Different Plant Species Have Common Sequence Features Related to mRNA Degradation Intermediates

Abstract

mRNA degradation is an important cellular mechanism involved in the control of gene expression. Several genome-wide profiling methods have been developed for detecting mRNA degradation in plants and animals. However, because many of these techniques use poly (A) mRNA for library preparation, degradation intermediates are often only detected near the 3′-ends of transcripts. Previously, we developed the Truncated RNA End Sequencing (TREseq) method using Arabidopsis thaliana, and demonstrated that this method ameliorates 3′-end bias. In analyses using TREseq, we observed G-rich sequences near the 5′-ends of degradation intermediates. However, this finding remained to be confirmed in other plant species. Hence, in this study, we conducted TREseq analyses in Lactuca sativa (lettuce), Oryza sativa (rice) and Rosa hybrida (rose). These species including A. thaliana were selected to encompass a diverse range in the angiosperm phylogeny. The results revealed similar sequence features near the 5′-ends of degradation intermediates, and involvement of translation process in all four species. In addition, homologous genes have similar efficiencies of mRNA degradation in different plants, suggesting that similar mechanisms of mRNA degradation are conserved across plant species. These strong sequence features were not observed in previous degradome analyses among different species in plants.

Sequence features around cleavage sites are highly conserved among different species and a critical determinant for RNA cleavage position across eukaryotes

“…In degradome analysis, the term “cleavage score” was used to estimate RNA cleavage efficiencies in previous studies (Anderson et al 2018; Ueno et al 2018). In this analysis, we defined cleavage score at the site level (CS site ) as the number of 5’ degradation intermediates normalized against RNA abundance (Ueno et al 2018, 2020). In addition, as with efficiencies of RNA cleavage at the gene level, we defined the sum of CS site values in each gene as the CS gene value.…”

“…Subsequently, we discovered sequence motifs using sequences around (from − 10 to + 10), upstream (from − 20 to − 5), or downstream (from + 5 to + 20) of cleavage sites using DREME, and then used STAMP to carry out phylogenetic analyses based on similarities among the discovered motifs (Supplementary Figures S10–S12). We also obtained sequences around, upstream, or downstream of cleavage sites in different plant species ( Lactuca sativa [lettuce], Oryza sativa [rice], and Rosa hybrida [rose]) reported in a previous study (Ueno et al 2020), and added sequence motifs for phylogenetic analyses. Generally, similar G-rich sequence motifs were observed around the cleavage sites (from − 10 to + 10).…”

“…To increase the concentration of Cap-less RNA, we removed the majority of expected Cap RNA from the Cap-less RNA data during the mapping process. Because Cap (7-methylguanosine) is not encoded in the genome and nucleotide of Cap position in the genome is Y (C or T) in eukaryotes (Carninci et al 2006; Adiconis et al 2018; Thieffry et al 2020; Lu and Lin 2019), the majority of Cap RNA in the Cap-less data could be removed by excluding Cap-less RNA with mismatches at the 5’ end of the read relative to the genome (Ueno et al 2020). In addition, we decreased the 3’ bias of the cleavage site using random primers and conducting rRNA depletion (Ueno et al 2018).…”

Translational gene regulation in plants: A green new deal

“…In the process, the exon junction complex is removed thus keeping the mRNA stable and the rate of eRF1 synthesis high. After Nyikó et al (2017) mRNAs are also degraded co-translationally where the 5'-3' exoribonuclease XRN4 follows a ribosome, whether it is actively translating or stalled (Merret et al, 2015;Ueno et al, 2019;Ueno, Yamasaki, Demura, & Kato, 2018;X. Yu, Willmann, Anderson, & Gregory, 2016).…”

“…P‐bodies also contain ribonucleases for RNA degradation. However, several recent studies have shown that mRNAs are also degraded co‐translationally where the 5'–3' exoribonuclease XRN4 follows a ribosome, whether it is actively translating or stalled (Merret et al, 2015; Ueno et al, 2019; Ueno, Yamasaki, Demura, & Kato, 2018; X. Yu, Willmann, Anderson, & Gregory, 2016). The evidence?…”