Decoding the informational properties of the RNA polymerase II Carboxy Terminal Domain

• Main Author: Karagiannis Jim
• Format: Article
• Language: English
• Published: BMC 2012-05-01
• Series: BMC Research Notes
• Subjects: Transcription; RNA polymerase II; Carboxy terminal domain; Information theory; Phosphorylation; Kinase; Phosphatase; Fission yeast; Budding yeast
• Online Access: http://www.biomedcentral.com/1756-0500/5/241

<p>Abstract</p> <p>Background</p> <p>The largest sub-unit of RNA polymerase II, Rpb1p, has long been known to be subject to post-translational modifications that influence various aspects of pre-mRNA processing. However, the portion of the Rpb1p molecule subject to these modifications – the carboxy-terminal domain or CTD – remains the subject of much fascination. Intriguingly, the CTD possesses a unique repetitive structure consisting of multiple repeats of the heptapeptide sequence, Y₁S₂P₃T₄S₅P₆S₇. While these repeats are critical for viability, they are not required for basal transcriptional activity in vitro. This suggests that – even though the CTD is not catalytically essential – it must perform other critical functions in eukaryotes.</p> <p>Presentation of the Hypothesis</p> <p>By formally applying the long-standing mathematical principles of information theory, I explore the hypothesis that complex post-translational modifications of the CTD represent a means for the dynamic “programming” of Rpb1p and thus for the discrete modulation of the expression of specific gene subsets in eukaryotes.</p> <p>Testing the Hypothesis</p> <p>Empirical means for testing the informational capacity and regulatory potential of the CTD – based on simple genetic analysis in yeast model systems – are put forward and discussed.</p> <p>Implications of the Hypothesis</p> <p>These ideas imply that the controlled manipulation of CTD effectors could be used to “program” the CTD and thus to manipulate biological processes in eukaryotes in a definable manner.</p>