@article{b3911924371e417188bfecd4dc46f13a,
title = "Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates",
abstract = "Experimentally guided multi-scale modeling of the cotranscriptional folding pathway of the E. coli signal recognition particle (SRP) RNA reveals that it undergoes an internal toehold-mediated strand-displacement process that requires local structural fluctuations. An intermediate of this pathway is a substrate for RNase P, suggesting concurrent transcription and processing.",
keywords = "cotranscriptional RNA folding, molecular dynamics, RNA, RNA fluctuations, RNA folding dynamics, RNA structure, SHAPE-seq, signal recognition particle, toehold strand displacement, transcription",
author = "Yu, {Angela M.} and Gasper, {Paul M.} and Luyi Cheng and Lai, {Lien B.} and Simi Kaur and Venkat Gopalan and Chen, {Alan A.} and Lucks, {Julius B.}",
note = "Funding Information: We thank Eric Siggia (Rockefeller University) and Dave Matthews (University of Rochester) for foundational conversations, Daniel Aalberts (Williams College) for assistance with plotting RNAbow plots, Gregory Phillips and Nicholas Backes (Iowa State University) for discussions and protocols, Katherine Berman for cloning SRP RNA sequence mutants, Eric Strobel and Kyle Watters for help with cotranscriptional SHAPE-seq, and Molly Evans for SHAPE-seq protocol discussions and improvements. We also thank Shannon Yan, Shingo Fukuda, and Carlos Bustamante (University of California, Berkeley) for helpful discussions. Support for this work was provided by the Tri-Institutional Training Program in Computational Biology and Medicine (via National Institutes of Health [NIH] training grant T32GM083937 to A.M.Y., NIH grant 1DP2GM110838 to J.B.L., NIH grant GM120582 to V.G. and J.B.L., National Science Foundation [NSF] grant MCB1651877 to A.A.C., and NSF grant 1914567 to J.B.L.), and Searle Funds at The Chicago Community Trust (J.B.L.). This work used the Extreme Science and Engineering Discovery Environment (XSEDE) (allocation TG-MCB140273 to A.A.C.), which is supported by NSF grant ACI-1548562 , as well as the Quest high performance computing facility at Northwestern University . The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. Publisher Copyright: {\textcopyright} 2020 Elsevier Inc.",
year = "2021",
month = feb,
day = "18",
doi = "10.1016/j.molcel.2020.12.017",
language = "English (US)",
volume = "81",
pages = "870--883.e10",
journal = "Molecular Cell",
issn = "1097-2765",
publisher = "Cell Press",
number = "4",
}