Sequence-specific targeting of RNA.

Post-transcriptional modifications play an important role in several processes, including translation, splicing, and RNA degradation in eukaryotic cells. To investigate the function of specific modifications it is of high interest to develop tools for sequence-specific RNA-targeting. This work focuses on two abundant modifications of eukaryotic mRNA, namely methylation of the guanine-N7 position of the 5'-cap and internal N6-methyladenosine (m6A). We describe the sequence-specific targeting of model RNA transcripts via RNA-binding proteins, such as nuclease-deficient RNA-targeting Cas9 (RCas9) and the Pumilio homology domain (PumHD) fused to two different effector enzymes, the dioxygenase FTO and the guanine-N7 methyltransferase Ecm1. With this tool, we were able to install and remove the methylation at the respective positions with high specificity.

Sequence-specific m6A demethylation in RNA by FTO fused to RCas9.

N6-methyladenosine (m6A) is the most common internal modification in eukaryotic mRNA and associated with numerous cellular processes in health and disease. Up- and down-regulation of its "writer" or "eraser" proteins alter the global m6A level; however, modifying distinct m6A sites has remained elusive. We genetically fused the dioxygenase FTO responsible for m6A demethylation to RCas9 as an RNA-targeting module. The resulting RCas9-FTO retained demethylation activity and bound to RNA in a sequence-specific manner depending on the sgRNA and PAMmer. Using SCARLET analysis, we quantified the m6A level at a specific site and analyzed the effect of the PAM-to-m6A distance on activity. Sequence-specific demethylation by RCas9-FTO was tested on different RNA combinations and showed up to 15-fold sequence preference for target RNA compared to off-target RNA. Taken together, RCas9-FTO represents a new tool for sequence-specific demethylation of m6A in RNA that can be readily adapted to any given RNA sequence and opens the door to studying the function of distinct m6A sites.

Fragmentation of the CRISPR-Cas Type I-B signature protein Cas8b.

BACKGROUND: CRISPR arrays are transcribed into long precursor RNA species, which are further processed into mature CRISPR RNAs (crRNAs). Cas proteins utilize these crRNAs, which contain spacer sequences that can be derived from mobile genetic elements, to mediate immunity during a reoccurring virus infection. Type I CRISPR-Cas systems are defined by the presence of different Cascade interference complexes containing large and small subunits that play major roles during target DNA selection. METHODS: Here, we produce the protein and crRNA components of the Type I-B CRISPR-Cas complex of Clostridium thermocellum and Methanococcus maripaludis. The C. thermocellum Cascade complexes were reconstituted and analyzed via size-exclusion chromatography. Activity of the heterologous M. maripaludis CRISPR-Cas system was followed using phage lambda plaques assays. RESULTS: The reconstituted Type-I-B Cascade complex contains Cas7, Cas5, Cas6b and the large subunit Cas8b. Cas6b can be omitted from the reconstitution protocol. The large subunit Cas8b was found to be represented by two tightly associated protein fragments and a small C-terminal Cas8b segment was identified in recombinant complexes and C. thermocellum cell lysate. CONCLUSIONS: Production of Cas8b generates a small C-terminal fragment, which is suggested to fulfill the role of the missing small subunit. A heterologous, synthetic M. maripaludis Type I-B system is active in E. coli against phage lambda, highlighting a potential for genome editing using endogenous Type-I-B CRISPR-Cas machineries. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.

CRISPR/Cas9: A New Tool for RNA Imaging in Live Cells.

Cas9 can be implemented as an RNA-targeting system to track mRNA in living cells. Nuclear export is enabled by efficient targeting of GFP-fused Cas9 to an endogenous mRNA. The approach provides a new and versatile platform for RNA-targeting with applications in RNA imaging and beyond.

Nucleoside-modified AdoMet analogues for differential methyltransferase targeting.

Methyltransferases (MTases) modify a wide range of biomolecules using S-adenosyl-l-methionine (AdoMet) as the cosubstrate. Synthetic AdoMet analogues are powerful tools to site-specifically introduce a variety of functional groups and exhibit potential to be converted only by distinct MTases. Extending the size of the substituent at the sulfur/selenium atom provides selectivity among MTases but is insufficient to discriminate between promiscuous MTases. We present a panel of AdoMet analogues differing in the nucleoside moiety (NM-AdoMets). These NM-AdoMets were efficiently produced by a previously uncharacterized methionine adenosyltransferase (MAT) from methionine and ATP analogues, such as ITP and N6-propargyl-ATP. The N6-modification changed the relative activity of three representative MTases up to 13-fold resulting in discrimination of substrates for the methyl transfer and could also be combined with transfer of allyl and propargyl groups.

Making the Message Clear: Concepts for mRNA Imaging.

The transcriptome of each individual cell contains numerous RNA species, each of which can be controlled by multiple mechanisms during their lifetime. The standard transcriptome analysis focuses on the expression levels of the genes of interest. To gain additional insights into spatiotemporal RNA distribution and the underlying trafficking processes, RNA labeling and imaging are necessary-ideally in living cells. This perspective will summarize state-of-the-art RNA imaging methods including their strengths and weaknesses.

Safety of the Ullorex oral intragastric balloon for the treatment of obesity.

BACKGROUND: Intragastric balloons have been used for weight loss with varying success. Widespread use of intragastric balloons has been limited because balloons must be placed in, and removed from, the stomach endoscopically. Development of a balloon that does not require endoscopy suggests that obesity treatment with intragastric balloons is feasible. The purpose of this study was to test the Ullorex oral intragastric balloon (OIB) in a sample of human participants. METHODS: The Ullorex OIB is a large capsule that is injected with citric acid and swallowed. After 4 minutes, the balloon inflates to 300 cm(3). Stomach acid degrades a plug on the balloon over 25-30 days, when the balloon deflates and passes in feces. The Ullorex OIB was tested in 12 humans (two participants received placebo capsules). Body weight was monitored before and after balloon placement, and test meals quantified food intake among 6 of the 12 participants, all of whom received one balloon. RESULTS: A single significant adverse event occurred. The one participant randomized to receive three balloons developed nausea and vomiting, requiring intravenous fluids, which was likely influenced by noncompliance (eating solid foods after balloon placement). Participants who received balloons had a significant mean weight loss over 2 weeks, amounting to 1.5 kg (p < 0.05). A marginally significant food intake reduction from baseline to week 1 was found (149 kcal, 24.4%) (p = 0.055). CONCLUSIONS: The Ullorex OIB was successfully utilized in this study, with one serious adverse event that was likely influenced by noncompliance. Body weight and food intake data suggest that the Ullorex OIB be tested further as a possible treatment for obesity.