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Nat Commun. 2017 May 12;8:15233. doi: 10.1038/ncomms15233.

Phosphorylation induces sequence-specific conformational switches in the RNA polymerase II C-terminal domain.

Author information

1
Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
2
Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
3
Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
4
Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA.
5
Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.

Abstract

The carboxy-terminal domain (CTD) of the RNA polymerase II (Pol II) large subunit cycles through phosphorylation states that correlate with progression through the transcription cycle and regulate nascent mRNA processing. Structural analyses of yeast and mammalian CTD are hampered by their repetitive sequences. Here we identify a region of the Drosophila melanogaster CTD that is essential for Pol II function in vivo and capitalize on natural sequence variations within it to facilitate structural analysis. Mass spectrometry and NMR spectroscopy reveal that hyper-Ser5 phosphorylation transforms the local structure of this region via proline isomerization. The sequence context of this switch tunes the activity of the phosphatase Ssu72, leading to the preferential de-phosphorylation of specific heptads. Together, context-dependent conformational switches and biased dephosphorylation suggest a mechanism for the selective recruitment of cis-proline-specific regulatory factors and region-specific modulation of the CTD code that may augment gene regulation in developmentally complex organisms.

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