Fig. 8: Accumulation of MTR4 substrate ncRNAs could be involved in altered expression of protein coding genes.

A Pie plot showing the population of upregulated mRNAs with MTR4 binding. n = 361. B Cumulative distribution of the expression changes of mRNAs in Mtr4-cKO germ cells compared to the corresponding Cntls. mRNAs are categorized into those with highly-upregulated, mildly-upregulated and no-changed PROMPT. Highly-up, n = 1367; mildly-up, n = 1631; n/c, n = 613. P-values are based on the one-sided Kolmogorov-Smirnov test. C Pie plot showing the population of upregulated mRNAs without MTR4 binding possessing upregulated PROMPT. D Screenshots of RNA-seq signals of upregulated Zfp397 with upregulated PROMPT. E Pie plot showing the distribution of MTR4 binding reads mapped to the indicated RNA classes. Categories are mutually exclusive. n = 1,631,508. F Pie plot showing the distribution of MTR4 binding reads mapped to the indicated repeat elements (RE). Categories are mutually exclusive. G Bar plot showing the distribution of reads mapped to the indicated RNA classes in Cntl and Mtr4-cKO RNA-seq data. Categories are mutually exclusive. Cntl, n = 94,489,710; Mtr4-cKO, n = 96,925,892. H Volcano plots showing the expression changes of SINEs (38,475 genes analyzed, left), LINEs (4890 genes analyzed, middle) and LTRs (6144 genes analyzed, right) in Mtr4-cKO germ cells compared to the corresponding Cntls. I Metaprofile showing MTR4 signals on SINEs exhibiting upregulated and no-changed or downregulated expression based on merged LACE-seq data. Up, n = 606; n/c or down, n = 4231. J Cumulative distribution of the expression changes of mRNAs in Mtr4-cKO germ cells compared to the corresponding Cntls. mRNAs are categorized into those with highly-upregulated, mildly-upregulated and no-changed B2 SINE. Highly-up, n = 361; mildly-up, n = 527; n/c, n = 1098. P-values are based on the one-sided Kolmogorov-Smirnov test. K Pie plot showing the population of downregulated mRNAs possessing upregulated B2 SINE.