Direct RNA sequencing dataset of SMG1 KO mutant Physcomitrella (Physcomitrium patens)

Abstract

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.

Keywords

• Transcriptomics
• Nonsense-mediated decay
• Direct RNA sequencing
• Physcomitrella (Physcomitrium patens)
• SMG1 knockout