MERVL ERVs are derepressed in HP1α and HP1β KO mESCs but HP1α and HP1β show relatively low enrichment at these ERVs. (A) RNA-seq analysis of retroelement expression in HP1α and HP1β KO mESCs. RNA-seq data for HP1α and HP1β KO mESCs and the HM1 parent line was generated, and Z-scores were calculated for all retroelements and plotted. Note that MERVL elements show relatively high levels of derepression in both KO lines. (B) MERVL elements are upregulated in HP1α and HP1β KO mESCs. Expression of MERVL, IAP and MMERVK10C ERVs was analyzed by qRT-PCR in HM1 wt, HP1α and HP1β KO lines. Mean (+/-SD) expression levels (normalized to β-actin) are shown, relative to the wt line for three technical replicates. (C-F) IAPEz elements show significantly higher levels of HP1α and HP1β enrichment than do MERVL elements. Cross-linked ChIP was performed with antibodies specific for HP1α or HP1β in HM1 and the corresponding KO cell line. IgG was used as a negative control. The level of enrichment for each IP was determined by qPCR, and the mean and standard deviation of three technical replicates are shown for each experiment. IgG, immunoglobulin G; IP, immunoprecipitation; SD, standard deviation.