Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo.

Autor:	Ritchey LE; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.; Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA., Su Z; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA., Tang Y; Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, PA 16802, USA., Tack DC; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA., Assmann SM; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA., Bevilacqua PC; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.; Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.; Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2017 Aug 21; Vol. 45 (14), pp. e135.
DOI:	10.1093/nar/gkx533
Abstrakt:	RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage. We also present a variation of Structure-seq2 in which a biotinylated nucleotide is incorporated during reverse transcription, which greatly facilitates the protocol by eliminating two PAGE purification steps. We benchmark Structure-seq2 on both mRNA and rRNA structure in rice (Oryza sativa). We demonstrate that Structure-seq2 can lead to new biological insights. Our Structure-seq2 datasets uncover hidden breaks in chloroplast rRNA and identify a previously unreported N1-methyladenosine (m1A) in a nuclear-encoded Oryza sativa rRNA. Overall, Structure-seq2 is a rapid, sensitive, and unbiased method to probe RNA in vivo and genome-wide that facilitates new insights into RNA biology. (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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