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Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
Yoav Arava, Yulei Wang, John D. Storey, Chih Long Liu, Patrick O. Brown and Daniel Herschlag
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Supplemental Material
Supplemental Figure 4: Distribution of ribosome occupancy values.

The percentage of each mRNA found in ribosome-containing fractions (Fractions 6-14) was determined, and the values for 5701 genes are plotted.

(Also available in Portable Document Format [PDF] )

Supplemental Figure 5: Ribosome density distributions.

Distribution of ribosome density values for the subset of 739 genes that have a peak fraction assigned to one fraction with 95% confidence level, the subset of 2128 genes with peak fraction assigned to two adjacent fractions, and for all 5701 genes.

(Also available in Portable Document Format [PDF] )

Supplemental Figure 6: Correlations of ribosome density with mRNA features.

Scatter plot of density values with codon bias index, codon adaptation index, mRNA abundance and mRNA half-life.

(Also available in Portable Document Format [PDF] )

Supplemental Figure 7: Testing the effects from potential incorrect assignment of number of ribosomes in the fast-migrating fractions.

Correlation of ORF length with ribosome density when analyzing only the well-resolved fractions, when assigning extreme error margins for the number of ribosomes in fractions or when assigning ribosome density by a weighted average across the polysomal gradient.

(Also available in Portable Document Format [PDF] )

Supplemental Figure 8: Correlation of ribosome density and ORF length within subsets of genes.

Correlation of ORF length with ribosome density for subsets of genes with a similar localization of their mRNA (membrane or mitochondria) or similar localization of the encoded protein (ribosome or mitochondria)

(Also available in Portable Document Format [PDF] )

Supplemental Figure 9: Correlation of ribosome density and ORF length in mammalian cells.

Correlation of ribosome density and ORF length observed in mouse cells by Northern analysis (Cataldo L. Mol. Human Repro. 1999, 5 pp. 206-213).

(Also available in Portable Document Format [PDF] )

Excel workbook

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Supplemental Table 1: List of genes which less than 50% of their mRNAs are associated with ribosome(s).

List of genes with ribosome occupancy values lower than 50%. For each gene, two values are presented: percent associated with one ribosome or more (sum of fractions 6-14) and percent associated with two or more ribosomes ((sum of fractions 8-14). For each gene, its annotated function in MIPS) are also presented.

Excel workbook

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Supplemental Table 2: List of mRNAs predominantly associated with one ribosome.

List of genes which had a peak fraction in fractions 6 or 7. This list was extracted from the 2128 genes data set (Containing genes with their bootstrap 95% Confidence intervals for peak fraction assignment containing at most two adjacent fractions). Also presented for each gene is its annotated function in SGD, its functional group (from MIPS), and the number of AUGs located in its 140 nts upstream to the start site.

Excel workbook

(1.4 MB)
Supplemental Table 3: Protein synthesis estimates.

To predict relative translation rates we simply multiply the ribosome occupancy by the ribosome density. This estimate assumes elongation and termination are equal for all genes and there are no large biases from different shape of polysome distributions. In order to estimate proteins synthesis rates (proteins/sec), the relative translation values were multiplied by the mRNA abundance and divided by the time needed to translate fragment of 100 nts (3.3 second, assuming elongation rate is 30 nts/sec, on every section along every mRNA ).

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Supplemental Table 4: Number of ribosomes associated with each fraction of the sucrose gradient.

Also available in PDF format.

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Supplemental Table 5: Summary of searches for motifs in the untranslated regions of the genes listed in supplemental Tables 1 and 2.

Two different search algorithms were used, MEME and BioProspector, to try and identify sequence motifs that might be involved in translation regulation.


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