Structure and Mechanism of RNA Mimics of Green Fluorescent Protein

Meng, Yuchuan; Jaffrey, Samie R.

doi:10.1146/annurev-biophys-060414-033954

Cited by 116 publications

(100 citation statements)

References 68 publications

Supporting

Mentioning

100

Contrasting

Order By: Relevance

“…The RNA aptamer, dubbed Spinach, as well as the second generation aptamer Spinach2, both require addition of exogenous Mg 2+ to fold properly; such addition could obviously also affect native RNA structures. The third generation Spinach reporter, Broccoli, eliminates this requirement (You & Jaffrey, 2015). …”

Section: Setting the Stagementioning

confidence: 99%

Bridging the gap betweenin vitroandin vivoRNA folding

Leamy

Assmann

Mathews

et al. 2016

Quart. Rev. Biophys.

124

132

View full text Add to dashboard Cite

Deciphering the folding pathways and predicting the structures of complex three-dimensional biomolecules is central to elucidating biological function. RNA is single-stranded, which gives it the freedom to fold into complex secondary and tertiary structures. These structures endow RNA with the ability to perform complex chemistries and functions ranging from enzymatic activity to gene regulation. Given that RNA is involved in many essential cellular processes, it is critical to understand how it folds and functions in vivo. Within the last few years, methods have been developed to probe RNA structures in vivo and genome-wide. These studies reveal that RNA often adopts very different structures in vivo and in vitro, and provide profound insights into RNA biology. Nonetheless, both in vitro and in vivo approaches have limitations: studies in the complex and uncontrolled cellular environment make it difficult to obtain insight into RNA folding pathways and thermodynamics, and studies in vitro often lack direct cellular relevance, leaving a gap in our knowledge of RNA folding in vivo. This gap is being bridged by biophysical and mechanistic studies of RNA structure and function under conditions that mimic the cellular environment. To date, most artificial cytoplasms have used various polymers as molecular crowding agents and a series of small molecules as cosolutes. Studies under such in vivo-like conditions are yielding fresh insights, such as cooperative folding of functional RNAs and increased activity of ribozymes. These observations are accounted for in part by molecular crowding effects and interactions with other molecules. In this review, we report milestones in RNA folding in vitro and in vivo and discuss ongoing experimental and computational efforts to bridge the gap between these two conditions in order to understand how RNA folds in the cell.

show abstract

Section: Setting the Stagementioning

confidence: 99%

Bridging the gap betweenin vitroandin vivoRNA folding

Leamy

Assmann

Mathews

et al. 2016

Quart. Rev. Biophys.

124

132

View full text Add to dashboard Cite

show abstract

“…The development of RNA aptamer based imaging methods provides another possibility of live-cell RNA imaging. This approach utilizes RNA aptamer sequences added to the transcript of interest and fluorogenic small molecules that can freely diffuse into the cell, and become fluorescent upon binding to the RNA aptamer (see also several recent reviews (17, 46–48)). While not quite suitable for live-cell imaging, earlier developments of malachite green (MG), thiazole orange (TO), and dimethyl indole red (DIR) aptamers, etc.…”

Section: Approaches To Study Rna Localizationmentioning

confidence: 99%

“…Despite their relatively broad applications in the area of metabolite sensing through engineering to various riboswitches (also see reviews (17, 46–48)), the use of RNA aptamers in single-molecule RNA imaging is still considered to be limited. This limited application of the aptamer-based method for single-molecule RNA imaging might be related to, e.g., the limited brightness of the tag, and the requirement for correct folding of the aptamer in vivo .…”

Section: Approaches To Study Rna Localizationmentioning

confidence: 99%

RNA Localization in Bacteria

Fei

Sharma

2018

Microbiol Spectr

View full text Add to dashboard Cite

Diverse mechanisms and functions of post-transcriptional regulation by small regulatory RNAs (sRNAs) and RNA binding proteins (RBPs) have been described in bacteria. In contrast, little is known about the spatial organization of RNAs in bacterial cells. In eukaryotes, subcellular localization and transport of RNAs play important roles in diverse physiological processes, such as embryonic patterning, asymmetric cell division, epithelial polarity, and neuronal plasticity. It is now clear that bacterial RNAs also can accumulate at distinct sites in the cell. However, due the small size of bacterial cells, localized RNA and translation are more challenging to study in bacterial cells, and the underlying molecular mechanisms of transcript localization are less understood. Here we review the emerging examples of RNAs localized to specific subcellular locations in bacteria, with indications that subcellular localization of transcripts might be important for regulatory processes. Diverse mechanisms for bacterial RNA localization have been suggested, including close association to their genomic site of transcription, or to the localizations of their protein products in translation-dependent or independent processes. We also provide an overview of the state-of-the-art of technologies to visualize and track bacterial RNAs, ranging from hybridization-based approaches in fixed cells to in vivo imaging approaches using fluorescent protein reporters and/or RNA aptamers in single living bacterial cells. We conclude with a discussion of open questions in the field and ongoing technological developments regarding RNA imaging in eukaryotic systems that might likewise provide novel insights into RNA localization in bacteria.

show abstract

“…In addition, it is expected that new technologies for functional characterization of lncRNAs will advance our research in the field. Recently, a group of investigators developed novel technology to trace RNA molecules in living cells 72 . In addition, Paige et al used Spinach, an RNA-fluorophore complex which is a kind of RNA aptamers that bind to fluorophores of green fluorescent protein, to encode the fluorescent specific RNA molecules and image their localization in living cells 73 .…”

Section: Future Perspectivesmentioning

confidence: 99%

Functional diversity of long non-coding RNAs in immune regulation

Geng

Tan

2016

Genes & Diseases

View full text Add to dashboard Cite

Precise and dynamic regulation of gene expression is a key feature of immunity. In recent years, rapid advances in transcriptome profiling analysis have led to recognize long non-coding RNAs (lncRNAs) as an additional layer of gene regulation context. In the immune system, lncRNAs are found to be widely expressed in immune cells including monocytes, macrophages, dendritic cells (DC), neutrophils, T cells and B cells during their development, differentiation and activation. However, the functional importance of immune-related lncRNAs is just emerging to be characterized. In this review, we discuss the up-to-date knowledge of lncRNAs in immune regulation.

show abstract

Structure and Mechanism of RNA Mimics of Green Fluorescent Protein

Cited by 116 publications

References 68 publications

Bridging the gap betweenin vitroandin vivoRNA folding

Bridging the gap betweenin vitroandin vivoRNA folding

RNA Localization in Bacteria

Functional diversity of long non-coding RNAs in immune regulation

Contact Info

Product

Resources

About