Forced expression of MSR repeat transcripts breaks heterochromatin organization

Mouse heterochromatin is characterized by transcriptionally competent major satellite repeat (MSR) sequences and it has been proposed that MSR repeat RNA contributes to the integrity of heterochromatin. We established an inducible dCas9-effector system in mouse embryonic fibroblasts, where we can target dCas9-VPR (transcriptional activator) and dCas9-KM (transcriptional repressor) to MSR repeat sequences. We show that induction of dCas9-VPR forces significant MSR RNA output, while induction of dCas9-KM silences MSR transcription. Both approaches perturb heterochromatin organization, where the dCas9-VPR leads to an immediate dispersion of heterochromatin and dCas9-KM induction results in a delayed aggregation of heterochromatin. MEF cells with the forced expression of MSR RNA are not viable and the defects in heterochromatin organization cannot be reverted. This study highlights the importance of restricting MSR RNA output to maintain heterochromatin integrity and also reveals that the structural organization of heterochromatin is governed by the transcriptional state of the underlying MSR repeats. Overall design: To investigate the effect of modulating MSR repeat transcription on repeat dysregulation genomewide. MEF cell lines were created where chromatin effectors can be inducibly expressed. These chromatin effectors are targeted to MSR repeats utilizing the CRISPR/dCas9 system: dCas9-control, dCas9-KM (transcriptional repressor), dCas9-VPR (transcriptional activator).