Fig. 7: TFIP11 knockdown induces intron retention. | Nature Communications

Fig. 7: TFIP11 knockdown induces intron retention.

From: DHX15-independent roles for TFIP11 in U6 snRNA modification, U4/U6.U5 tri-snRNP assembly and pre-mRNA splicing fidelity

Fig. 7

a Number of differential alternative 5′ splice site (A5SS), alternative 3′ splice site (A3SS), mutually exclusive exon (MXE), retained intron (RI), and skipped exon (SE) events identified with rMATS in cells transfected for 72 h with one TFIP11 siRNA (siTFIP11 #1) compared to control siRNA (siCtr). b–g RT-qPCR shows increased intron retention in mRNA encoding NXF1 (DPSI by RNA-seq: 0.07; overall p = 8.4e-4, p = 0.0027 for siTFIP11#1, p = 0.0032 for siTFIP11#2), THOC6 (DPSI by RNA-seq: 0.14; overall p = 0.0015, p = 0.0049 for siTFIP11#1, p = 0.042 for siTFIP11#2), SMC4 (DPSI by RNA-seq: 0.01, overall p = 0.0017, p = 0.0054 for siTFIP11#1, p = 0.0041 for siTFIP11#2), sororin (DPSI by RNA-seq: 0.11; overall p = 0.0041, p = 0.0072 for siTFIP11#1, p = 0.0052 for siTFIP11#2), CENPE (DPSI by RNA-seq: 0.09; overall p = 3.79e-4, p = 0,001 for siTFIP11#1, p = 0.0086 for siTFIP11#2) and Alyref (DPSI by RNA-seq: 0.06; overall p = 0.0014, p = 0.0055 for siTFIP11#1, p = 0.0064 for siTFIP11#2) in cells transfected with one of two TFIP11 siRNAs (siTFIP11 #1 and siTFIP11 #2) compared to control siRNA (siCtr) for 72 h or mock-transfected cells (No siRNA). n = 3 independent experiments. p-values calculated using one-way ANOVA with Tukey post-hoc test. Only p-values < 0.05 (relative to siCtr) are displayed. Box limits = 25th to 75th percentiles; line = median; whiskers = min to max. h Western blotting in HeLa cells transfected as in b shows decreased abundance of indicated proteins whose mRNAs have increased IR. i Sequences at 5′ and 3′ splice sites (SS), branch points and polypyrimidine tracts (PPT) for introns with increased retention in cells transfected as in a (n = 2311 introns) and introns from all detected splicing events (n = 104,230 introns). j Length of introns and their flanking exons. Control and retained introns as in i. p-values calculated using Welch’s two-sample t-test. k GC content near 5′ and 3′ splice sites. Control and retained introns as in i. l–m Strength and length of PPT of introns. Control and retained introns as in i. p-values calculated using Welch’s two-sample t-test. n Strength of 5′ and 3′ splice sites (SS). Control and retained introns as in i. MaxEntScores ≥ 0 are displayed. p-values calculated using all values with Welch’s two-sample t-test. Source data are provided as a Source Data file.

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