Plant genome response to incoming coding sequences: stochastic transcriptional activation independent of integration loci

Abstract

Horizontal gene transfer can occur between phylogenetically distant organisms, such as prokaryotes and eukaryotes. In these cases, how do the translocated genes acquire transcriptional competency in the alien genome environment? According to the conventional view, specific loci of the eukaryotic genome are thought to provide transcriptional competency to the incoming coding sequences. To examine this possibility, we randomly introduced the promoterless luciferase (LUC)-coding sequences into the genome of Arabidopsis thaliana cultured cells and performed a genome-wide “transgene location vs. expression” scan. We found that one-third of the 4,504 mapped LUC genes were transcribed. However, only 10% of them were explained by conventional transcriptional fusions with the annotated genes, and the remainder of the genes exhibited novel transcription that occurred independently of the chromatin configuration or transcriptional activity inherent to the given chromosomal locus; rather, their transcriptional activation occurred stochastically at about 30% of each insertion event, but independent of the integration sites. We termed this activation phenomenon as an integration-dependent stochastic transcriptional activation, a new type of response of the plant genome to incoming coding sequences. We discuss the possible roles of this phenomenon in the evolution of eukaryotic genomes.

Kozak sequence acts as a negative regulator for de novo transcription initiation of newborn coding sequences in the plant genome

“…As de novo TSSs occur without inherent promoter-like epigenetic profiles (Figure 4e), a transcription-supporting chromatin configuration in these cases is supposed to be formed after sequence insertion. We found analogous cases in transgenic plants, in which promoterless LUC genes became transcriptionally activated concomitant with chromatin remodelling around the LUC insertion loci (Kudo, Matsuo, and Satoh et al ., 2020; Hata and Takada et al ., 2020). From the massive analysis of transgenic cultured cells, we also found that transcriptional activation occurred stochastically at 30% of the insertion events across the genome and was independent of chromosomal loci, suggesting that this transcriptional activation reflects the stochastic nature of chromatin remodelling (Satoh and Hata et al ., 2020).…”

“…This putative positioning mechanism is buttressed by our previous observation. When core promoter regions were triplicated in front of the LUC ORF, the most proximal core promoter unit was predominantly utilized in transgenic plants (Kudo, Matsuo, and Satoh et al ., 2020). Therefore, the coding sequence is likely to act as a cis -determinant element of the pol II PIC recruitment.…”

“…By introducing promoterless coding sequences into the genome, promoter/gene-trapping screening also simulates gene origination processes (Friedrich and Soriano, 1991; Springer, 2000). A recent study reported that newly inserted promoterless coding sequences were transcribed without trapping any endogenous genes or transcription units, which indicated the origination of brand-new promoters in the plant genome (Kudo, Matsuo, and Satoh et al ., 2020). However, the throughput of these studies was too limited to illustrate the general features of how newborn genes acquire transcriptional competency.…”

De novoactivated transcription of inserted foreign coding sequences is inheritable in the plant genome

“…Importantly, to become functional, new genes must acquire a promoter during their evolution. To examine the mechanism via which new genes acquire their promoters in the plant genome, we previously carried out an artificial evolutionary experiment (Satoh and Hata et al , 2020). To mimic a gene-birth event, we introduced exogenous promoterless coding sequences into Arabidopsis thaliana T87 cultured cells and analysed their transcriptional fates at the genome-wide level (Satoh and Hata et al , 2020).…”

“…Differing from the comparative genomics approach, artificial evolutionary experiments can dissect the molecular mechanisms of how newly emerged coding sequences acquire their promoters in the timescales of molecular biology and genetics. Previously, to mimic a gene-birth event, we introduced exogenous promoterless coding sequences into A. thaliana T87 cultured cells and analysed their transcriptional fates at the genome-wide level [26] (unpublished data; available at https://doi.org/10.1101/2020.11.28.401992). Interestingly, we found that promoterless coding sequences became transcriptionally activated via two distinct mechanisms:…”