Transcriptional Modulation during Photomorphogenesis in Rice Seedlings

Abstract

Light is one of the most important factors regulating plant gene expression patterns, metabolism, physiology, growth, and development. To explore how light may induce or alter transcript splicing, we conducted RNA-Seq-based transcriptome analyses by comparing the samples harvested as etiolated seedlings grown under continuous dark conditions vs. the light-treated green seedlings. The study aims to reveal differentially regulated protein-coding genes and novel long noncoding RNAs (lncRNAs), their light-induced alternative splicing, and their association with biological pathways. We identified 14,766 differentially expressed genes, of which 4369 genes showed alternative splicing. We observed that genes mapped to the plastid-localized methyl-erythritol-phosphate (MEP) pathway were light-upregulated compared to the cytosolic mevalonate (MVA) pathway genes. Many of these genes also undergo splicing. These pathways provide crucial metabolite precursors for the biosynthesis of secondary metabolic compounds needed for chloroplast biogenesis, the establishment of a successful photosynthetic apparatus, and photomorphogenesis. In the chromosome-wide survey of the light-induced transcriptome, we observed intron retention as the most predominant splicing event. In addition, we identified 1709 novel lncRNA transcripts in our transcriptome data. This study provides insights on light-regulated gene expression and alternative splicing in rice.

Keywords: MVA and MEP pathways; RNA-Seq; alternative splicing; circadian clock; lncRNA; photomorphogenesis; rice; transcriptome.

Figure 1

Summary of differential gene expression and transcript splicing observed in rice seedling shoots undergoing photomorphogenesis. Expressed genes: total number of expressed genes in rice transcriptome; DE genes: differentially expressed genes; Non-DE genes: genes with no significant difference in expression; AS: alternatively spliced; DES: differentially expressed and spliced. Expressed and differentially expressed gene counts are represented by green shaded boxes, non-DE genes in blue shaded boxes, and AS genes in purple boxes. Mixed color boxes represent gene counts from overlapping AS, DE, and non-DE.

Figure 2

Pathway enrichment analysis using the Plant Reactome. (A) Plant Reactome pathway enrichment analysis plots. (B) Unique and shared pathways enriched for the light-upregulated and downregulated gene sets. (C) Counts of genes mapped to some of the common Plant Reactome pathways. Light-upregulated (green) and downregulated (grey).

Figure 3

Gene expression and splicing of cytosolic mevalonate (MVA) and plastid-localized methyl erythritol 4-phosphate (MEP) pathway genes. AACT, acetyl-CoA acetyltransferase; HMGS, hydroxymethyl glutaryl CoA synthase; HMGR, 3-hydroxy-3-methylglutaryl-coenzyme A reductase; MK, mevalonate kinase; PMK, phosphomevalonate kinase; MDD, mevalonate diphosphate decarboxylase; DXS, 1-deoxy-D-xylulose-5-phosphate synthase; DXR, 1-deoxy-D-xylulose-5-phosphate reductoisomerase; CDPMES, 2-C-methyl-D-erythritol4-phosphate cytidylyl transferase; CDPMEK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; MECPS, 2-C-methyl-D-erythritol2,4-cyclodiphosphate synthase; HDS, 4-hydroxy-3-methylbut-2-enyldiphosphate synthase; HDR, 4-hydroxy-3-methylbut-2-enyldiphosphate reductase. Blue: intron retention.

Figure 4

Classification of lncRNAs identified in the transcriptome of dark- and light-treated rice seedling samples.

Figure 5

Plant Reactome pathway enrichment showing light-regulated genes and reaction event coverage for the DNA biosynthesis pathway of the G1-to-S phase mitotic cell cycle. (A) shows enrichment in dark conditions and (B) shows enrichment in light conditions. Each reaction has several input and output entities and may be regulated or catalyzed by a protein and or a protein complex. Solid arrows depict the directionality. The view also shows overlaps between the sub-pathways. The boxes with yellow-painted areas show the gene coverage (the number of genes mapped to the protein or protein complex entity participating in the respective reaction).

Figure 5

Plant Reactome pathway enrichment showing light-regulated genes and reaction event coverage for the DNA biosynthesis pathway of the G1-to-S phase mitotic cell cycle. (A) shows enrichment in dark conditions and (B) shows enrichment in light conditions. Each reaction has several input and output entities and may be regulated or catalyzed by a protein and or a protein complex. Solid arrows depict the directionality. The view also shows overlaps between the sub-pathways. The boxes with yellow-painted areas show the gene coverage (the number of genes mapped to the protein or protein complex entity participating in the respective reaction).

Figure 6

Splicing and expression pattern (normalized counts) of nitrogen assimilation cycle genes under dark and light conditions. NRT: nitrate transporter; NR: nitrate reductase; NiR: nitrite reductase.