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The plant corepressor TPL is recruited to diverse chromatin contexts, yet its mechanism of repression remains unclear. Previously, we leveraged the fact that TPL retains its function in a synthetic transcriptional circuit in the yeast model Saccharomyces cerevisiae to localize repressive function to two distinct domains. Here, we employed two unbiased whole-genome approaches to map the physical and genetic interactions of TPL at a repressed locus. We identified SPT4, SPT5, and SPT6 as necessary for repression with SPT4 acting as a bridge connecting TPL to SPT5 and SPT6. We discovered the association of multiple additional constituents of the transcriptional preinitiation complex at TPL-repressed promoters, specifically those involved early in transcription initiation. These findings were validated in yeast and plants, including a novel method to analyze the conditional loss of function of essential genes in plants. Our findings support a model where TPL nucleates preassembly of the transcription activation machinery to facilitate the rapid onset of transcription once repression is relieved.
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http://dx.doi.org/10.1083/jcb.202404103 | DOI Listing |
Nucleic Acids Res
September 2025
Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, United States.
DDX6 is known to repress messenger RNA (mRNA) translation and promote mRNA decay in microRNA-mediated silencing. In embryonic stem cells (ESCs), DDX6 primarily functions at the translation level, independent of mRNA destabilization; however, the precise molecular mechanism of how DDX6 represses translation remains unclear. Here, we identify DDX3X as a key downstream target of DDX6-mediated translational repression in ESCs.
View Article and Find Full Text PDFCell Rep
September 2025
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA. Electronic address:
RNA polymerase II (RNAPII) is regulated by sequence-specific transcription factors (TFs) and the pre-initiation complex (PIC): TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and Mediator. TFs, Mediator, and RNAPII contain intrinsically disordered regions (IDRs) and form phase-separated condensates, but how IDRs control RNAPII function remains poorly understood. Using purified PIC factors, we developed a real-time in vitro fluorescence transcription (RIFT) assay for second-by-second visualization of transcription at hundreds of promoters simultaneously.
View Article and Find Full Text PDFNat Struct Mol Biol
September 2025
Department of Biochemistry 1, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany.
Transfer RNAs (tRNAs) are widely recognized for their role in translation. Here, we describe a previously unidentified function of tRNA as an assembly chaperone. During poxviral infection, tRNA lacking the anticodon mcmsU34 modification is specifically sequestered from the cellular tRNA pool to promote formation of a multisubunit poxviral RNA polymerase complex (vRNAP).
View Article and Find Full Text PDFJ Biol Chem
September 2025
Department of Basic Medicine, College of Medicine, Jiaxing University, 118 Jiahang Road, Jiaxing 314001, Zhejiang, P. R. China; Provincial Key Laboratory of Multimodal Perceiving and Intelligent Systems,Jiaxing University,Jiaxing,314001, China; Engineering Research Center of Intelligent Human Health
The nucleolus is an important nonmembranous organelle within the nucleus and is responsible for ribosome biogenesis. This process is frequently upregulated in tumors to support elevated protein synthesis and sustain tumor growth. The transcription of rDNA into pre-45S rRNA, a rate-limiting step in ribosomal biogenesis, has been reported to be enhanced to drive the progression of non-small cell lung cancer (NSCLC).
View Article and Find Full Text PDFbioRxiv
July 2025
Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, 10031, USA.
The DExH-box helicase DHX29 plays a critical role in mammalian translation initiation. It is required for the scanning of mRNAs with complex 5'UTRs. Despite its importance, the detailed mechanism of DHX29's action has remained debated.
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