PRELIMINARY ANALYSIS OF NUCLEAR TRANSCRIPTOME REVEALED THE EXTENSIVE NUCLEAR-ENRICHED SUBCELLULAR DISTRIBUTION PATTERN OF TRANSPOSABLE ELEMENT-DERIVED TRANSCRIPTS IN RICE

The complexity and its functional consequence of nuclear transcriptome have come to be documented in mammal cells. However, little is known about plant nuclear transcriptome. In this study, we explored the complexity of rice nuclear transcriptome via the profiling of whole protoplasts and isolated nucleus using rRNA-depleted RNA-seq strategy. The expression characteristics of the long non-protein coding RNAs, transposable element-related genes and conventional protein coding genes were investigated. These analyses found that the proportion of expressed TE-related genes and reads mapped to these genes in nucleus were four time of that in protoplasts. In particular, no obvious nuclear-enriched expression pattern of lncRNAs or conventional protein coding genes was observed. Therefore, the extensive transcription of TE-related genes was the major contribution of the larger diversity of nuclear RNA species. Further muti-tissues comparative transcriptome analysis indicated that the transcription of TE-related genes, especially for nuclear-specific expressed TE-related genes defined in this study, was likely to be underestimated by conventional bulk RNA-seq. Furthermore, Gene Ontology functional enrichment analysis indicated that some nuclear abundant lncRNAs were co expressed with nuclear-located RNA binding proteins. Together, the global features of rice nuclear transcriptome will prompt the functional characterization of the nuclear-expressed TE-related genes and lncRNAs.

Automated summary

This study investigated the complexity and characteristics of the rice nuclear transcriptome. The expression of transposable element-related genes was found to be higher in the nucleus compared to protoplasts. Additionally, nuclear-enriched long non-protein coding RNAs were found to be co-expressed with nuclear-located RNA binding proteins. These findings provide valuable insights into the functional characterization of nuclear-expressed transposable element-related genes and lncRNAs.