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.
