Article Figures & Data
Figures
- Figure 1.
Flow Chart of RepTAS.
[See online article for color version of this figure.]
- Figure 2.
Detection of Arabidopsis lincRNAs by RepTAS and ATH lincRNA v1 Arrays.
(A) Distribution in 200 tiling arrays of lincRNAs detected by RepTAS. Blue bars show predicted lincRNAs, whereas red bars show 85 to ∼140-nucleotide signal peaks or partial transcripts detected by only two neighboring positive probes. Such partial transcripts were considered to be false positives. See Methods for details.
(B) Changes of lincRNA expression levels in roots and leaves detected by custom array and RNA-seq. lincRNAs with more than twofold change in expression level are represented by blue solid circles. Gray dashed lines show a twofold change in expression level. FPKM, fragments per kilobase of exon per million fragments mapped (Cabili et al., 2011).
(C) Expression levels of lincRNAs, pri-miRNAs, and mRNAs in two independent flower samples detected by ATH lincRNA v1 arrays. The x axis and y axis give log2 values of signal intensity detected in two biological replicates. Blue solid circles, lincRNAs; green squares, mRNAs; red triangles, pri-miRNAs; and gray solid circles, lincRNAs with signal intensities below the background value. Shadow shows the range of twofold change in signal intensity of each transcript.
(D) Accumulative distribution of lincRNA, pri-miRNA, and mRNA expression levels detected by ATH lincRNA v1 arrays. Green, mRNAs; red, lincRNAs; blue, pri-miRNAs; and brown, negative control probes. Average signal values of two independent flower samples are given.
- Figure 3.
Expression Profiles of lincRNAs in Different Arabidopsis Plant Organs and in Response to Biotic and Abiotic Stresses.
(A) A Venn diagram showing preferential expression of lincRNAs in different organs. F, flowers; L, leaves; and R, roots.
(B) Organ preferential expression of three selected lincRNAs. Relative expression levels of lincRNAs were measured by qRT-PCR. Other examples are shown in Supplemental Data Set 12 online.
(C) and (D) Detection and experimental verification of At5NC056820, a predicted lincRNA. Expression levels are given with sd bars (n = 3). Note that At5NC056820 was highly induced by elf18 and moderately induced by ABA and drought treatment.
[See online article for color version of this figure.]
- Figure 4.
Global Changes of Expression Levels of Three Transcript Categories in 11 Arabidopsis Mutants.
(A) Global changes of transcript levels in 11 mutants compared with the wild type. Plant organs are shown in cartoon formats. Dark-green “++” shows highly upregulated transcripts compared with the wild type. Light-green “+” shows slightly upregulated transcripts compared with the wild type. Red “-” shows downregulated transcripts compared with the wild type. Brown “nc” indicates no change.
(B) A Venn diagram of upregulated (green) and downregulated (red) lincRNAs in se-2 and cbp20/80 double mutant.
(C) Heat maps of 734 lincRNAs in se-2 and the cbp20/80 double mutant. Data in (B) were used for this analysis.
(D) Detection of lincRNA splicing using RT-PCR. Primers of PCR/RT-PCR are shown by arrows.
(E) Two intron retention events in two lincRNAs (AT2G07042 and AT4G23205) detected by RT-PCR in se, cbp20, cbp80, and the cbp20/80 double mutant. We used hyl1-2 as a negative control of splicing regulated by SE, CBP20, and CBP80. The AT1G13880 is an mRNA previously shown to be regulated by SE, CBP20, and CBP80 (Laubinger et al., 2008); this served as a positive control. RT-PCR products were verified by sequencing. gDNA, genomic DNA.
Tables
TU Type Other RNAs EST Tiling Array Analysis (Seedlings) Tiling Array Analysis (Seeds) RepTAS RNA-seq lincRNAs 36 36 32 61 6,480 278 GATUs 52 69 369 434 * 370 TUCPs 5 0 0 0 22 7 RCTUs 55 83 172 237 6,728 678 OITUs 1 8 1 6 * 7 Total intergenic TUs 149 196 574 738 13,230 1,340 *In our RepTAS analysis (Methods), GATUs and OITUs could not meet the identification criteria and therefore these TUs were filtered out.
Additional Files
Supplemental Data
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