SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

Research output: Contribution to journalJournal articlepeer-review

Standard

SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data. / Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R; Krogh, Anders; Vinther, Jeppe.

In: R N A, Vol. 21, No. 5, 2015, p. 1042-1052.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Poulsen, LD, Kielpinski, LJ, Salama, SR, Krogh, A & Vinther, J 2015, 'SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data', R N A, vol. 21, no. 5, pp. 1042-1052. https://doi.org/10.1261/rna.047068.114

APA

Poulsen, L. D., Kielpinski, L. J., Salama, S. R., Krogh, A., & Vinther, J. (2015). SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data. R N A, 21(5), 1042-1052. https://doi.org/10.1261/rna.047068.114

Vancouver

Poulsen LD, Kielpinski LJ, Salama SR, Krogh A, Vinther J. SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data. R N A. 2015;21(5):1042-1052. https://doi.org/10.1261/rna.047068.114

Author

Poulsen, Line Dahl ; Kielpinski, Lukasz Jan ; Salama, Sofie R ; Krogh, Anders ; Vinther, Jeppe. / SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data. In: R N A. 2015 ; Vol. 21, No. 5. pp. 1042-1052.

Bibtex

@article{f571ccc9e2ce4e18a0c5f608ddc954d2,
title = "SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data",
abstract = "Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA-RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing.",
author = "Poulsen, {Line Dahl} and Kielpinski, {Lukasz Jan} and Salama, {Sofie R} and Anders Krogh and Jeppe Vinther",
note = "{\textcopyright} 2015 Poulsen et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.",
year = "2015",
doi = "10.1261/rna.047068.114",
language = "English",
volume = "21",
pages = "1042--1052",
journal = "RNA",
issn = "1355-8382",
publisher = "Cold Spring Harbor Laboratory Press",
number = "5",

}

RIS

TY - JOUR

T1 - SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

AU - Poulsen, Line Dahl

AU - Kielpinski, Lukasz Jan

AU - Salama, Sofie R

AU - Krogh, Anders

AU - Vinther, Jeppe

N1 - © 2015 Poulsen et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

PY - 2015

Y1 - 2015

N2 - Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA-RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing.

AB - Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA-RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing.

U2 - 10.1261/rna.047068.114

DO - 10.1261/rna.047068.114

M3 - Journal article

C2 - 25805860

VL - 21

SP - 1042

EP - 1052

JO - RNA

JF - RNA

SN - 1355-8382

IS - 5

ER -

ID: 136791443