8 results on '"Guarnacci M"'
Search Results
2. Simultaneous identification of m6A and m5C reveals coordinated RNA modification at single-molecule resolution
- Author
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Mateos, P. Acera, primary, Sethi, A.J., additional, Ravindran, A., additional, Guarnacci, M., additional, Srivastava, A., additional, Xu, J., additional, Woodward, K., additional, Yuen, Z.W.S., additional, Hamilton, W., additional, Gao, J., additional, Starrs, L.M., additional, Hayashi, R., additional, Wickramasinghe, V., additional, Preiss, T., additional, Burgio, G., additional, Dehorter, N., additional, Shirokikh, N., additional, and Eyras, E., additional
- Published
- 2022
- Full Text
- View/download PDF
3. Substrate diversity of NSUN enzymes and links of 5-methylcytosine to mRNA translation and turnover.
- Author
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Guarnacci M, Zhang PH, Kanchi M, Hung YT, Lin H, Shirokikh NE, Yang L, and Preiss T
- Subjects
- Humans, HeLa Cells, RNA-Binding Proteins metabolism, RNA-Binding Proteins genetics, Substrate Specificity, Methylation, RNA Stability genetics, tRNA Methyltransferases, 5-Methylcytosine metabolism, RNA, Messenger metabolism, RNA, Messenger genetics, Protein Biosynthesis, Methyltransferases metabolism, Methyltransferases genetics
- Abstract
Maps of the RNA modification 5-methylcytosine (m
5 C) often diverge markedly not only because of differences in detection methods, data depand analysis pipelines but also biological factors. We re-analysed bisulfite RNA sequencing datasets from five human cell lines and seven tissues using a coherent m5 C site calling pipeline. With the resulting union list of 6,393 m5 C sites, we studied site distribution, enzymology, interaction with RNA-binding proteins and molecular function. We confirmed tRNA:m5 C methyltransferases NSUN2 and NSUN6 as the main mRNA m5 C "writers," but further showed that the rRNA:m5 C methyltransferase NSUN5 can also modify mRNA. Each enzyme recognises mRNA features that strongly resemble their canonical substrates. By analysing proximity between mRNA m5 C sites and footprints of RNA-binding proteins, we identified new candidates for functional interactions, including the RNA helicases DDX3X, involved in mRNA translation, and UPF1, an mRNA decay factor. We found that lack of NSUN2 in HeLa cells affected both steady-state levels of, and UPF1-binding to, target mRNAs. Our studies emphasise the emerging diversity of m5 C writers and readers and their effect on mRNA function., (© 2024 Guarnacci et al.)- Published
- 2024
- Full Text
- View/download PDF
4. The je ne sais quoi of 5-methylcytosine in messenger RNA.
- Author
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Guarnacci M and Preiss T
- Subjects
- RNA, Messenger genetics, 5-Methylcytosine, RNA
- Abstract
The potential presence of 5-methylcytosine as a sparse internal modification of mRNA was first raised in 1975, and a first map of the modification was also part of the epitranscriptomics "big bang" in 2012. Since then, the evidence for its presence in mRNA has firmed up, and initial insights have been gained into the molecular function and broader biological relevance of 5-methylcytosine when present in mRNA. Here, we summarize the status quo of the field, outline some of its current challenges, and suggest how to address them in future work., (© 2024 Guarnacci and Preiss; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)
- Published
- 2024
- Full Text
- View/download PDF
5. Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer.
- Author
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Ortiz-Barahona V, Soler M, Davalos V, García-Prieto CA, Janin M, Setien F, Fernández-Rebollo I, Bech-Serra JJ, De La Torre C, Guil S, Villanueva A, Zhang PH, Yang L, Guarnacci M, Schumann U, Preiss T, Balaseviciute U, Montal R, Llovet JM, and Esteller M
- Subjects
- Humans, 5-Methylcytosine, CpG Islands, DNA Methylation, Epigenesis, Genetic, Gene Expression Regulation, Neoplastic, Proteomics, RNA, Messenger metabolism, RNA-Binding Proteins metabolism, Transcription Factors genetics, Liver Neoplasms genetics, Methyltransferases genetics, Methyltransferases metabolism
- Abstract
Background: RNA modifications are important regulators of transcript activity and an increasingly emerging body of data suggests that the epitranscriptome and its associated enzymes are altered in human tumors., Methods: Combining data mining and conventional experimental procedures, NSUN7 methylation and expression status was assessed in liver cancer cell lines and primary tumors. Loss-of-function and transfection-mediated recovery experiments coupled with RNA bisulfite sequencing and proteomics determined the activity of NSUN7 in downstream targets and drug sensitivity., Results: In this study, the initial screening for genetic and epigenetic defects of 5-methylcytosine RNA methyltransferases in transformed cell lines, identified that the NOL1/NOP2/Sun domain family member 7 (NSUN7) undergoes promoter CpG island hypermethylation-associated with transcriptional silencing in a cancer-specific manner. NSUN7 epigenetic inactivation was common in liver malignant cells and we coupled bisulfite conversion of cellular RNA with next-generation sequencing (bsRNA-seq) to find the RNA targets of this poorly characterized putative RNA methyltransferase. Using knock-out and restoration-of-function models, we observed that the mRNA of the coiled-coil domain containing 9B (CCDC9B) gene required NSUN7-mediated methylation for transcript stability. Most importantly, proteomic analyses determined that CCDC9B loss impaired protein levels of its partner, the MYC-regulator Influenza Virus NS1A Binding Protein (IVNS1ABP), creating sensitivity to bromodomain inhibitors in liver cancer cells exhibiting NSUN7 epigenetic silencing. The DNA methylation-associated loss of NSUN7 was also observed in primary liver tumors where it was associated with poor overall survival. Interestingly, NSUN7 unmethylated status was enriched in the immune active subclass of liver tumors., Conclusion: The 5-methylcytosine RNA methyltransferase NSUN7 undergoes epigenetic inactivation in liver cancer that prevents correct mRNA methylation. Furthermore, NSUN7 DNA methylation-associated silencing is associated with clinical outcome and distinct therapeutic vulnerability., (© 2023. The Author(s).)
- Published
- 2023
- Full Text
- View/download PDF
6. Target-Specific Profiling of RNA m 5 C Methylation Level Using Amplicon Sequencing.
- Author
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Sibbritt T, Schumann U, Shafik A, Guarnacci M, Clark SJ, and Preiss T
- Subjects
- 5-Methylcytosine, High-Throughput Nucleotide Sequencing, Methylation, RNA genetics, Sequence Analysis, DNA
- Abstract
Mapping the position and quantifying the level of 5-methylcytosine (m
5 C) as a modification in different types of cellular RNA is an important objective in the field of epitranscriptomics. Bisulfite conversion has long been the gold standard for the detection of m5 C in DNA, but it can also be applied to RNA. Here, we detail methods for bisulfite treatment of RNA, locus-specific PCR amplification, and detection of candidate sites by sequencing on the Illumina MiSeq platform., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)- Published
- 2022
- Full Text
- View/download PDF
7. CircVAMP3: A circRNA with a Role in Alveolar Rhabdomyosarcoma Cell Cycle Progression.
- Author
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Rossi F, Centrón-Broco A, Dattilo D, Di Timoteo G, Guarnacci M, Colantoni A, Beltran Nebot M, and Bozzoni I
- Subjects
- Cell Division genetics, Cell Line, Tumor, Gene Expression Regulation, Neoplastic genetics, Humans, Myoblasts metabolism, Oncogene Protein v-akt genetics, RNA Splicing genetics, Rhabdomyosarcoma, Alveolar pathology, Cell Cycle genetics, RNA genetics, RNA, Circular genetics, Rhabdomyosarcoma, Alveolar genetics
- Abstract
Circular RNAs (circRNAs), a class of covalently closed RNAs formed by a back-splicing reaction, have been involved in the regulation of diverse oncogenic processes. In this article we describe circVAMP3, a novel circular RNA overexpressed in RH4, a representative cell line of alveolar rhabdomyosarcoma. We demonstrated that circVAMP3 has a differential m
6 A pattern opposed to its linear counterpart, suggesting that the two isoforms can be differently regulated by such RNA modification. Moreover, we show how circVAMP3 depletion in alveolar rhabdomyosarcoma cells can impair cell cycle progression, through the alteration of the AKT-related pathways, pointing to this non-coding RNA as a novel regulator of the alveolar rhabdomyosarcoma progression and as a putative future therapeutic target.- Published
- 2021
- Full Text
- View/download PDF
8. Modulation of circRNA Metabolism by m 6 A Modification.
- Author
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Di Timoteo G, Dattilo D, Centrón-Broco A, Colantoni A, Guarnacci M, Rossi F, Incarnato D, Oliviero S, Fatica A, Morlando M, and Bozzoni I
- Subjects
- Adenosine metabolism, Alternative Splicing, Child, Preschool, Female, HEK293 Cells, HeLa Cells, Humans, Male, Nerve Tissue Proteins, RNA Splicing Factors, Adenosine analogs & derivatives, Methyltransferases metabolism, RNA, Circular metabolism
- Abstract
N
6 -methyladenosine (m6 A) is an RNA modification well-known for its contribution to different processes controlling RNA metabolism, including splicing, stability, and translation of mRNA. Conversely, the role of m6 A on the biogenesis and function of circular RNAs (circRNAs) has yet to be addressed. circRNAs belong to a class of covalently closed transcripts produced via a back-splicing reaction whereby a downstream 5' splice donor site fuses to an upstream 3' splice acceptor site. Starting from circ-ZNF609 as a study case, we discover that specific m6 As control its accumulation and that METTL3 and YTHDC1 are required to direct the back-splicing reaction. This feature is shared with other circRNAs because we find a significant direct correlation among METTL3 requirement, YTHDC1 binding, and the ability of m6 A exons to undergo back-splicing. Finally, because circ-ZNF609 displays the ability to be translated, we show that m6 A modifications, through recognition by YTHDF3 and eIF4G2, modulate its translation., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2020
- Full Text
- View/download PDF
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