Fig. 7: MTR4 binds to specific regions on its substrate RNAs.

A A diagram for the cell sorting and LACE-seq experimental approach. B Violin plot showing the normalized MTR4 binding counts on RNAs of varying length expressed in Cntl germ cells. n = 2130; 2130; 2130; 2130; 2130 from left to right. P-values are based on the two-sided unpaired Wilcoxon test. Medians are shown in the plot. C Violin plot showing the normalized MTR4 binding counts on RNAs with varying intron numbers expressed in Cntl germ cells. n = 3422; 1161; 1944; 2031; 2022 from left to right. P-values are based on the two-sided unpaired Wilcoxon test. Medians are shown in the plot. D Metaprofile showing the MTR4 signals on mRNAs exhibiting upregulated, no-changed, and downregulated expression based on merged LACE-seq data. Up, n = 340; n/c, n = 11,115; down, n = 2661. E Same as (D), except that MTR4 signals on ptRNAs are shown. Up, n = 419; n/c, n = 396. F Same as (D), except that MTR4 signals on RDH and RIH mRNAs are shown. RDH, n = 65; RIH, n = 14. G Heatmap showing the expression of RDH and RIH genes in Cntl and Mtr4-cKO germ cells. H Screenshots of RNA-seq signals of representative upregulated RDH (left) and no-changed RIH (right) genes in Cntl and Mtr4-cKO germ cells. I Same as (D), except that MTR4 signals on histone mRNAs are shown. Up, n = 51; n/c, n = 18. J Bar plot showing the population of RDH and RIH genes exhibiting upregulated, no-changed, and downregulated expression in hMTR4 KD HeLa cells relative to the corresponding Cntls based on rRNA depleted RNA-seq. RDH, n = 61; RIH, n = 10. Data in (B, C) are presented as box and whisker plots. The central lines denote median value, while the bounds of box mark the 25th to 75th percentiles and whiskers refer to minimum and maxima values. Source data are provided as a Source Data file.