Talk abstracts
Talk on Saturday 09:00-09:15am submitted by Shardul Kulkarni
Human CCR4-NOT is a global regulator of gene expression and is a novel silencer of retrotransposon activation
Shardul Kulkarni (Center for Eukaryotic Gene Regulation and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA), Alexis Morrissey, Courtney Smith, Oluwasegun T. Akinniyi, Shaun Mahony (Center for Eukaryotic Gene Regulation and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA), Aswathy Sebastian, Istvan Albert (Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA), Cheryl A. Keller, Belinda Giardine, Istvan Albert (Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA), Alexei Arnaoutov (Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA), Joseph C. Reese (Center for Eukaryotic Gene Regulation and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA)
Abstract:
CCR4-NOT regulates multiple steps in gene regulation, including transcription, mRNA decay, protein ubiquitylation, and translation. It has been well studied in budding yeast; however, relatively less is known about its regulation and functions in mammals. To characterize the functions of the human CCR4-NOT complex, we developed a rapid auxin-induced degron system to deplete CNOT1 (the scaffold of the complex) and CNOT4 (E3 ubiquitin ligase) in cell culture. Transcriptome-wide measurements of gene-expression revealed that depleting CNOT1 changed several thousand transcripts, wherein most mRNAs were increased and resulted in a global decrease in mRNA decay rates. In contrast to what was observed in CNOT1-depleted cells, CNOT4 depletion only modestly changed RNA steady-state levels and, surprisingly, led to a global acceleration in mRNA decay. To further investigate the role of CCR4-NOT in transcription, we used transient transcriptome sequencing (TT-seq) to measure ongoing RNA synthesis. Depletion of either subunit resulted in increased RNA synthesis of several thousand genes. In contrast to most of the genome, a rapid reduction in the synthesis of KRAB-Zinc-Finger-proteins (KZNFs) genes, especially those clustered on chromosome 19, was observed. KZNFs are transcriptional repressors of retro-transposable elements (rTEs), and consistent with the decreased KZNFs expression, we observed a significant and rapid activation of rTEs, mainly Long interspersed Nuclear Elements (LINEs). Our data reveal that CCR4-NOT regulates gene expression and silences retrotransposons across the genome by maintaining KZNF expression. These data establish CCR4-NOT as a global regulator of gene expression, and we have identified a novel mammalian-specific function of the complex, the suppression of rTEs.
Keywords: CCR4-NOT, Retrotranspsons, KRAB Zinc finger proteins (KZFPs)