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Chang HW , Hsieh FK , Patel SS , Studitsky VM
Time-resolved analysis of transcription through chromatin
Methods. 2019 Apr 15;159-160 :90-95
PMID: 30707952 PMCID: PMC6589111 URL: https://www.ncbi.nlm.nih.gov/pubmed/30707952
AbstractDuring transcription along nucleosomal DNA, RNA polymerase II (Pol II) pauses at multiple positions and induces formation of multiple intermediates that aid in maintaining proper chromatin structure. To describe the kinetics of this multiple-step reaction, we utilized a computational model-based approach and KinTek Explorer software to analyze the time courses. Here we describe the stepwise protocol for analysis of the kinetics of transcription through a nucleosome that provides the rate constants for each step of this complex process. We also present an example where this time-resolved approach was applied to study the mechanism of histone chaperone FACT action during Pol II transcription through a single nucleosome by comparing the rate constants derived in the presence or in the absence of FACT.
Notes1095-9130 Chang, Han-Wen Hsieh, Fu-Kai Patel, Smita S Studitsky, Vasily M R35 GM118086/GM/NIGMS NIH HHS/United States Journal Article United States Methods. 2019 Jan 29. pii: S1046-2023(18)30294-9. doi: 10.1016/j.ymeth.2019.01.016.