Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis

Abstract

Recent research on long noncoding RNAs (lncRNAs) has expanded our understanding of gene transcription regulation and the generation of cellular complexity. Depending on their genomic origins, lncRNAs can be transcribed from intergenic or intragenic regions or from introns of protein-coding genes. We have recently reported more than 6000 intergenic lncRNAs in Arabidopsis. Here, we systematically identified long noncoding natural antisense transcripts (lncNATs), defined as lncRNAs transcribed from the opposite DNA strand of coding or noncoding genes. We found a total of 37,238 sense-antisense transcript pairs and 70% of annotated mRNAs to be associated with antisense transcripts in Arabidopsis. These lncNATs could be reproducibly detected by different technical platforms, including strand-specific tiling arrays, Agilent custom expression arrays, strand-specific RNA-seq, and qRT-PCR experiments. Moreover, we investigated the expression profiles of sense-antisense pairs in response to light and observed spatial and developmental-specific light effects on 626 concordant and 766 discordant NAT pairs. Genes for a large number of the light-responsive NAT pairs are associated with histone modification peaks, and histone acetylation is dynamically correlated with light-responsive expression changes of NATs.

Figure 1.

Identification and profiling of lncNATs in Arabidopsis. (A) Pipeline for the identification of lncNATs in Arabidopsis. NAT pairs were identified from mRNAs and RepTAS-uncovered novel intragenic transcripts. NAT pairs were verified by different platforms, including ATH NAT custom array, strand-specific RNA-seq (ssRNA-seq), and quantitative RT-PCR (qRT-PCR). (B) Detection of lncNATs in 200 tiling arrays. The x-axis represents the percentage of tiling arrays in which the transcripts could be detected, and the y-axis represents the percentage of detectable transcripts. Blue bars show lncNATs and red bars show false positives. (C) Reproducible detection of NAT pairs by ATH NAT custom array. The y-axis represents the number of detectable NAT pairs in all three biological replicates of each sample. (R) Roots; (L) leaves; (F) inflorescences. (D) Accumulative frequency of mRNA expression levels (green line), pre-miRNAs (red line), lncNATs (blue line), and transposable element transcripts (gray line) in roots. The x-axis represents the log2 value of normalized signal intensity and the y-axis represents accumulative frequency. (E) Venn diagram showing the number of organ-specific NAT pairs in roots (blue), leaves (green), and inflorescences (red). (F) Correlation between ATH NAT array and ssRNA-seq in the detection of organ-specific NAT pairs. The fold-change between leaves and inflorescences of sense transcript levels is represented by blue circles, and antisense transcript levels by pink circles. Gray circles are transcripts that do not show expression differences (less than twofold) between the two organs. (r.s) Correlation for sense transcripts; (r.as) correlation for antisense transcripts. (G) Correlation between ATH NAT array and qRT-PCR in the detection of light-responsive NATs. The x-axis gives the log2 value of fold change detected by ATH NAT array and the y-axis gives the value detected by qRT-PCR. Gray circles represent NATs that do not change more than twofold in expression after light treatment. (6h) Samples treated with 6 h of continuous white light; (D) etiolated seedlings.

Figure 2.

Light-regulated coding and noncoding transcripts. (A) Heat map representing fold change (log2 value) of light-regulated transcript levels at 1 h and 6 h in cotyledons. (B) Organ-preferential expression of light-regulated lncRNAs. Venn diagrams show number of light-regulated transcripts in each organ. (C) Signal intensity and (D) validation by qRT-PCR of an organ-specific light-induced lncNAT. (E) Signal intensity and (F) validation by qRT-PCR of an organ-specific light-repressed lncNAT. Error bar gives standard error (SE) (n = 3). (C) cotyledon; (H) hypocotyl; (R) root; (D) dark; (1) 1-h light; (6) 6-h light.

Figure 3.

Light-regulated NAT pairs. (A) Clustering of light-regulated concordant (positively correlated) NAT pairs. Each blue line represents a light-regulated concordant NAT pair in cotyledon, hypocotyl, and root at 1 h and 6 h. (B) Heat map of discordant (negatively correlated) NAT pairs at 1 h. Expression levels of discordant sense (S) and antisense (AS) transcripts in cotyledon, hypocotyl, and root. (C) Clustering of light-regulated discordant (negatively correlated) NAT pairs. Each red line represents a light-regulated discordant NAT pair in cotyledon, hypocotyl, and root at 1 h and 6 h. (D,E) Validation of light-regulated concordant and discordant NAT pairs by qRT-PCR. Bar plot represents relative expression level. Error bar gives standard error (SE) (n = 3). (C) cotyledon; (H) hypocotyl; (R) root; (D) dark; (1) 1-h light; (6) 6-h light.

Figure 4.

Light effects on histone modifications associated with genes encoding NATs. (A) Association of four kinds of histone modifications and light-regulated genes for NATs. Percentage of histone modification associated with genes for noncoding and coding NATs. (B) Histone modifications of genes for light-induced NATs. Each line represents a gene for the corresponding light-induced transcript. (C) Histone modifications of genes for dark-induced NATs. Each line represents a gene for the corresponding dark-induced transcript.

Figure 5.

H3K9ac is associated with the regulation of a light-responsive discordant NAT pair. (A,B) Detection of a discordant NAT pair by ATH NAT array and qRT-PCR. Error bar gives standard error (SE) (n = 3). (C) cotyledon; (H) hypocotyl; (R) root; (D) dark; (6) 6-h light. (C) Gene structures of AT2G18280 and AT2G18290 and H3K9ac peaks at this locus in darkness and light (6 h).