Fig. 3
Chromatin modifiers regulate the type-specific expression of TEs. a Number of significantly deregulated TE types for the indicated shRNA knockdown (P values < 0.05, Benjamini & Hochberg corrected, absolute fold-change >2, relative to shLuc). See Supplementary Data 1 for detailed sample information. b Boxplots of log2 (fold-change (FC) versus shLuc) for all significantly deregulated TE types. In the boxplot, outliers represent the mean of a TE type. TE types significantly upregulated > 4 fold are indicated in red and the number is marked. c Western blot of chromatin marks, from the indicated shRNA knockdowns. Molecular weight is indicated as Mr (K). This experiment was performed twice with similar results. d Boxplots of the expression level for all TE types with either High or Low levels of the indicated chromatin mark. High was defined as those TE types with > 2-fold enrichment of the indicated chromatin mark. Low sites were selected by ranking the TEs by fold enrichment, and taking TEs from the bottom of the list until it was the same length as the High list. e Genomic views of MMERVK10C-int and IAPEz-int showing chromatin marks and RNA-seq in the indicated shRNA knockdown. f MA-scatter (log-fold-change, mean average expression) plot showing shPrmt5 knockdown relative to shLuc. Blue dots are significantly different genes or TEs (P value < 0.05, Benjamini & Hochberg corrected, absolute fold-change > 2, relative to shLuc). Red dots indicate IAP or LINE1 elements, or the Prmt5 gene. RNA-seq data was from 2 biological replicates. g Genome view of H4R3me2 ChIP-seq data and shPrmt5 RNA-seq data for L1Md_F3 LINE1. h RT-qPCR expression of the LINE1 L1Md_F2, and RLTR13G, relative to shLuc control knockdown. P values are from a one-tailed Student’s t-test. The circles are the mean of three technical replicates, the red bar is the mean of the three biological replicates, and the error bars are the standard error of the mean. Source data are provided as a Source Data file. Primers used are described in Supplementary Data 7. For the boxplots, the midline indicates the median, boxes indicate the upper and lower quartiles and the whiskers indicate 1.5*interquartile range
