Essential roles of RNA cap-proximal ribose methylation in mammalian embryonic development and fertility

Dohnálková, Michaela; Krasnykov, Kyrylo; Mendel, Mateusz; Li, Lingyun; Panasenko, Olesya O.; Fleury-Olela, Fabienne; Vågbø, Cathrine Broberg; Homolka, David; Pillai, Ramesh S.

doi:10.1016/j.celrep.2023.112786

Cited by 12 publications

(8 citation statements)

References 74 publications

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“…It is important to note here that the role of cap1 modification goes beyond marking mRNA as 'self' and serves as a mechanism for epitranscriptomic regulation of gene expression. It has been demonstrated that CMTR1-catalyzed methylation of cellular transcripts is essential for promoting histone and ribosomal gene expression in the process of differentiation of embryonic stem cells (Liang et al 2022) and in the development and fertility of mammalian embryos (Dohnalkova et al 2023).…”

Section: Discussionmentioning

confidence: 99%

Cap-related modifications of RNA regulate binding to IFIT proteins

Geng,

Chrabaszczewska,

Kurpiejewski

et al. 2024

Preprint

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All cells in our body are equipped with receptors to recognize pathogens and trigger a rapid defense response. As a result, foreign molecules are blocked and cells are alerted to the danger. Among the many molecules produced in response to viral infection are interferon-induced proteins with tetratricopeptide repeats (IFITs). Their role is to recognize foreign mRNA and eliminate it from the translational pool of transcripts. In the present study, we used biophysical methods to characterize the interactions between IFIT1 protein and its partners IFIT2 and IFIT3. IFIT1 interacts with IFIT3 with nanomolar binding affinity, which did not change significantly in the presence of the preformed IFIT2/3 complex. The interactions between IFIT2 and IFIT3 and IFIT1 and IFIT2 were one order of magnitude weaker. We also present kinetic data of the interactions between the IFIT protein complex and short RNA bearing various modifications at the 5’ end. We show kinetic parameters for interaction between IFIT complex and RNA with m6Ammodification. The results show that the cap adjacent m6Ammodification is a stronger signature than cap1 alone. It blocks the formation of a complex between IFIT proteins and m7Gpppm6Am-RNA much more effectively than other cap modifications. In contrast, m6A in the 5’UTR is not recognized by IFIT proteins and does not contribute to translation repression by IFIT proteins. The data obtained are important for understanding the regulation of expression of genetic information. They indicate that 2’-Oand m6Ammodifications modulate the availability of mRNA molecules for proteins of innate immune response.

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Section: Discussionmentioning

confidence: 99%

Cap-related modifications of RNA regulate binding to IFIT proteins

Geng,

Chrabaszczewska,

Kurpiejewski

et al. 2024

Preprint

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show abstract

“…In mice, deletion of CMTR1 in the adult liver resulted in the up-regulation of several ISGs, including IFIT1, possibly by sensing of endogenous transcripts. CMTR1 was also found to be essential for mouse embryonic development without activating the type I IFN response, as the ability to produce IFNs is inactive during the early stage of development ( Gázquez-Gutiérrez et al 2021 ; Dohnalkova et al 2023 ; Mueller et al 2024 ). In addition to CMTR1, the absence of CMTR2 in HEK293T also results in activation of the type I IFN response in a RIG-I-dependent manner ( Despic and Jeffrey 2023 ).…”

Section: Functions Of the 5′-end Sensors And Modifying Enzymes Beyond...mentioning

confidence: 99%

“…In addition to CMTR1, the absence of CMTR2 in HEK293T also results in activation of the type I IFN response in a RIG-I-dependent manner ( Despic and Jeffrey 2023 ). Interestingly, CMTR2 is also essential for mouse embryonic development ( Dohnalkova et al 2023 ).…”

Section: Functions Of the 5′-end Sensors And Modifying Enzymes Beyond...mentioning

confidence: 99%

The molecular language of RNA 5′ ends: guardians of RNA identity and immunity

Avila-Bonilla,

Macias

2024

RNA

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RNA caps are deposited at the 5’end of RNA-polymerase II transcripts. This modification regulates several steps of gene expression, in addition to marking transcripts as self to enable the innate immune system to distinguish them from uncapped foreign RNAs, including those derived from viruses. Specialized immune sensors, such as RIG-I and IFITs, trigger antiviral responses upon recognition of uncapped cytoplasmic transcripts. Interestingly, uncapped transcripts can also be produced by mammalian hosts. For instance, 5'-triphosphate RNAs are generated by RNA-polymerase III transcription, including tRNAs, Alu RNAs, or vault RNAs. These RNAs have emerged as key players of innate immunity, as they can be recognised by the antiviral sensors. Mechanisms that regulate the presence of 5-triphosphates, such as 5' end dephosphorylation or RNA editing, prevent immune recognition of endogenous RNAs and excessive inflammation. Here, we provide a comprehensive overview of the complexity of RNA cap structures and 5'-triphosphate RNAs, highlighting their roles in transcript identity, immune surveillance, and disease.

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“…Several proteins involved in innate immune response avidly recognize 5′-triphosphate RNAs and even RNAs carrying cap-0, whereas cap-1 RNAs are recognized with much lower affinity . Recent studies revealed the importance of cap-1 and cap-2 for mammalian development …”

Section: Why Cap Mrna?mentioning

confidence: 99%

“…17 Recent studies revealed the importance of cap-1 and cap-2 for mammalian development. 18 The importance of the 5′-cap for mRNA stability, translation, and evasion of the innate immune response requires that any linear mRNA delivered as a therapeutic agent must be capped. In the cell, mRNA capping is realized at an early stage of transcription, by a complex of three enzymatic activities.…”

Section: Why Cap Mrna?mentioning

confidence: 99%

Chemical Modifications of mRNA Ends for Therapeutic Applications

Warminski,

Mamot,

Depaix

et al. 2023

Acc. Chem. Res.

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Metrics & MoreArticle Recommendations CONSPECTUS: Messenger ribonucleic acid (mRNA) is the universal cellular instruction for ribosomes to produce proteins. Proteins are responsible for most of the functions of living organisms, and their abnormal structure or activity is the cause of many diseases. mRNA, which is expressed in the cytoplasm and, unlike DNA, does not need to be delivered into the nucleus, appears to be an ideal vehicle for pursuing the idea of gene therapy in which genetic information about proteins is introduced into an organism to exert a therapeutic effect. mRNA molecules of any sequence can be synthesized using the same set of reagents in a cell-free system via a process called in vitro transcription (IVT), which is very convenient for therapeutic applications. However, this does not mean that the path from the idea to the first mRNA-based therapeutic was short and easy. It took 30 years of trial and error in the search for solutions that eventually led to the first mRNA vaccines created in record time during the SARS-CoV-2 pandemic. One of the fundamental problems in the development of RNA-based therapeutics is the legendary instability of mRNA, due to the transient nature of this macromolecule. From the chemical point of view, mRNA is a linear biopolymer composed of four types of ribonucleic subunits ranging in length from a few hundred to hundreds of thousands of nucleotides, with unique structures at its ends: a 5′-cap at the 5′-end and a poly(A) tail at the 3′-end. Both are extremely important for the regulation of translation and mRNA durability. These elements are also convenient sites for sequence-independent labeling of mRNA to create probes for enzymatic assays and tracking of the fate of mRNA in cells and living organisms. Synthetic 5′-cap analogs have played an important role in the studies of mRNA metabolism, and some of them have also been shown to significantly improve the translational properties of mRNA or affect mRNA stability and reactogenicity. The most effective of these is used in clinical trials of mRNA-based anticancer vaccines. Interestingly, thanks to the knowledge gained from the biophysical studies of cap-related processes, even relatively large modifications such as fluorescent tags can be attached to the cap structure without significant effects on the biological properties of the mRNA, if properly designed cap analogs are used. This has been exploited in the development of molecular tools (fluorescently labeled mRNAs) to track these macromolecules in complex biological systems, including organisms. These tools are extremely valuable for better understanding of the cellular mechanisms involved in mRNA metabolism but also for designing therapeutic mRNAs with superior properties. Much less is known about the usefulness/utility of poly(A) tail modifications in the therapeutic context, but it is clear that chemical modifications of poly(A) can also affect biochemical properties of mRNA. This Account is devoted to chemical modifications of both the 5′-and 3′-ends of mR...

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Essential roles of RNA cap-proximal ribose methylation in mammalian embryonic development and fertility

Cited by 12 publications

References 74 publications

Cap-related modifications of RNA regulate binding to IFIT proteins

Cap-related modifications of RNA regulate binding to IFIT proteins

The molecular language of RNA 5′ ends: guardians of RNA identity and immunity

Chemical Modifications of mRNA Ends for Therapeutic Applications

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