Direct RNA sequencing dataset of SMG1 KO mutant Physcomitrella (Physcomitrium patens)
Nonsense-mediated mRNA decay (NMD) is a system that controls the quality of mRNA transcripts in eukaryotes by degradation of aberrant transcripts in a pioneer round of translation. In mammals, NMD targets one-third of mutated, disease-causing mRNAs and ∼10% of unmutated mRNAs, facilitating appropria...
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| Format: | Article |
| Language: | English |
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Elsevier
2020-12-01
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| Series: | Data in Brief |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340920314827 |
| _version_ | 1818449894523797504 |
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| author | Andrey Knyazev Anna Glushkevich Igor Fesenko |
| author_facet | Andrey Knyazev Anna Glushkevich Igor Fesenko |
| author_sort | Andrey Knyazev |
| collection | DOAJ |
| description | Nonsense-mediated mRNA decay (NMD) is a system that controls the quality of mRNA transcripts in eukaryotes by degradation of aberrant transcripts in a pioneer round of translation. In mammals, NMD targets one-third of mutated, disease-causing mRNAs and ∼10% of unmutated mRNAs, facilitating appropriate cellular responses to environmental changes [1]. In plants, NMD plays an important role in development and regulating abiotic and biotic stress responses [2]. The transcripts with premature termination codons (PTCs), upstream ORFs or long 3′-UTRs can be targeted to NMD. It was shown that alternative splicing plays a crucial role in regulation of NMD triggering, for example, by the introduction of a PTC in transcripts. Therefore, the correct identification of mRNA isoforms is a key step in the study of the principles of regulation of the cell transcriptome by the NMD pathway. Here, we performed long-read sequencing of Physcomitrella (Physcomitrium patens) mutant smg1Δ line 2 native transcriptome by Oxford Nanopore Technology (ONT). The smg1Δ is a knockout (KO) mutant deficient in SMG1 kinase is a key component of NMD system in plants and animals [3]. RNA was isolated with Trizol from 5 day old protonemata and sequenced using kit SQK-RNA002, flow cells FLO-MIN106 and a MinION device (Oxford Nanopore Technologies Ltd., UK (ONT)) in three biological repeats. Basecalling was performed with Guppy v.4.0.15. The presented transcriptomes give advantages in the identification and functional characterization of RNA transcripts that are direct targets of the Nonsense-mediated mRNA decay system. |
| first_indexed | 2024-12-14T20:42:40Z |
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| id | doaj.art-5d6dd54ca5a644b1a6e50ba99f1d7296 |
| institution | Directory Open Access Journal |
| issn | 2352-3409 |
| language | English |
| last_indexed | 2024-12-14T20:42:40Z |
| publishDate | 2020-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj.art-5d6dd54ca5a644b1a6e50ba99f1d72962022-12-21T22:48:11ZengElsevierData in Brief2352-34092020-12-0133106602Direct RNA sequencing dataset of SMG1 KO mutant Physcomitrella (Physcomitrium patens)Andrey Knyazev0Anna Glushkevich1Igor Fesenko2Corresponding author.; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Ulitsa Miklukho-Maklaya, Moscow, 117997, Russian FederationShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Ulitsa Miklukho-Maklaya, Moscow, 117997, Russian FederationShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Ulitsa Miklukho-Maklaya, Moscow, 117997, Russian FederationNonsense-mediated mRNA decay (NMD) is a system that controls the quality of mRNA transcripts in eukaryotes by degradation of aberrant transcripts in a pioneer round of translation. In mammals, NMD targets one-third of mutated, disease-causing mRNAs and ∼10% of unmutated mRNAs, facilitating appropriate cellular responses to environmental changes [1]. In plants, NMD plays an important role in development and regulating abiotic and biotic stress responses [2]. The transcripts with premature termination codons (PTCs), upstream ORFs or long 3′-UTRs can be targeted to NMD. It was shown that alternative splicing plays a crucial role in regulation of NMD triggering, for example, by the introduction of a PTC in transcripts. Therefore, the correct identification of mRNA isoforms is a key step in the study of the principles of regulation of the cell transcriptome by the NMD pathway. Here, we performed long-read sequencing of Physcomitrella (Physcomitrium patens) mutant smg1Δ line 2 native transcriptome by Oxford Nanopore Technology (ONT). The smg1Δ is a knockout (KO) mutant deficient in SMG1 kinase is a key component of NMD system in plants and animals [3]. RNA was isolated with Trizol from 5 day old protonemata and sequenced using kit SQK-RNA002, flow cells FLO-MIN106 and a MinION device (Oxford Nanopore Technologies Ltd., UK (ONT)) in three biological repeats. Basecalling was performed with Guppy v.4.0.15. The presented transcriptomes give advantages in the identification and functional characterization of RNA transcripts that are direct targets of the Nonsense-mediated mRNA decay system.http://www.sciencedirect.com/science/article/pii/S2352340920314827TranscriptomicsNonsense-mediated decayDirect RNA sequencingPhyscomitrella (Physcomitrium patens)SMG1 knockout |
| spellingShingle | Andrey Knyazev Anna Glushkevich Igor Fesenko Direct RNA sequencing dataset of SMG1 KO mutant Physcomitrella (Physcomitrium patens) Data in Brief Transcriptomics Nonsense-mediated decay Direct RNA sequencing Physcomitrella (Physcomitrium patens) SMG1 knockout |
| title | Direct RNA sequencing dataset of SMG1 KO mutant Physcomitrella (Physcomitrium patens) |
| title_full | Direct RNA sequencing dataset of SMG1 KO mutant Physcomitrella (Physcomitrium patens) |
| title_fullStr | Direct RNA sequencing dataset of SMG1 KO mutant Physcomitrella (Physcomitrium patens) |
| title_full_unstemmed | Direct RNA sequencing dataset of SMG1 KO mutant Physcomitrella (Physcomitrium patens) |
| title_short | Direct RNA sequencing dataset of SMG1 KO mutant Physcomitrella (Physcomitrium patens) |
| title_sort | direct rna sequencing dataset of smg1 ko mutant physcomitrella physcomitrium patens |
| topic | Transcriptomics Nonsense-mediated decay Direct RNA sequencing Physcomitrella (Physcomitrium patens) SMG1 knockout |
| url | http://www.sciencedirect.com/science/article/pii/S2352340920314827 |
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