Control of mammalian translation by mRNA structure near caps

Jeremy Babendure, Jennie Bever, Jian Hua Ding, Roger Y. Tsien

Research output: Contribution to journalArticle

135 Citations (Scopus)

Abstract

The scanning model of RNA translation proposes that highly stable secondary structures within mRNAs can inhibit translation, while structures of lower thermal stability also affect translation if close enough to the 5′ methyl G cap. However, only fragmentary information is available about the dependence of translation efficiency in live mammalian cells on the thermodynamic stability, location, and GC content of RNA structures in the 5′-untranslated region. We devised a two-color fluorescence assay for translation efficiency in single live cells and compared a wide range of hairpins with predicted thermal stabilities ranging from -10 to -50 kcal/mol and 5′ G cap-to-hairpin distances of 1-46 bases. Translation efficiency decreased abruptly as hairpin stabilities increased from ΔG = -25 to -35 kcal/mol. Shifting a hairpin as little as nine bases relative to the 5′ cap could modulate translation more than 50-fold. Increasing GC content diminished translation efficiency when predicted thermal stability and cap-to-hairpin distances were held constant. We additionally found naturally occurring 5′-untranslated regions affected translation differently in live cells compared with translation in in vitro lysates. Our study will assist scientists in designing experiments that deliberately modulate mammalian translation with designed 5′ UTRs.

Original languageEnglish (US)
Pages (from-to)851-861
Number of pages11
JournalRNA
Volume12
Issue number5
DOIs
StatePublished - May 1 2006
Externally publishedYes

Fingerprint

5' Untranslated Regions
Protein Biosynthesis
Hot Temperature
Base Composition
RNA
Thermodynamics
Color
Fluorescence
Messenger RNA

Keywords

  • Fluorescence
  • Hairpin
  • RNA
  • Structure
  • Thermal stability
  • Translation

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Control of mammalian translation by mRNA structure near caps. / Babendure, Jeremy; Bever, Jennie; Ding, Jian Hua; Tsien, Roger Y.

In: RNA, Vol. 12, No. 5, 01.05.2006, p. 851-861.

Research output: Contribution to journalArticle

Babendure, J, Bever, J, Ding, JH & Tsien, RY 2006, 'Control of mammalian translation by mRNA structure near caps', RNA, vol. 12, no. 5, pp. 851-861. https://doi.org/10.1261/rna.2309906
Babendure, Jeremy ; Bever, Jennie ; Ding, Jian Hua ; Tsien, Roger Y. / Control of mammalian translation by mRNA structure near caps. In: RNA. 2006 ; Vol. 12, No. 5. pp. 851-861.
@article{9c502d676e5446f689339601ec5f092e,
title = "Control of mammalian translation by mRNA structure near caps",
abstract = "The scanning model of RNA translation proposes that highly stable secondary structures within mRNAs can inhibit translation, while structures of lower thermal stability also affect translation if close enough to the 5′ methyl G cap. However, only fragmentary information is available about the dependence of translation efficiency in live mammalian cells on the thermodynamic stability, location, and GC content of RNA structures in the 5′-untranslated region. We devised a two-color fluorescence assay for translation efficiency in single live cells and compared a wide range of hairpins with predicted thermal stabilities ranging from -10 to -50 kcal/mol and 5′ G cap-to-hairpin distances of 1-46 bases. Translation efficiency decreased abruptly as hairpin stabilities increased from ΔG = -25 to -35 kcal/mol. Shifting a hairpin as little as nine bases relative to the 5′ cap could modulate translation more than 50-fold. Increasing GC content diminished translation efficiency when predicted thermal stability and cap-to-hairpin distances were held constant. We additionally found naturally occurring 5′-untranslated regions affected translation differently in live cells compared with translation in in vitro lysates. Our study will assist scientists in designing experiments that deliberately modulate mammalian translation with designed 5′ UTRs.",
keywords = "Fluorescence, Hairpin, RNA, Structure, Thermal stability, Translation",
author = "Jeremy Babendure and Jennie Bever and Ding, {Jian Hua} and Tsien, {Roger Y.}",
year = "2006",
month = "5",
day = "1",
doi = "10.1261/rna.2309906",
language = "English (US)",
volume = "12",
pages = "851--861",
journal = "RNA",
issn = "1355-8382",
publisher = "Cold Spring Harbor Laboratory Press",
number = "5",

}

TY - JOUR

T1 - Control of mammalian translation by mRNA structure near caps

AU - Babendure, Jeremy

AU - Bever, Jennie

AU - Ding, Jian Hua

AU - Tsien, Roger Y.

PY - 2006/5/1

Y1 - 2006/5/1

N2 - The scanning model of RNA translation proposes that highly stable secondary structures within mRNAs can inhibit translation, while structures of lower thermal stability also affect translation if close enough to the 5′ methyl G cap. However, only fragmentary information is available about the dependence of translation efficiency in live mammalian cells on the thermodynamic stability, location, and GC content of RNA structures in the 5′-untranslated region. We devised a two-color fluorescence assay for translation efficiency in single live cells and compared a wide range of hairpins with predicted thermal stabilities ranging from -10 to -50 kcal/mol and 5′ G cap-to-hairpin distances of 1-46 bases. Translation efficiency decreased abruptly as hairpin stabilities increased from ΔG = -25 to -35 kcal/mol. Shifting a hairpin as little as nine bases relative to the 5′ cap could modulate translation more than 50-fold. Increasing GC content diminished translation efficiency when predicted thermal stability and cap-to-hairpin distances were held constant. We additionally found naturally occurring 5′-untranslated regions affected translation differently in live cells compared with translation in in vitro lysates. Our study will assist scientists in designing experiments that deliberately modulate mammalian translation with designed 5′ UTRs.

AB - The scanning model of RNA translation proposes that highly stable secondary structures within mRNAs can inhibit translation, while structures of lower thermal stability also affect translation if close enough to the 5′ methyl G cap. However, only fragmentary information is available about the dependence of translation efficiency in live mammalian cells on the thermodynamic stability, location, and GC content of RNA structures in the 5′-untranslated region. We devised a two-color fluorescence assay for translation efficiency in single live cells and compared a wide range of hairpins with predicted thermal stabilities ranging from -10 to -50 kcal/mol and 5′ G cap-to-hairpin distances of 1-46 bases. Translation efficiency decreased abruptly as hairpin stabilities increased from ΔG = -25 to -35 kcal/mol. Shifting a hairpin as little as nine bases relative to the 5′ cap could modulate translation more than 50-fold. Increasing GC content diminished translation efficiency when predicted thermal stability and cap-to-hairpin distances were held constant. We additionally found naturally occurring 5′-untranslated regions affected translation differently in live cells compared with translation in in vitro lysates. Our study will assist scientists in designing experiments that deliberately modulate mammalian translation with designed 5′ UTRs.

KW - Fluorescence

KW - Hairpin

KW - RNA

KW - Structure

KW - Thermal stability

KW - Translation

UR - http://www.scopus.com/inward/record.url?scp=33646193306&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33646193306&partnerID=8YFLogxK

U2 - 10.1261/rna.2309906

DO - 10.1261/rna.2309906

M3 - Article

C2 - 16540693

AN - SCOPUS:33646193306

VL - 12

SP - 851

EP - 861

JO - RNA

JF - RNA

SN - 1355-8382

IS - 5

ER -