CCR4-NOT is required for suppressing pervasive transcription and retrotransposable elements

CCR4-NOT regulates multiple steps in gene regulation and has been well studied in yeast. Although the human complex is known to play an essential role in cytoplasmic mRNA degradation, its nuclear functions are poorly characterized. Here, we used auxin-induced degradation to deplete the scaffold subunit CNOT1 and the E3 ligase CNOT4 to characterize the complex's regulation of transcription. Transient transcriptome profiling (TT-Seq) revealed that depleting either subunit led to widespread activation of RNA synthesis in genic and intergenic regions. Interestingly, fewer genes were down-regulated, including KRAB-zinc-finger protein (KZNF) genes. KZNFs repress genes and retrotransposable elements (rTEs), and consistent with decreased KZNF expression, rTEs, mainly long interspersed nuclear elements, were activated. Full-length active long interspersed nuclear elements and rTEs located outside of genes were activated too, suggesting that the increased transcription is not the direct result of transcription of the genes in which the rTEs are embedded. Most of the activated transcription events occurred near KZNF binding sites, suggesting that KZNF regulation plays a role in suppressing both genic and rTE transcription. Finally, we demonstrate that CCR4-NOT regulates the stability of rTE RNAs, indicating that the complex tightly controls transposon expression by repressing transcription and targeting their RNAs for degradation.