Extended Data Fig. 7: Endo-siRNA targeting rules in mouse oocytes.
From: Global profiling of RNA-binding protein target sites by LACE-seq
a, Ago2-IP enriched small RNAs. b, Boxplots showing that endo-siRNAs (n = top 200) are preferably loaded into Ago2 than miRNAs (n = top 200) due to their relative abundance in oocytes. P-values were calculated by two-tailed Wilcoxon test. The centre line represents the median, the box borders represent the first (Q1) and third (Q3) quartiles, and the whiskers are the most extreme data points within 1.5× the interquartile range (from Q1 to Q3). c, Scatter plot showing the preference of endo-siRNA base-paired with class I or class II Ago2 clusters. Each point represents an endo-siRNA, and different colours indicate the source for endo-siRNA. The horizontal axis represents the difference in the average MFE of all the potential hybrids formed between each class of clusters and a given endo-siRNA. The vertical axis represents the difference in the proportion of clusters that could form hybrids with each endo-siRNA. As a positive control, miRNAs mostly pair with class II clusters. d, Endo-siRNAs paired with class II RNAs have a significantly lower MEF value than random controls. Two-tailed unpaired Student’s t-test was used to calculate the P-value. Ago2-IP enriched smRNA-seq data in a-d represent results from a single experiment. e, The single-nucleotide mutation at the seed region compromises the repression mediated by endo-siRNA-336 in oocytes. Data are mean ± s.e.m.; n = 3 biological replicates, two-tailed unpaired Student’s t-test.
