Human CCR4-NOT suppresses pervasive transcription and retrotransposable elements

Area of Science:

• Molecular Biology
• Gene Regulation
• Epigenetics

Background:

• The CCR4-NOT complex is crucial for gene regulation, particularly mRNA degradation in the cytoplasm.
• Its nuclear functions in human cells remain largely uncharacterized.
• Key subunits include scaffold protein CNOT1 and E3 ligase CNOT4.

Purpose of the Study:

• To investigate the nuclear transcriptional functions of the human CCR4-NOT complex.
• To understand the impact of CNOT1 and CNOT4 depletion on gene expression and retrotransposable element (rTE) activity.

Main Methods:

• Utilized auxin-induced degradation to rapidly deplete CNOT1 and CNOT4 in human cells.
• Employed transient transcriptome profiling (TT-Seq) to measure ongoing RNA synthesis.
• Analyzed changes in gene expression and rTE activation.

Main Results:

• Depletion of CCR4-NOT subunits led to widespread activation of RNA synthesis across genic and intergenic regions.
• Repression of genes, including KRAB-Zinc-Finger-protein (KZNF) genes, decreased.
• Activation of retrotransposable elements (rTEs), particularly Long Interspersed Nuclear Elements (LINEs), was observed, often near KZNF binding sites.
• CCR4-NOT was shown to regulate rTE RNA stability, targeting them for decay.

Conclusions:

• The human CCR4-NOT complex plays a significant nuclear role in suppressing transcription, including that of rTEs.
• KZNF proteins contribute to this suppression, and their regulation by CCR4-NOT impacts rTE activity.
• CCR4-NOT tightly controls transposon expression through both transcriptional repression and RNA degradation pathways.