Role of general regulatory factors in the control of gene expression and transcription fidelity

Abstract : The last decades have been marked by the discovery of pervasive transcription. Indeed, many studies have shown that transcription by RNA polymerase II is not restricted to annotated regions but is widespread in eukaryotic genomes, leading to the production of a plethora of non-coding RNAs. Precise delimitation of transcriptional units appears to be essential to ensure robust fidelity of gene expression and to maintain the integrity of DNA-associated events by preventing the occurrence of conflicts with transcription. In this respect, accurate transcription initiation and termination represent crucial mechanisms to partition the genome and define the correct processing of RNA molecules. Here, we show that yeast general regulatory factors (GRFs), a class of highly expressed transcription regulators, control pervasive transcription at the level of initiation and termination and are also involved in the fidelity of initiation of mRNA-coding genes. We demonstrate that GRFs bound at promoter regions can elicit transcription termination by physically impeding the progression of polymerases mainly deriving from readthrough transcription at upstream canonical termination sites. We provide evidence that this termination pathway named roadblock is widespread throughout the yeast genome and protects promoter regions from transcriptional interference. Furthermore, we establish that the presence of general regulatory factors also limits pervasive transcription at the level of initiation, notably by occluding spurious transcription start sites present in the vicinity of their binding sites. We also unveil the importance of these factors in promoting correct transcription start site selection at mRNA-coding genes thus favouring the synthesis of transcripts with an appropriate coding potential. Finally, we determine that the role of GRFs in controlling proper initiation is intimately linked to their ability to correctly position nucleosomes in promoters, a role that occurs independently from but in cooperation with chromatin remodelers.
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Drice Challal. Role of general regulatory factors in the control of gene expression and transcription fidelity. Biochemistry, Molecular Biology. Université Paris-Saclay, 2019. English. ⟨NNT : 2019SACLS176⟩. ⟨tel-02272934⟩

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