Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models. (April 2018)

• Record Type: Journal Article
• Authors: Unarta, Ilona Christy; Zhu, Lizhe; Tse, Carmen Ka Man; Cheung, Peter Pak-Hang; Yu, Jin; Huang, Xuhui
• Is Part Of: Current opinion in structural biology. Volume 49(2018)
• Page Start: 54
• Page End: 62
• Publication Date: 2018-04
• Subjects: Molecular biology -- Periodicals; 570
• DOI: 10.1016/j.sbi.2018.01.002
• Languages: English
• ISSNs: 0959-440X

Abstract

Graphical abstract: Highlights: We introduce the general protocol to build Markov State Model (MSM). Latest findings of MSM and other computational studies of Pol II TEC are reviewed. We introduce and explain how to build kinetic network models of the whole TEC. Sequence dependent KNM may be used to predict transcription error in the genome. Abstract : Transcription elongation cycle (TEC) of RNA polymerase II (Pol II) is a process of adding a nucleoside triphosphate to the growing messenger RNA chain. Due to the long timescale events in Pol II TEC, an advanced computational technique, such as Markov State Model (MSM), is needed to provide atomistic mechanism and reaction rates. The combination of MSM and experimental results can be used to build a kinetic network model (KNM) of the whole TEC. This review provides a brief protocol to build MSM and KNM of the whole TEC, along with the latest findings of MSM and other computational studies of Pol II TEC. Lastly, we offer a perspective on potentially using a sequence dependent KNM to predict genome-wide transcription error.