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. Author manuscript; available in PMC: 2020 Aug 8.
Published in final edited form as: Mol Cell. 2019 Jul 3;75(3):631–643.e8. doi: 10.1016/j.molcel.2019.06.006

Figure 5. mRNA expression level and mRNA half-life depending on TSS.

Figure 5.

A. mRNAs with an annotated m6Am start nucleotide show higher mRNA expression than other mRNAs. mRNA expression level in wild-type HEK293T cells was based on the first annotated nucleotide and an earlier m6Am map (Mauer et al., 2017a) . Transcripts that start with m6Am are significantly upregulated. ****, P < 2.2 × 10-16, Student’s t-test. Cumulative distribution plot and boxplot represent the expression for mRNAs starting with m6Am, Am, Cm, Gm and Um. Data shown are the average gene expression measured from two replicates for HEK293T cells.

B. m6Am mRNAs annotated using the PCIF1 knockout (KO) miCLIP dataset show increased expression compared to mRNAs with other start nucleotides. Cumulative distribution plots were prepared as in A using the high-confidence m6Am dataset. The transcripts start with m6Am are significantly upregulated as in A. ****, P < 2.2 × 10-16, Student’s t-test.

C. mRNAs with an annotated m6Am start nucleotide show higher mRNA half-life than other mRNAs. Annotated mRNA half-lives were based on the first annotated nucleotide and an earlier m6Am map (Mauer et al., 2017a). mRNAs with an annotated m6Am exhibit a significantly elevated mRNA half-life than mRNAs with other annotated start nucleotides. ****, P < 2.2 × 10-16, Student’s t-test.

D. m6Am mRNAs annotated using the PCIF1 KO miCLIP dataset show increased expression compared to mRNAs with other start nucleotides. Transcripts with m6Am have significantly longer half-life with similar P-value. ****, P < 2.2 × 10-16, Student’s t-test.

E. Influence of PCIF1 depletion on mRNA half-life for transcripts in the lower half of gene expression. Transcripts with m6Am have significantly shorter half-life in comparison to mRNAs with other annotated start nucleotides. *, P = 0.0258 by Student’s t-test.

F. Influence of PCIF1 depletion on mRNA half-life for highly expressed transcripts. Transcripts with m6Am show no significant decrease in mRNA half-life in comparison to mRNAs with other annotated start nucleotides. n.s., Student’s t-test.

See also Figure S4.