Figure S2.

Sequence features of C. elegans 3′ UTRs, related to Figure 2

(A) Boxplots of Kyte Doolittle scores indicating hydrophobicity of CDS regions, 3′ UTRs and maximum hydrophobicity score (max. score) of a 21AA window (average TA length) within 3′ UTRs in C. elegans and human.

(B) Relationship of nucleotide composition and sequence properties. Left: nucleotide composition in C. elegans of coding sequences (CDSs), red; TMD transcripts, gray; 3′ UTRs, blue. Right: correlation of 3′ UTR nucleotide composition and hydrophobicity of their translated peptides. U-content positively correlates with hydrophobicity in C. elegans.

(C) Correlation analysis of nucleotide composition and tAI score indicates a negative correlation between U-content and codon optimality.

(D) Occurrence of in-frame stop codons in 3′ UTRs. 3′ UTRs typically contain at least one stop codon before the poly(A) tail (∼90%) in all three reading frames.

(E) Expression of 3-color reporter constructs for either hydrophilic (top) or hydrophobic (bottom) 3′ UTR fusion proteins. Representative fluorescence microscopy images (overlay) of either YFP:mScarlet (left, ratio of YFP to mScarlet) or mScarlet:CFP (right, ratio of mScarlet to CFP) channels are shown.

(F) Representative ratiometric analysis of YFP by mScarlet ratios performed on images shown in (D). The mScarlet channel was used to outline the muscle cells expressing the reporter construct. Linear regression analysis was applied to values of each pixel (for the corresponding channel). The resulting slope was used to express the ratios depicted in Figures 2E, 2F, 3D, and 3E.