Structural heterogeneity in the intrinsically disordered RNA polymerase II C-terminal domain

Bede Portz, Feiyue Lu, Eric B. Gibbs, Joshua E. Mayfield, M. Rachel Mehaffey, Yan Jessie Zhang, Jennifer S. Brodbelt, Scott A. Showalter and David S. Gilmour ()
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Bede Portz: Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park
Feiyue Lu: Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park
Eric B. Gibbs: The Pennsylvania State University
Joshua E. Mayfield: University of Texas
M. Rachel Mehaffey: University of Texas
Yan Jessie Zhang: University of Texas
Jennifer S. Brodbelt: University of Texas
Scott A. Showalter: Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park
David S. Gilmour: Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park

Nature Communications, 2017, vol. 8, issue 1, 1-12

Abstract: Abstract RNA polymerase II contains a repetitive, intrinsically disordered, C-terminal domain (CTD) composed of heptads of the consensus sequence YSPTSPS. The CTD is heavily phosphorylated and serves as a scaffold, interacting with factors involved in transcription initiation, elongation and termination, RNA processing and chromatin modification. Despite being a nexus of eukaryotic gene regulation, the structure of the CTD and the structural implications of phosphorylation are poorly understood. Here we present a biophysical and biochemical interrogation of the structure of the full length CTD of Drosophila melanogaster, which we conclude is a compact random coil. Surprisingly, we find that the repetitive CTD is structurally heterogeneous. Phosphorylation causes increases in radius, protein accessibility and stiffness, without disrupting local structural heterogeneity. Additionally, we show the human CTD is also structurally heterogeneous and able to substitute for the D. melanogaster CTD in supporting fly development to adulthood. This finding implicates conserved structural organization, not a precise array of heptad motifs, as important to CTD function.

Date: 2017
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DOI: 10.1038/ncomms15231

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