Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the drosha cleavage site

Kaycee A. Quarles, Debashish Sahu, Mallory A. Havens, Ellen R. Forsyth, Christopher Wostenberg, Michelle L. Hastings, Scott A. Showalter

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Most noncoding RNAs function properly only when folded into complex three-dimensional (3D) structures, but the experimental determination of these structures remains challenging. Understanding of primary microRNA (miRNA) maturation is currently limited by a lack of determined structures for nonprocessed forms of the RNA. SHAPE chemistry efficiently determines RNA secondary structural information with single-nucleotide resolution, providing constraints suitable for input into MC-Pipeline for refinement of 3D structure models. Here we combine these approaches to analyze three structurally diverse primary microRNAs, revealing deviations from canonical double-stranded RNA structure in the stem adjacent to the Drosha cut site for all three. The necessity of these deformable sites for efficient processing is demonstrated through Drosha processing assays. The structure models generated herein support the hypothesis that deformable sequences spaced roughly once per turn of A-form helix, created by noncanonical structure elements, combine with the necessary single-stranded RNA-double-stranded RNA junction to define the correct Drosha cleavage site.

Original languageEnglish (US)
Pages (from-to)795-807
Number of pages13
JournalBiochemistry
Volume52
Issue number5
DOIs
StatePublished - Feb 5 2013

Fingerprint

Double-Stranded RNA
Model structures
MicroRNAs
RNA
Untranslated RNA
Processing
Assays
Nucleotides
Pipelines

All Science Journal Classification (ASJC) codes

  • Biochemistry

Cite this

Quarles, Kaycee A. ; Sahu, Debashish ; Havens, Mallory A. ; Forsyth, Ellen R. ; Wostenberg, Christopher ; Hastings, Michelle L. ; Showalter, Scott A. / Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the drosha cleavage site. In: Biochemistry. 2013 ; Vol. 52, No. 5. pp. 795-807.
@article{6e9b7ebefea940718e33d49f21e95533,
title = "Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the drosha cleavage site",
abstract = "Most noncoding RNAs function properly only when folded into complex three-dimensional (3D) structures, but the experimental determination of these structures remains challenging. Understanding of primary microRNA (miRNA) maturation is currently limited by a lack of determined structures for nonprocessed forms of the RNA. SHAPE chemistry efficiently determines RNA secondary structural information with single-nucleotide resolution, providing constraints suitable for input into MC-Pipeline for refinement of 3D structure models. Here we combine these approaches to analyze three structurally diverse primary microRNAs, revealing deviations from canonical double-stranded RNA structure in the stem adjacent to the Drosha cut site for all three. The necessity of these deformable sites for efficient processing is demonstrated through Drosha processing assays. The structure models generated herein support the hypothesis that deformable sequences spaced roughly once per turn of A-form helix, created by noncanonical structure elements, combine with the necessary single-stranded RNA-double-stranded RNA junction to define the correct Drosha cleavage site.",
author = "Quarles, {Kaycee A.} and Debashish Sahu and Havens, {Mallory A.} and Forsyth, {Ellen R.} and Christopher Wostenberg and Hastings, {Michelle L.} and Showalter, {Scott A.}",
year = "2013",
month = "2",
day = "5",
doi = "10.1021/bi301452a",
language = "English (US)",
volume = "52",
pages = "795--807",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "5",

}

Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the drosha cleavage site. / Quarles, Kaycee A.; Sahu, Debashish; Havens, Mallory A.; Forsyth, Ellen R.; Wostenberg, Christopher; Hastings, Michelle L.; Showalter, Scott A.

In: Biochemistry, Vol. 52, No. 5, 05.02.2013, p. 795-807.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the drosha cleavage site

AU - Quarles, Kaycee A.

AU - Sahu, Debashish

AU - Havens, Mallory A.

AU - Forsyth, Ellen R.

AU - Wostenberg, Christopher

AU - Hastings, Michelle L.

AU - Showalter, Scott A.

PY - 2013/2/5

Y1 - 2013/2/5

N2 - Most noncoding RNAs function properly only when folded into complex three-dimensional (3D) structures, but the experimental determination of these structures remains challenging. Understanding of primary microRNA (miRNA) maturation is currently limited by a lack of determined structures for nonprocessed forms of the RNA. SHAPE chemistry efficiently determines RNA secondary structural information with single-nucleotide resolution, providing constraints suitable for input into MC-Pipeline for refinement of 3D structure models. Here we combine these approaches to analyze three structurally diverse primary microRNAs, revealing deviations from canonical double-stranded RNA structure in the stem adjacent to the Drosha cut site for all three. The necessity of these deformable sites for efficient processing is demonstrated through Drosha processing assays. The structure models generated herein support the hypothesis that deformable sequences spaced roughly once per turn of A-form helix, created by noncanonical structure elements, combine with the necessary single-stranded RNA-double-stranded RNA junction to define the correct Drosha cleavage site.

AB - Most noncoding RNAs function properly only when folded into complex three-dimensional (3D) structures, but the experimental determination of these structures remains challenging. Understanding of primary microRNA (miRNA) maturation is currently limited by a lack of determined structures for nonprocessed forms of the RNA. SHAPE chemistry efficiently determines RNA secondary structural information with single-nucleotide resolution, providing constraints suitable for input into MC-Pipeline for refinement of 3D structure models. Here we combine these approaches to analyze three structurally diverse primary microRNAs, revealing deviations from canonical double-stranded RNA structure in the stem adjacent to the Drosha cut site for all three. The necessity of these deformable sites for efficient processing is demonstrated through Drosha processing assays. The structure models generated herein support the hypothesis that deformable sequences spaced roughly once per turn of A-form helix, created by noncanonical structure elements, combine with the necessary single-stranded RNA-double-stranded RNA junction to define the correct Drosha cleavage site.

UR - http://www.scopus.com/inward/record.url?scp=84873365736&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84873365736&partnerID=8YFLogxK

U2 - 10.1021/bi301452a

DO - 10.1021/bi301452a

M3 - Article

C2 - 23305493

AN - SCOPUS:84873365736

VL - 52

SP - 795

EP - 807

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 5

ER -