Data from: Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom

Description

Chapter 1: Eukaryotic protein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of this context in different species is unclear. We tested this concept in two pathogenic Cryptococcus yeast species by genome-wide mapping of translation and of mRNA 5' and 3' ends. We observed thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to translation repression. uORF use depends on the Kozak sequence context of its start codon, and uORFs with strong contexts promote nonsense-mediated mRNA decay. Transcript leaders in Cryptococcus and other fungi are substantially longer and more AUG-dense than in Saccharomyces. Numerous Cryptococcus mRNAs encode predicted dual-localized proteins, including many aminoacyl-tRNA synthetases, in which a leaky AUG start codon is followed by a strong Kozak context in-frame AUG, separated by mitochondrial-targeting sequence. Analysis of other fungal species shows that such dual-localization is also predicted to be common in the ascomycete mould, Neurospora crassa. Kozak-controlled regulation is correlated with insertions in…

Description from Zenodo, shortened.

Files (29)

• XLSXChapter_1_Table_S1_sequencing_numbers.xlsx16 kB
• XLSXChapter_1_Table_S5_tRNAsynthetases6fungi.xlsx86 kB
• TXTChapter_1_Table_S4_dvsaATG_highdiffw_enoughRNA_H99.txt5.5 kB
• XLSXChapter_1_Table_S3_cytoribosome_Proteins.xlsx35 kB
• TXTChapter_1_Table_S6_dualAUG_aaRS_contexts_cc.txt1.1 kB
• XLSXChapter_1_Table_S7_eIF3.xlsx15 kB
• XLSXChapter_3_Table_S3.xlsx1.5 MB
• XLSXChapter_3_Table_S4.xlsx2.5 MB
• XLSXChapter_1_Table_S8_oligos.xlsx13 kB
• XLSXChapter_3_Table_S1.xlsx136 kB
• XLSXChapter_2_Table_S4.xlsx6.6 MB
• XLSXChapter_3_Table_S8.xlsx475 kB
• XLSXChapter_2_Table_S5.xlsx200 kB
• XLSXChapter_2_Table_S6.xlsx12 kB
• TXTChapter_1_Table_S2_upf1E30vsWT_complete.txt1.1 MB
• XLSXChapter_3_Table_S9.xlsx21 kB
• CSVChapter_2_Table_S1.csv158 kB
• XLSXChapter_2_Table_S2.xlsx12 kB
• XLSXChapter_4_Supp_Table_6_TMT-MS_RBM5-2.xlsx46 kB
• XLSXChapter_3_Table_S5.xlsx4.3 MB
• XLSXChapter_4_Supp_Table_7_Proteomes-2.xlsx10 kB
• XLSXChapter_4_Supp_Table_5_TMT-MS_RBM17-2.xlsx968 kB
• XLSXChapter_3_Table_S6.xlsx15 kB
• XLSXChapter_2_Table_S3.xlsx7.6 MB
• XLSXChapter_3_Table_S2.xlsx1.3 MB
• XLSXChapter_4_Supp_Table_4_TMT-MS_GPATCH1-2.xlsx1.1 MB
• XLSXChapter_4_Supp_Table_3_JUM_output_total.xlsx3.9 MB
• XLSXChapter_3_Table_S7.xlsx371 kB
• XLSXChapter_4_Supp_Table_1_hsSpliceosome_core-2.xlsx37 kB

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