Standardization of RNA chemical mapping experiments.
Chemical mapping experiments offer powerful information about RNA structure but currently involve ad hoc assumptions in data processing. We show that simple dilutions, referencing standards (GAGUA hairpins), and HiTRACE/MAPseeker analysis allow rigorous overmodification correction, background subtraction, and normalization for electrophoretic data and a ligation bias correction needed for accurate deep sequencing data. Comparisons across six noncoding RNAs stringently test the proposed standardization of dimethyl sulfate (DMS), 2'-OH acylation (SHAPE), and carbodiimide measurements. Identification of new signatures for extrahelical bulges and DMS "hot spot" pockets (including tRNA A58, methylated in vivo) illustrates the utility and necessity of standardization for quantitative RNA mapping.
Department of Biochemistry, Stanford University , Stanford, California 94305, United States.
Wipapat
W
Kladwang
Thomas H
TH
Mann
Alex
A
Becka
Siqi
S
Tian
Hanjoo
H
Kim
Sungroh
S
Yoon
Rhiju
R
Das
D000215:Acylation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013463:Sulfuric Acid Esters / Q000737:chemistry*
D013463:Sulfuric Acid Esters; D012313:RNA; C007482:dimethyl sulfate