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Filatova A, Reveguk I, Piatkova M, Bessonova D, Kuziakova O, Demakova V, Romanishin A, Fishman V, Imanmalik Y, Chekanov N, Skitchenko R, Barbitoff Y, Kardymon O, Skoblov M. Annotation of uORFs in the OMIM genes allows to reveal pathogenic variants in 5'UTRs. Nucleic Acids Res 2023; 51:1229-1244. [PMID: 36651276 PMCID: PMC9943669 DOI: 10.1093/nar/gkac1247] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 11/29/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023] Open
Abstract
An increasing number of studies emphasize the role of non-coding variants in the development of hereditary diseases. However, the interpretation of such variants in clinical genetic testing still remains a critical challenge due to poor knowledge of their pathogenicity mechanisms. It was previously shown that variants in 5'-untranslated regions (5'UTRs) can lead to hereditary diseases due to disruption of upstream open reading frames (uORFs). Here, we performed a manual annotation of upstream translation initiation sites (TISs) in human disease-associated genes from the OMIM database and revealed ∼4.7 thousand of TISs related to uORFs. We compared our TISs with the previous studies and provided a list of 'high confidence' uORFs. Using a luciferase assay, we experimentally validated the translation of uORFs in the ETFDH, PAX9, MAST1, HTT, TTN,GLI2 and COL2A1 genes, as well as existence of N-terminal CDS extension in the ZIC2 gene. Besides, we created a tool to annotate the effects of genetic variants located in uORFs. We revealed the variants from the HGMD and ClinVar databases that disrupt uORFs and thereby could lead to Mendelian disorders. We also showed that the distribution of uORFs-affecting variants differs between pathogenic and population variants. Finally, drawing on manually curated data, we developed a machine-learning algorithm that allows us to predict the TISs in other human genes.
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Affiliation(s)
- Alexandra Filatova
- To whom correspondence should be addressed. Tel: +7 916 335 33 29; Fax: +7 499 324 07 02;
| | - Ivan Reveguk
- Laboratoire de Biologie Structurale de la Cellule, École Polytechnique, Paris, France
| | - Maria Piatkova
- Institute of Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia,Institute of high technologies and advanced materials, Far Eastern Federal University, Vladivostok, Russia
| | - Daria Bessonova
- Medical Center, Far Eastern Federal University, Vladivostok, Russia
| | - Olga Kuziakova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | | | - Alexander Romanishin
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia,Institute of Life Sciences, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Veniamin Fishman
- Artificial Intelligence Research Institute, Moscow, Russia,Molecular Mechanisms of Ontogenesis, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | | | | | | | - Yury Barbitoff
- Bioinformatics Institute, St. Petersburg, Russia,Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, St. Petersburg, Russia,Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Olga Kardymon
- Artificial Intelligence Research Institute, Moscow, Russia
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Long-read assays shed new light on the transcriptome complexity of a viral pathogen. Sci Rep 2020; 10:13822. [PMID: 32796917 PMCID: PMC7427789 DOI: 10.1038/s41598-020-70794-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022] Open
Abstract
Characterization of global transcriptomes using conventional short-read sequencing is challenging due to the insensitivity of these platforms to transcripts isoforms, multigenic RNA molecules, and transcriptional overlaps. Long-read sequencing (LRS) can overcome these limitations by reading full-length transcripts. Employment of these technologies has led to the redefinition of transcriptional complexities in reported organisms. In this study, we applied LRS platforms from Pacific Biosciences and Oxford Nanopore Technologies to profile the vaccinia virus (VACV) transcriptome. We performed cDNA and direct RNA sequencing analyses and revealed an extremely complex transcriptional landscape of this virus. In particular, VACV genes produce large numbers of transcript isoforms that vary in their start and termination sites. A significant fraction of VACV transcripts start or end within coding regions of neighbouring genes. This study provides new insights into the transcriptomic profile of this viral pathogen.
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Bohlen J, Fenzl K, Kramer G, Bukau B, Teleman AA. Selective 40S Footprinting Reveals Cap-Tethered Ribosome Scanning in Human Cells. Mol Cell 2020; 79:561-574.e5. [DOI: 10.1016/j.molcel.2020.06.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 04/10/2020] [Accepted: 05/18/2020] [Indexed: 11/27/2022]
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