Illuminating RNA biology through imaging

Le, Phuong; Ahmed, Noorsher; Yeo, G

doi:10.1038/s41556-022-00933-9

Cited by 54 publications

(48 citation statements)

References 151 publications

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“…Recent advances in microscopy enable robust live-cell imaging of diffusing granule proteins, providing biophysical data of granule material properties. Fluorescence in situ hybridization and the MS2 tagging system can be used for fixed and live tracking of RNAs (Le et al, 2022).…”

Section: Technologies For Investigating Rna Granulesmentioning

confidence: 99%

Aging RNA granule dynamics in neurodegeneration

Rhine

Al-Azzam

Chen

et al. 2022

Front. Mol. Biosci.

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Disordered RNA-binding proteins and repetitive RNA sequences are the main genetic causes of several neurodegenerative diseases, including amyotrophic lateral sclerosis and Huntington’s disease. Importantly, these components also seed the formation of cytoplasmic liquid-like granules, like stress granules and P bodies. Emerging evidence demonstrates that healthy granules formed via liquid-liquid phase separation can mature into solid- or gel-like inclusions that persist within the cell. These solidified inclusions are a precursor to the aggregates identified in patients, demonstrating that dysregulation of RNA granule biology is an important component of neurodegeneration. Here, we review recent literature highlighting how RNA molecules seed proteinaceous granules, the mechanisms of healthy turnover of RNA granules in cells, which biophysical properties underly a transition to solid- or gel-like material states, and why persistent granules disrupt the cellular homeostasis of neurons. We also identify various methods that will illuminate the contributions of disordered proteins and RNAs to neurodegeneration in ongoing research efforts.

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Section: Technologies For Investigating Rna Granulesmentioning

confidence: 99%

Aging RNA granule dynamics in neurodegeneration

Rhine

Al-Azzam

Chen

et al. 2022

Front. Mol. Biosci.

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“…Yeo's bias, he says, is to study neuronal RNAs. And they are on the move, which is best tracked by imaging rather than a stack of many snapshots 9 . Such 'stills' can't be collected for all transcripts at a time in both the nucleus and cytoplasm.…”

Section: Being An Rna Personmentioning

confidence: 99%

Some roads ahead for noncoding RNAs

Marx

2022

Nat Methods

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“…Probe modified oligonucleotides have widespread applications in imaging, diagnostics, nanotechnology, and medicine. [1][2][3] Modified nucleic acids are commonly produced by incorporating functionalized nucleotides during solid-phase synthesis using phosphoramidite chemistry. In addition, several alternative techniques exist that rely on chemical or enzymatic modification of nucleobases or the sugar backbone.…”

Section: Introductionmentioning

confidence: 99%

Site-specific Covalent Labeling of DNA Substrates by an RNA Transglycosylase

Tota

Devaraj

2023

Preprint

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Bacterial tRNA guanine transglycosylases (TGTs) catalyze the exchange of guanine for the 7-deazaguanine queuine precursor, prequeuosine1 (preQ1). While the native nucleic acid substrate for bacterial TGTs is the anticodon loop of queuine-cognate tRNAs, the minimum recognition sequence for the enzyme is a structured hairpin containing the target G nucleobase in a "UGU" loop motif. Previous work has established an RNA modification system, RNA-TAG, in which E. coli TGT exchanges the target G on an RNA of interest for chemically modified preQ1 substrates linked to a small molecule reporter such as biotin or a fluorophore. While extending the substrate scope of RNA transglycosylases to include DNA would enable numerous applications, it has been previously reported that TGT is incapable of modifying native DNA. Here we demonstrate that TGT can in fact recognize and label specific DNA substrates. Through iterative testing of rationally mutated DNA hairpin sequences, we determined the minimal sequence requirements for transglycosylation of unmodified DNA by E. coli TGT. Controlling steric constraint in the DNA hairpin dramatically affects labeling efficiency, and, when optimized, can lead to near quantitative site-specific modification. We demonstrate the utility of our newly developed DNA-TAG system by rapidly synthesizing probes for fluorescent Northern blotting of spliceosomal U6 RNA and RNA FISH visualization of the long noncoding RNA, MALAT1. The ease and convenience of the DNA-TAG system will provide researchers with a tool for accessing a wide variety of affordable modified DNA substrates.

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Illuminating RNA biology through imaging

Cited by 54 publications

References 151 publications

Aging RNA granule dynamics in neurodegeneration

Aging RNA granule dynamics in neurodegeneration

Some roads ahead for noncoding RNAs

Site-specific Covalent Labeling of DNA Substrates by an RNA Transglycosylase

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