LNA-enhanced DNA FIT-probes for multicolour RNA imaging

F. Hövelmann; I. Gaspar; J. Chamiolo; M. Kasper; J. Steffen; A. Ephrussi; O. Seitz

doi:10.1039/c5sc03053f

LNA-enhanced DNA FIT-probes for multicolour RNA imaging

Chemical Science ◽

10.1039/c5sc03053f ◽

2016 ◽

Vol 7 (1) ◽

pp. 128-135 ◽

Cited By ~ 35

Author(s):

F. Hövelmann ◽

I. Gaspar ◽

J. Chamiolo ◽

M. Kasper ◽

J. Steffen ◽

...

Keyword(s):

Rna Binding ◽

Red Fluorescence ◽

Rna Imaging ◽

Polyadenylated Mrna

A surrogate nucleobase based on 4,4'-cyanine provided up to 195-fold enhancement of red fluorescence upon complementary RNA binding. A mixture of FIT probes allowed the localization of oskar mRNA and other polyadenylated mRNA molecules in developing oocytes from Drosphila melanogaster by wash-free FISH and STED.

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Current techniques for visualizing RNA in cells

F1000Research ◽

10.12688/f1000research.8151.1 ◽

2016 ◽

Vol 5 ◽

pp. 775 ◽

Cited By ~ 9

Author(s):

Lilith V.J.C. Mannack ◽

Sebastian Eising ◽

Andrea Rentmeister

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

State Of The Art ◽

Living Cells ◽

Enzymatic Modification ◽

Current State ◽

Rna Imaging ◽

In Cells ◽

Art Techniques

Labeling RNA is of utmost interest, particularly in living cells, and thus RNA imaging is an emerging field. There are numerous methods relying on different concepts ranging from hybridization-based probes, over RNA-binding proteins to chemo-enzymatic modification of RNA. These methods have different benefits and limitations. This review aims to outline the current state-of-the-art techniques and point out their benefits and limitations.

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N6-methyladenosine dynamics during early vertebrate embryogenesis

10.1101/528422 ◽

2019 ◽

Author(s):

Håvard Aanes ◽

Dominique Engelsen ◽

Adeel Manaf ◽

Endalkachew Ashenafi Alemu ◽

Cathrine Broberg Vågbø ◽

...

Keyword(s):

Translational Regulation ◽

Rna Binding ◽

Rna Binding Proteins ◽

Rna Degradation ◽

Translational Efficiency ◽

Mrna Levels ◽

Maternal Transcripts ◽

Post Transcriptional Regulation ◽

Genome Activation ◽

Polyadenylated Mrna

AbstractEarly vertebrate embryogenesis is characterized by extensive post-transcriptional regulation during the maternal-to-zygotic transition. The N6-methyladenosine (m6A) modifications on mRNA have been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with polyadenylated mRNA levels. The majority (>70%) of maternal transcripts harbor m6A, and there is a substantial increase of m6A in the polyadenylated mRNA fraction between 0 and 2 hours post fertilization. Notably, we find strong associations between m6A, cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation (ZGA). Interestingly, the relationship between m6A and translation is strongest for peaks located in the 3’UTR, but not overlapping stop codons. Sequence analyses revealed enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. After ZGA, m6A seem to diminish the effect of miR-430 mediated degradation. The reported results improve our understanding of the combinatorial code behind post-transcriptional mRNA regulation during embryonic reprogramming and early differentiation.

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Seeing Is Believing: Visualizing Circular RNAs

Non-Coding RNA ◽

10.3390/ncrna6040045 ◽

2020 ◽

Vol 6 (4) ◽

pp. 45

Author(s):

Pruthvi Raj Bejugam ◽

Aniruddha Das ◽

Amaresh Chandra Panda

Keyword(s):

Single Molecule ◽

Rna Binding ◽

Rna Binding Proteins ◽

Imaging Techniques ◽

Sequence Similarity ◽

Rna Aptamers ◽

Circular Rnas ◽

Cellular Processes ◽

Imaging Probes ◽

Rna Imaging

Advancement in the RNA sequencing techniques has discovered hundreds of thousands of circular RNAs (circRNAs) in humans. However, the physiological function of most of the identified circRNAs remains unexplored. Recent studies have established that spliceosomal machinery and RNA-binding proteins modulate circRNA biogenesis. Furthermore, circRNAs have been implicated in regulating crucial cellular processes by interacting with various proteins and microRNAs. However, there are several challenges in understanding the mechanism of circRNA biogenesis, transport, and their interaction with cellular factors to regulate cellular events because of their low abundance and sequence similarity with linear RNA. Addressing these challenges requires systematic studies that directly visualize the circRNAs in cells at single-molecule resolution along with the molecular regulators. In this review, we present the design, benefits, and weaknesses of RNA imaging techniques such as single-molecule RNA fluorescence in situ hybridization and BaseScope in fixed cells and fluorescent RNA aptamers in live-cell imaging of circRNAs. Furthermore, we propose the potential use of molecular beacons, multiply labeled tetravalent RNA imaging probes, and Cas-derived systems to visualize circRNAs.

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A molecular brake that modulates spliceosome pausing at detained introns contributes to neurodegeneration

10.1101/2022.01.11.475943 ◽

2022 ◽

Author(s):

Yichang Jia

Keyword(s):

Rna Binding ◽

Rna Binding Protein ◽

Conditional Knockout ◽

Interacting Protein ◽

U2 Snrna ◽

Mrna Pool ◽

Splicing Efficiency ◽

Underlying Mechanisms ◽

Molecular Brake ◽

Polyadenylated Mrna

Emerging evidence suggests that intron-detaining transcripts (IDTs) are a nucleus-detained and polyadenylated mRNA pool for cell to quickly and effectively respond to environmental stimuli and stress. However, the underlying mechanisms of detained intron (DI) splicing are still largely unknown. Here, we suggest that post-transcriptional DI splicing is paused at Bact 29 state, an active spliceosome but not catalytically primed, which depends on SNIP1 (Smad Nuclear Interacting Protein 1) and RNPS1 (a serine-rich RNA binding protein) interaction. RNPS1 and Bact component preferentially dock at DIs and the RNPS1 docking is sufficient to trigger spliceosome pausing. Haploinsufficiency of Snip1 attenuates neurodegeneration and globally rescues IDT accumulation caused by a previously reported mutant U2 snRNA, a basal spliceosomal component. Snip1 conditional knockout in cerebellum decreases DI splicing efficiency and causes neurodegeneration. Therefore, we suggest that SNIP1 and RNPS1 form a molecular brake for the spliceosome pausing, and that its misregulation contributes to neurodegeneration.

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