In vivo SHAPE-seq: A method to determine the in-cell structure of RNA

Timothy R. Abbott, Kyle E. Watters, Julius B. Lucks

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Motivation · RNA is versatile, easy to design, and characterize [1] · RNAe regulate transcription, RNA degradation, and translation · SHAPE-Seq (elective 2'-ydroxyl ucylation analyzed by primer ntension puencing) is a powerful technique for characterizing RNA by determining structure [2], but can only measure in vitro transcribed RNA · We wish to know cellular RNA strscture to better understand their structure and function inside the cellular environment In-Cell SHAPE-Seq 1) Fluorescence assay allows discovering RNA regulator structure- function relationships 2) Modular platform allows probing almost any RNA with uniform set of primers Probing Results · Structure of cis-repreeeed (Cr) and trans-activating (ta) riboregulators differ slightly from proposed structure [3] · Ribosome binding site )RBS) nucleotide (nt) reactivity correlates well with fluorescence increase Conclusions · In-cell SHAPE-Seq is a powerful method to determine RNA structure with nucleotide resolution · Structural variations and increase in RBS nt reactivity were detected in cr and ta riboregulators Future Studies · Probe CRISPR (plustered regularly ntersperaed gpacer palindromic Lepeats) small guide RNA5 )5gRNA) to find structure- function relationships · Discover cellular structure, mechanism of small transcription activating RNA5 (STARs) [4] · Formulate design princtples for directed RNA engineering.

Original languageEnglish (US)
Title of host publicationFood, Pharmaceutical and Bioengineering Division 2014 - Core Programming Area at the 2014 AIChE Annual Meeting
PublisherAIChE
Number of pages1
Volume2
ISBN (Electronic)9781510812598
StatePublished - Jan 1 2014
EventFood, Pharmaceutical and Bioengineering Division 2014 - Core Programming Area at the 2014 AIChE Annual Meeting - Atlanta, United States
Duration: Nov 16 2014Nov 21 2014

Other

OtherFood, Pharmaceutical and Bioengineering Division 2014 - Core Programming Area at the 2014 AIChE Annual Meeting
CountryUnited States
CityAtlanta
Period11/16/1411/21/14

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Pharmaceutical Science
  • Bioengineering

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