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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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Human CCR4-NOT suppresses pervasive transcription and retrotransposable elements.

Shardul Kulkarni1,2, Alexis Morrissey1,2, Aswathy Sebastian3

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Biorxiv : the Preprint Server for Biology
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Summary

The human CCR4-NOT complex controls gene expression. Depleting it activates RNA synthesis and retrotransposable elements (rTEs), revealing its nuclear role in suppressing transcription and degrading rTE RNAs.

Keywords:
CCR4-NOTKrab Zinc finger proteins (KZFPs)LINE elementsRetrotransposonstranscription

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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.