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Fig. 2 | Genome Biology

Fig. 2

From: The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation

Fig. 2

MKRN1 binds upstream of A-rich stretches in 3′ UTRs. a MKRN1 binds upstream of A-rich stretches in the 3′ UTR of the LARP1 gene. Genome browser view of GFP-MKRN1 iCLIP data showing crosslink events per nt (merged replicates) together with binding sites (lilac) and associated A-rich stretches (dark green). b MKRN1 predominantly binds in the 3′ UTR of protein-coding genes. Pie charts summarizing the distribution of MKRN1 binding sites to different RNA biotypes (7331 binding sites, top) and different regions within protein-coding transcripts (6913 binding sites, bottom). c MKRN1 binding sites display a downstream enrichment of AAAA homopolymers. Frequency per nucleotide (nt) for four homopolymeric 4-mers in a 101-nt window around the midpoints of the top 20% MKRN1 binding sites (according to signal-over-background; see the “Materials and methods” section). d MKRN1 crosslink events accumulate upstream of A-rich stretches. Metaprofile (top) shows the mean crosslink events per nt in a 201-nt window around the start position of 1412 MKRN1-associated A-rich stretches in 3′ UTRs. Heatmap visualization (bottom) displays crosslink events per nt (see color scale) in a 101-nt window around the MKRN1-associated A-rich stretches. e MKRN1 binding site strength (signal-over-background, SOB) increases with the number of continuous A’s within the A-rich stretch. Mean and standard deviation of MKRN1 binding site strengths associated with A-rich stretches harboring continuous A runs of increasing length (x-axis). MKRN1 binding sites without associated A-rich stretches are shown for comparison on the left. Number of binding sites in each category indicated as bar chart above

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