![]() ![]() (B) Northern blot analysis of U6 snRNA as a loading control for transcription shutoff/mRNA decay analysis of CRIP1, LSM8, and SPTSSA amino acid stretch reporters in Fig 2G. ![]() Amino acids indicated in magenta are significantly stabilizing or destabilizing in both datasets R = 0.91, p = 3.1 x 10 −8 (Pearson correlation test). Dark blue line represents linear regression trendline. (A) Scatterplot comparing amino acid stabilization coefficients (AASC) between HeLa and CHO datasets. ![]() S2 Fig: mRNAs containing destabilizing amino acid stretches show accelerated deadenylation (related to Fig 3). See also S1 Table for northern probe sequences and reporter ORF sequences and S2 Table for tAI and CSC values. Codons indicated in magenta are significantly stabilizing or destabilizing in both datasets R = 0.88, p < 2.2 x 10 −16 (Pearson correlation test). (G) Scatterplot comparing codon stability coefficients (CSC) between HeLa and CHO datasets. R = 0.6, p = 3.0 x 10 −7 (Pearson correlation test). (F) Scatterplot comparing codon stability coefficients (CSC) calculated from HeLa endogenous mRNA half-life datasets used in this study and in a parallel study by Wu and colleagues. Timepoints represent time elapsed after shutoff of transcription with doxycycline. (E) Northern blot analysis of actin mRNA as a loading control for mRNA decay analysis of CFTR ΔF508 variable codon optimality reporters in Fig 1E. (D) Northern blot analysis of U6 snRNA as a loading control for mRNA decay analysis of MECP2 variable codon optimality reporters in Fig 1D. (C) Northern blot analysis of U6 snRNA as a loading control for mRNA decay analysis of Firefly luciferase variable codon optimality reporters in Fig 1C. (B) Plot of frequency of codons with G or C at the 3’-nucleotide position (GC3) within variable optimality Firefly reporter ORF sequences. P-value and confidence intervals indicate results of Fisher’s exact test for difference in proportion of GC3 versus AT3 codons designated as optimal. (A) Two by two table detailing proportions of optimal vs non-optimal codons (as defined by HEK293T tRNA sequencing) with G or C at the at the 3’-nucleotide position (GC3) versus A or T (AT3). S1 Fig: Optimal codon content modulates mRNA stability in human cells (related to Fig 1). ![]()
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