RNA structure characterization from chemical mapping experiments

Sharon Aviran, Julius B. Lucks, Lior Pachter

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

29 Scopus citations

Abstract

Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem to determine structure from sequence. Among experimental approaches, a promising candidate is the "chemical modification strategy", which involves application of chemicals to RNA that are sensitive to structure and that result in modifications that can be assayed via sequencing technologies. One approach that can reveal paired nucleotides via chemical modification followed by sequencing is SHAPE, and it has been used in conjunction with capillary electrophoresis (SHAPE-CE) and high-throughput sequencing (SHAPE-Seq). The solution of mathematical inverse problems is needed to relate the sequence data to the modified sites, and a number of approaches have been previously suggested for SHAPE-CE, and separately for SHAPE-Seq analysis. Here we introduce a new model for inference of chemical modification experiments, whose formulation results in closed-form maximum likelihood estimates that can be easily applied to data. The model can be specialized to both SHAPE-CE and SHAPE-Seq, and therefore allows for a direct comparison of the two technologies. We then show that the extra information obtained with SHAPE-Seq but not with SHAPE-CE is valuable with respect to ML estimation.

Original languageEnglish (US)
Title of host publication2011 49th Annual Allerton Conference on Communication, Control, and Computing, Allerton 2011
Pages1743-1750
Number of pages8
DOIs
StatePublished - Dec 1 2011
Event2011 49th Annual Allerton Conference on Communication, Control, and Computing, Allerton 2011 - Monticello, IL, United States
Duration: Sep 28 2011Sep 30 2011

Other

Other2011 49th Annual Allerton Conference on Communication, Control, and Computing, Allerton 2011
CountryUnited States
CityMonticello, IL
Period9/28/119/30/11

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Control and Systems Engineering

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  • Cite this

    Aviran, S., Lucks, J. B., & Pachter, L. (2011). RNA structure characterization from chemical mapping experiments. In 2011 49th Annual Allerton Conference on Communication, Control, and Computing, Allerton 2011 (pp. 1743-1750). [6120379] https://doi.org/10.1109/Allerton.2011.6120379