Extended Data Fig. 4: Strong asymmetric H3K9me3 distribution is detected at “young” and long L1s.
From: Asymmetric distribution of parental H3K9me3 in S phase silences L1 elements
a. All HO L1 families with more than 195 copies in mES (left) and HeLa cells (right) were ranked from left to right based on average H3K9me3 eSPAN bias. See Source Data for numbers of L1s in each family. Data were plotted as mean ± SD. Note that L1Md_T and L1Md_A in mES and L1PA in HeLa cells, which have been reported as young and full-length L1s in mouse and human, respectively, show bigger bias. b. Pearson correlations between H3K9me3 eSPAN bias at HO L1s surrounding origins and their corresponding ages in mES (left) and HeLa (right) cells. Each dot represents a L1 subfamily and the size of the dot is proportional to its copy numbers around replication origins. Note that some of the youngest L1s with high H3K9me3 eSPAN bias were highlighted in orange. c. Distribution of the length of H3K9me3-bound HO L1s with the lowest H3K9me3 eSPAN bias (red, bottom 25%) and highest H3K9me3 eSPAN bias (blue, top 25%) in mES (left) and HeLa (right) cells. The Y axis was fragmented to better show the details of LINE distribution. Note that L1s with the lowest H3K9me3 bias were shorter than L1s with the highest bias. d. Box plots of H3K9me3 eSPAN bias at HO L1s that were separated into three groups based on their size in mES and HeLa cells. HO L1s were ranked from short to long according to their lengths. The shortest 1/3 was grouped as short (HeLa, n = 3,747; mES, n = 4,225), the middle 1/3 as mid (HeLa, n = 3,767; mES, n = 4,230) and the longest 1/3 as long (HeLa, n = 3,754; mES, n = 4,224). e. Heatmaps of H3K9me3, MPP8 and TASOR ChIP-seq density and H3K9me3 eSPAN bias at HO L1s sorted by L1 length in mES cells, with the size range for long, mid and short L1 groups indicated. The relative position of a full-length L1 was shown in blue. Box plots (d) show the median, 25% and 75% quartiles and minimal and maximal values with p values by two-sided Mann–Whitney–Wilcoxon tests, and Bonferroni correction for multiple comparisons. Each panel is a representative of at least two independent experiments. See Materials and Methods for more details.
