Experiment / E7BCT5PVF5' UTR / Translation Efficiency MPRA (MPTA)

PoLib-seq ribosome loading of yeast uORFs

Unraveling the influences of sequence and position on yeast uORF activity using massively parallel reporter systems and machine learning

A polysome-library sequencing MPRA measured how natural yeast transcript leaders and matched AAG start-codon mutants distribute between translating and non-translating sucrose-gradient fractions. The processed table reports uORF effects on ribosome loading in wildtype BY4741 yeast.

Download processed table (CSV)Raw source data API documentation

Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.

Organism: Budding yeast
Taxonomy ID: NCBITaxon:4932
Biosample: UNMAPPED:Saccharomyces_cerevisiae_BY4741
Reference genome: Not reported / not applicable
Design focus: Other
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated; BY4741 wildtype in log-phase growth

Reporter-bearing yeast lysates were separated on 7–47% sucrose gradients. The source analysis grouped 40S, 60S, and monosome fractions as non-translating and 2-, 3-, 4-, and >5-ribosome fractions as translating; the top fraction was excluded. Replicate 1 monosome reads were downsampled by 0.8626 to balance translating and non-translating reads. Targeted RNA sequencing of each fraction was used to calculate a log2(WT/AAG) ribosome-loading effect from the translated/non-translated reporter ratio.

Processed data

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Visible columns (43 of 43)

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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 43 definitions

element_id: Unique reporter-context identifier formed from the source uORF ID, source UTR ID, and assay condition.
uorf_id: Source identifier for the assayed upstream or overlapping open reading frame.
utr_id: Source identifier for the natural transcript leader containing the tested uORF.
assay_condition: Reporter host condition; all retained PoLib-seq rows are wildtype_BY4741.
source_species: Species from which the natural transcript-leader sequence was derived.
orf_type: Source annotation: uORF or overlapping ORF (oORF).
spealman_2018: Whether the source table marks the element as present in Spealman et al. 2018.
uorf_length_nt: Length of the uORF coding sequence in nucleotides, when defined by the source table.
cap_distance_nt: Distance from the designed transcript start/5′ cap to the uORF start codon in nucleotides.
cds_distance_nt: Distance from the uORF stop codon to the downstream YFP/main ORF start in nucleotides.
kozak_context: Sequence context surrounding the tested uORF start codon.
start_codon: Native uORF initiation codon in the reporter.
mutant_start_codon: Start codon in the matched nonfunctional reporter mutant; AAG for this assay.
mutant_construct_id: Source construct identifier for the AAG mutant reporter.
wildtype_construct_id: Source construct identifier for the native/wildtype reporter.
replicate_1_aag_fraction_counts: Semicolon-delimited source counts for the AAG reporter across PoLib-seq replicate-1 gradient fractions.
replicate_1_wt_fraction_counts: Semicolon-delimited source counts for the native reporter across PoLib-seq replicate-1 gradient fractions.
replicate_1_aag_translated_reads: AAG reporter reads in translating fractions for PoLib-seq replicate 1.
replicate_1_aag_nontranslating_reads: AAG reporter reads in non-translating fractions for PoLib-seq replicate 1.
replicate_1_wt_translated_reads: Native reporter reads in translating fractions for PoLib-seq replicate 1.
replicate_1_wt_nontranslating_reads: Native reporter reads in non-translating fractions for PoLib-seq replicate 1.
replicate_1_pair_total_fraction_reads: Source total fraction-count value for the matched AAG/native reporter pair in replicate 1.
replicate_1_aag_translation_efficiency: Source TE-like translated-fraction summary for the AAG reporter in replicate 1.
replicate_1_wt_translation_efficiency: Source TE-like translated-fraction summary for the native reporter in replicate 1.
replicate_1_log2_wt_over_aag: Per-replicate log2(native reporter/AAG mutant) ribosome-loading effect in PoLib-seq replicate 1.
replicate_2_aag_fraction_counts: Semicolon-delimited source counts for the AAG reporter across PoLib-seq replicate-2 gradient fractions.
replicate_2_wt_fraction_counts: Semicolon-delimited source counts for the native reporter across PoLib-seq replicate-2 gradient fractions.
replicate_2_aag_translated_reads: AAG reporter reads in translating fractions for PoLib-seq replicate 2.
replicate_2_aag_nontranslating_reads: AAG reporter reads in non-translating fractions for PoLib-seq replicate 2.
replicate_2_wt_translated_reads: Native reporter reads in translating fractions for PoLib-seq replicate 2.
replicate_2_wt_nontranslating_reads: Native reporter reads in non-translating fractions for PoLib-seq replicate 2.
replicate_2_pair_total_fraction_reads: Source total fraction-count value for the matched AAG/native reporter pair in replicate 2.
replicate_2_aag_translation_efficiency: Source TE-like translated-fraction summary for the AAG reporter in replicate 2.
replicate_2_wt_translation_efficiency: Source TE-like translated-fraction summary for the native reporter in replicate 2.
replicate_2_log2_wt_over_aag: Per-replicate log2(native reporter/AAG mutant) ribosome-loading effect in PoLib-seq replicate 2.
combined_total_reads: Summed source read count used for the PoLib-seq minimum-read QC cutoff.
combined_log2_wt_over_aag: Source combined log2(native reporter/AAG mutant) ribosome-loading effect; negative values indicate reduced native ribosome loading in the presence of the uORF.
chi_square: Source Cochran-Mantel-Haenszel/chi-square statistic for the combined comparison.
raw_p: Unadjusted significance p-value for the combined PoLib-seq comparison.
adjusted_p: Benjamini-Hochberg-adjusted p-value for the combined PoLib-seq comparison.
consistent_direction: Source flag indicating whether the replicate effects have the same direction.
significant_fdr_0_05: Source flag indicating significance after FDR correction at 0.05.
source_qc_pass: Whether the row met the source PoLib-seq minimum-read QC; all retained rows are true.

Quality control

The paper required at least 5,000 summed reads across capped and uncapped wildtype/AAG comparisons in both PoLib-seq replicates. It tested consistent-direction effects using a Cochran-Mantel-Haenszel test and controlled the false-discovery rate at 5% with Benjamini-Hochberg correction. The processed table retains all 2,209 source rows meeting the 5,000-read cutoff, including non-significant effects.

Curation notes

PoLib-seq was performed in wildtype BY4741; the paper used it as an orthogonal translation/ribosome-loading assay to compare with FACS-uORF. The source workbook reports 2,209 rows with TotalReads ≥5,001. Fraction-count strings are retained because they preserve the seven-position source readout, while the main summary effect is combined_log2_wt_over_aag. The paper does not specify a genome assembly, so reference_genome is null.

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