; ****p<0.0001; n.s, not significant (I) Box blots comparing number of introns per gene in SE target genes and non-targets. SE targets are significantly enriched for low numbers of introns compared to non-SE targets (Wilcoxon-Mann-Whitney test). ****p<0.0001.
Figure 1—figure supplement 1. SE mainly binds to protein-coding genes.
