Learning noncoding RNA biology from viruses

2021 ◽  
Author(s):  
Demián Cazalla
Keyword(s):  
Noncoding Rna ◽  
Rna Biology

scholarly journals An RNA-centric view on gut Bacteroidetes

2020 ◽  
Vol 402 (1) ◽  
pp. 55-72
Author(s):  
Daniel Ryan ◽  
Gianluca Prezza ◽  
Alexander J. Westermann
Keyword(s):  
Noncoding Rna ◽  
Case Reports ◽  
Model Organism ◽  
Global Gene Expression ◽  
Host Cells ◽  
Human Gut ◽  
Open Questions ◽  
Obligate Anaerobic ◽  
Bacterial Rna ◽  
Rna Biology

AbstractBacteria employ noncoding RNAs to maintain cellular physiology, adapt global gene expression to fluctuating environments, sense nutrients, coordinate their interaction with companion microbes and host cells, and protect themselves against bacteriophages. While bacterial RNA research has made fundamental contributions to biomedicine and biotechnology, the bulk of our knowledge of RNA biology stems from the study of a handful of aerobic model species. In comparison, RNA research is lagging in many medically relevant obligate anaerobic species, in particular the numerous commensal bacteria comprising our gut microbiota. This review presents a guide to RNA-based regulatory mechanisms in the phylum Bacteroidetes, focusing on the most abundant bacterial genus in the human gut, Bacteroides spp. This includes recent case reports on riboswitches, an mRNA leader, cis- and trans-encoded small RNAs (sRNAs) in Bacteroides spp., and a survey of CRISPR-Cas systems across Bacteroidetes. Recent work from our laboratory now suggests the existence of hundreds of noncoding RNA candidates in Bacteroides thetaiotaomicron, the emerging model organism for functional microbiota research. Based on these collective observations, we predict mechanistic and functional commonalities and differences between Bacteroides sRNAs and those of other model bacteria, and outline open questions and tools needed to boost Bacteroidetes RNA research.

scholarly journals Enzymatic RNA Biotinylation for Affinity Purification and Identification of RNA-protein Interactions

2020 ◽  
Author(s):  
Kayla N. Busby ◽  
Amitkumar Fulzele ◽  
Dongyang Zhang ◽  
Eric J. Bennett ◽  
Neal K. Devaraj
Keyword(s):  
Protein Interactions ◽  
Mammalian Cells ◽  
Noncoding Rna ◽  
Affinity Purification ◽  
Functional Characterization ◽  
Selective Enrichment ◽  
Binding Partners ◽  
Nucleotide Mutation ◽  
Rna Biology ◽  
And Function

ABSTRACTThroughout their cellular lifetime, RNA transcripts are bound to proteins, playing crucial roles in RNA metabolism, trafficking, and function. Despite the importance of these interactions, identifying the proteins that interact with an RNA of interest in mammalian cells represents a major challenge in RNA biology. Leveraging the ability to site-specifically and covalently label an RNA of interest using E. Coli tRNA guanine transglycosylase and an unnatural nucleobase substrate, we establish the identification of RNA-protein interactions and the selective enrichment of cellular RNA in mammalian systems. We demonstrate the utility of this approach through the identification of known binding partners of 7SK snRNA via mass spectrometry. Through a minimal 4-nucleotide mutation of the long noncoding RNA HOTAIR, enzymatic biotinylation enables identification putative HOTAIR binding partners in MCF7 breast cancer cells that suggest new potential pathways for oncogenic function. Furthermore, using RNA sequencing and qPCR, we establish that an engineered enzyme variant achieves high levels of labeling selectivity against the human transcriptome allowing for 145-fold enrichment of cellular RNA directly from mammalian cell lysates. The flexibility and breadth of this approach suggests that this system could be routinely applied to the functional characterization of RNA, greatly expanding the toolbox available for studying mammalian RNA biology.

scholarly journals Capturing RNA–protein interaction via CRUIS

2020 ◽  
Vol 48 (9) ◽  
pp. e52-e52 ◽  
Author(s):  
Ziheng Zhang ◽  
Weiping Sun ◽  
Tiezhu Shi ◽  
Pengfei Lu ◽  
Min Zhuang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Dna Damage ◽  
Protein Interactions ◽  
Noncoding Rna ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Living Cells ◽  
Innovative Methods ◽  
Rna Biology

Abstract No RNA is completely naked from birth to death. RNAs function with and are regulated by a range of proteins that bind to them. Therefore, the development of innovative methods for studying RNA–protein interactions is very important. Here, we developed a new tool, the CRISPR-based RNA-United Interacting System (CRUIS), which captures RNA–protein interactions in living cells by combining the power of CRISPR and PUP-IT, a novel proximity targeting system. In CRUIS, dCas13a is used as a tracker to target specific RNAs, while proximity enzyme PafA is fused to dCas13a to label the surrounding RNA-binding proteins, which are then identified by mass spectrometry. To identify the efficiency of CRUIS, we employed NORAD (Noncoding RNA activated by DNA damage) as a target, and the results show that a similar interactome profile of NORAD can be obtained as by using CLIP (crosslinking and immunoprecipitation)-based methods. Importantly, several novel NORAD RNA-binding proteins were also identified by CRUIS. The use of CRUIS facilitates the study of RNA–protein interactions in their natural environment, and provides new insights into RNA biology.

scholarly journals The emerging molecular biology toolbox for the study of long noncoding RNA biology

Epigenomics ◽  
2017 ◽  
Vol 9 (10) ◽  
pp. 1317-1327 ◽  
Author(s):  
Ezio T Fok ◽  
Janine Scholefield ◽  
Stephanie Fanucchi ◽  
Musa M Mhlanga
Keyword(s):  
Molecular Biology ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Rna Biology

An introduction to the themed issue on RNA biology in China

2020 ◽  
Vol 64 (6) ◽  
pp. 863-866
Author(s):  
Zhe Wu
Keyword(s):  
Molecular Biology ◽  
Chinese Society ◽  
Fortieth Anniversary ◽  
Rna Biology ◽  
Research And Education ◽  
Education In China

Abstract The year 2019 marked the fortieth anniversary of the Chinese Society of Biochemistry and Molecular Biology (CSBMB), whose mission is to promote biomolecular research and education in China. The last 40 years have witnessed tremendous growth and achievements in biomolecular research by Chinese scientists and Essays in Biochemistry is delighted to publish this themed issue that focuses on exciting areas within RNA biology, with each review contributed by key experts from China.

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