Fig. 5

5′P-RDO changes within the soluble RNA pool correlate with codon optimality upon Not4 and Not5 depletion. Scatterplot analyses comparing pairwise changes in 5′P-RDOs relative to WT in: A soluble RNAs upon Not4 and Not5 (left) or Not1 and Not5 (right) depletion; B soluble RNAs for Not1 and Not4 depletion for all mRNAs (left), all mRNAs excluding mRNAs of the red and green categories of Fig. 2C (middle) or only for mRNAs of the red and green categories (right); C for total RNAs upon Not1, Not4, and Not5 depletion. D tRNA microarray analysis of aminoacyl-tRNA levels in Not1 depleted and corresponding wild-type strain (top lane) and the relative total tRNA abundance (bottom lane). The abundance was measured relative to the wild-type strain. The arrays are an average of three biological replicates. Confidence intervals between replicate 1 and 2, 1 and 3, and 2 and 3 were 97%, 98%, and 98% for the charging arrays of the Not1 depleted cells; 97%, 97%, and 97% for the abundance arrays of the Not1 depleted cells; 97%, 97%, and 97% for charging arrays of the wild-type; and 95%, 94%, and 98% for the abundance arrays, respectively. tRNA probes are depicted with their cognate codon and the corresponding amino acid