Fig. 3: LSM1 interacts with major satellite RNA and regulates its decay.

a Scheme for the LSM1 RIP-seq and RIP-qPCR experiments. b Volcano plot showing LSM1-binding RNAs in zygotes. The red dots represent the top 10 targets of LSM1 in zygotes. p-values (two-sided) attained by the Wald test are corrected for multiple testing using the Benjamini and Hochberg method by default (n = 2 biologically independent samples). c Bar graph showing the LSM1 binding ratios in different RNA classes. d Venn diagrams showing the overlap of LSM1-binding protein-coding genes and up-/downregulated genes in Lsm1_KD zygotes. e Violin plot showing the distribution of LSM1-binding reads in different repeat families. f Venn diagrams showing the overlap of LSM1-binding repeats and up-/downregulated repeats in Lsm1_KD zygotes. g Heatmap showing differentially expressed repeats between Ctrl and Lsm1_KD zygotes. h Genome browser tracks showing LSM1 RIP-seq peaks and Lsm1_KD zygote RNA-seq peaks at the MajSat locus. i RIP-qPCR validation of target binding by LSM1. The statistical data are expressed as mean ± SEM, *p < 0.05 (MajSat: p = 0.0182, MinSat: p = 0.0228) by two-sided Student’s t test for each comparison. Each reaction for RIP-qPCR analysis contains 3 biological replicates, with each replicate from 300 zygotes. j Measurement of MajSat RNA decay in Ctrl and Lsm1_KD zygotes. Samples were collected following transcriptional inhibition using actinomycin D (ActD) for the indicated time. MajSat RNA amounts were measured by qPCR according to 18S RNA. The statistical data are expressed as mean ± SEM, *p < 0.05 (p = 0.0189 for 4 hours and p = 0.0112 for 8 h) and ns (p = 0.8217 for 2 h) means not significant by two-sided Student’s t test for each comparison. Each reaction for qPCR contains 3 biological replicates, with each replicate from ~50 zygotes.