Engineering regulatory RNAs

Davidson, Eric A.; Ellington, Andrew D.

doi:10.1016/j.tibtech.2005.01.006

Cited by 28 publications

(17 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In bacteria, am ethodh as recently been described to control gene expression using small noncodingR NAs to modulate secondary structure at the Shine-Dalgarno site (Isaacse ta l. 2004;Davidson and Ellington 2005). Bayer and Smolke (2005) recently modulated trans-binding RNAs to control reporter protein expression in yeast.…”

Section: Discussionmentioning

confidence: 99%

Control of mammalian translation by mRNA structure near caps

Babendure

Ding

et al. 2006

RNA

296

302

View full text Add to dashboard Cite

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 9 methyl Gc ap. 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 9 -untranslated region. We devised at wo-color fluorescence assay for translation efficiency in single live cells and compared aw ide range of hairpins with predicted thermal stabilities ranging from ÿ 10 to ÿ 50 kcal/mol and 5 9 Gcap-to-hairpin distances of 1-46 bases. Translation efficiency decreased abruptly as hairpin stabilities increased from D G = ÿ 25 to ÿ 35 kcal/mol. Shifting ahairpin as little as nine bases relative to the 5 9 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 9 -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 9 UTRs.

show abstract

Section: Discussionmentioning

confidence: 99%

Control of mammalian translation by mRNA structure near caps

Babendure

Ding

et al. 2006

RNA

296

302

View full text Add to dashboard Cite

show abstract

“…In light of the recentp rogress in natural and artificialRNA-based generegulatory mechanisms in bacteria (Isaacsetal. 2004;Davidson and Ellington 2005) and yeast (Suesse ta l. 2003; Buskirk et al 2004;Bayer and Smolke 2005), small molecule-regulatedR NA genetic switches in mammalian cells should further advance our understanding of the roleso fR NA in gene regulationa sw ell as their applications.…”

Section: Chiumentioning

confidence: 99%

Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer–small molecule interaction

An¹,

Trinh²,

Yokobayashi³

2006

RNA

135

View full text Add to dashboard Cite

Recent studies have uncovered extensive presence and functions of small noncoding RNAs in gene regulation in eukaryotes. In particular, RNA interference (RNAi) has been the subject of significant investigations for its unique role in post-transcriptional gene regulation and utility as at ool for artificial gene knockdown. Here, we describe an ovel strategy for post-transcriptional gene regulation in mammalian cells in which RNAi is specifically modulated through RNA aptamer-small molecule interaction. Incorporation of an RNA aptamer for theophylline in the loop region of as hort hairpin RNA (shRNA) designed to silence fluorescent reporter genes led to dose-dependent inhibition of RNAi by theophylline. shRNA cleavage experiments using recombinant Dicer demonstrated that theophylline inhibited cleavage of an aptamer-fused shRNA by Dicer in vitro. Inhibition of siRNA production by theophylline was also observed in vivo. The results presented here provide the first evidence of specific RNA-small molecule interaction affecting RNAi, and an ovel strategy to regulate mammalian gene expression by small molecules without engineered proteins.

show abstract

“…Many riboswitches have been found in nature, mainly in prokaryotes, and play important roles in the regulation of metabolism (Winkler and Breaker 2005). Artificial RNAs with similar switching function have been constructed by combining two modules: an aptamer module, which binds to a specific compound (ligand), and a regulator module, which changes its conformation depending on ligand binding to regulate gene expression (Davidson and Ellington 2005;Isaacs et al 2006;Suess and Weigand 2008). Such riboregulators are classified into several types based on the regulation mechanisms, such as those that directly induce or repress gene expression downstream in cis (Suess et al 2003(Suess et al , 2004Desai and Gallivan 2004;Lynch et al 2007;Sharma et al 2008;Weigand et al 2008;Ogawa 2011), those that alter the degree of hybridization resulting in induction or repression of genes in trans (Bayer and Smolke 2005), and those that induce ribozyme activity resulting in alteration of gene expression (Robertson and Ellington 1999;Breaker 1999b, 2000;Piganeau et al 2000; Thompson et al 2002;Yen et al 2004;Wieland and Hartig 2008;Wieland et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system: Modeling of ligand-dependent and -independent expression

Kobori

Ichihashi²,

Kazuta³

et al. 2012

RNA

View full text Add to dashboard Cite

Aptazymes are useful as RNA-based switches of gene expression responsive to several types of compounds. One of the most important properties of the switching ability is the signal/noise (S/N) ratio, i.e., the ratio of gene expression in the presence of ligand to that in the absence of ligand. The present study was performed to gain a quantitative understanding of how the aptazyme S/N ratio is determined by factors involved in gene expression, such as transcription, RNA self-cleavage, RNA degradation, protein translation, and their ligand dependencies. We performed switching of gene expression using two onswitch aptazymes with different properties in a cell-free translation system, and constructed a kinetic model that quantitatively describes the dynamics of RNA and protein species involved in switching. Both theoretical and experimental analyses consistently demonstrated that factors determining both the absolute value and the dynamics of the S/N ratio are highly dependent on the routes of translation in the absence of ligand: translation from the ligand-independently cleaved RNA or leaky translation from the noncleaved RNA. The model obtained here is useful to assess the factors that restrict the S/N ratio and to improve aptazymes more efficiently.

show abstract

Engineering regulatory RNAs

Cited by 28 publications

References 21 publications

Control of mammalian translation by mRNA structure near caps

Control of mammalian translation by mRNA structure near caps

Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer–small molecule interaction

Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system: Modeling of ligand-dependent and -independent expression

Contact Info

Product

Resources

About