Biology subjects

Akinniyi, O. T.

Publications and source records attributed to Akinniyi, O. T..

3 recordsLinked to original sources

bioRxiv2026

Human CCR4-NOT suppresses pervasive transcription and retrotransposable elements

CCR4-NOT regulates multiple steps in gene regulation and has been well studied in budding yeast. Although primarily cytoplasmic, where it plays an essential role in mRNA degradation, the human complex has poorly characterized nuclear functions. Here, we used auxin-induced degradation to rapidly deplete the scaffold subunit CNOT1 and the E3 ligase CNOT4, and characterized the transcriptional functions of the human CCR4-NOT complex. Using transient transcriptome profiling (TT-Seq) to measure ongoing transcription, we found widespread activation of RNA synthesis in depleted cells across genic and intergenic regions. Interestingly, fewer genes were repressed, including KRAB-Zinc-Finger-protein (KZNF) genes, especially those on chromosome 19. KZNFs repress genes and retrotransposable elements (rTEs), and consistent with decreased KZNF expression, rTEs, mainly Long Interspersed Nuclear Elements (LINEs), were activated. Full-length active LINEs and rTEs lying outside of genes were activated, suggesting that the increased transcription is not the direct result of transcription of the genes the rTEs are embedded in. We found that most activated transcription events were in proximity to KZNF binding sites, suggesting that KZNF regulation contributes to the suppression of 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 decay.

molecular biology↗

bioRxiv2024

The DNA damage response and RNA Polymerase II regulator Def1 has posttranscriptional functions in the cytoplasm

Def1 is a yeast protein that promotes transcription elongation and regulates the degradation of RNA polymerase II during transcription stress. Although Def1 is localized in the cytoplasm, its functions in this cellular compartment are not yet understood. Despite its well-established roles in transcription, a comprehensive genome-wide analysis of its impact on gene expression has not been conducted. Here, we performed RNA sequencing (RNA-seq) analysis on cells lacking DEF1 and surprisingly found that only a few hundred genes exhibited altered expression, both upregulated and downregulated. To evaluate mRNA synthesis and decay rates in these DEF1-deficient cells, we used a nascent transcription metabolic labeling technique called RATE-SEQ. As expected, we observed reduced synthesis rates across the genome in these cells. Additionally, a global decrease in mRNA decay rates was observed, suggesting that Def1 plays a role in the post-transcriptional regulation of mRNAs. The changes in synthesis and decay rates showed a strong correlation, indicating that this compensation helps buffer steady-state mRNA levels. To gain further insight into Def1s functions, we conducted proximity labeling experiments to identify its protein binding partners within the cells. Our findings revealed that Def1 primarily interacts with cytoplasmic regulators involved in post-transcriptional processes, including proteins responsible for deadenylation, decapping, and translation regulation. Using an mRNA decay reporter assay, we demonstrated that recruiting Def1 to mRNA reduces its expression and accelerates its turnover. In summary, we have identified a novel cytoplasmic function for Def1, establishing it as a key regulator of gene expression in both transcription and mRNA decay.

molecular biology↗

bioRxiv2024

Human CCR4-NOT is a global regulator of gene expression and is a novel silencer of retrotransposon activation

CCR4-NOT regulates multiple steps in gene regulation and has been well studied in budding yeast, but much less is known about the human complex. Auxin-induced degradation was used to rapidly deplete the scaffold subunit CNOT1, and CNOT4, to characterize the functions of human CCR4-NOT in gene regulation. Depleting CNOT1 increased RNA levels and caused a widespread decrease in RNA decay. In contrast, CNOT4 depletion only modestly changed steady-state RNA levels and, surprisingly, led to a global acceleration in mRNA decay. Further, depleting either subunit resulted in a global increase in RNA synthesis. In contrast to most of the genome, the transcription of KRAB-Zinc-Finger-protein (KZNFs) genes, especially those on chromosome 19, was repressed. KZNFs are transcriptional repressors of retrotransposable elements (rTEs), and consistent with the decreased KZNFs expression, rTEs, mainly Long Interspersed Nuclear Elements (LINEs), were activated. These data establish CCR4-NOT as a global regulator of gene expression and a novel silencer of rTEs.

molecular biology↗