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Research ArticleLARGE-SCALE BIOLOGY ARTICLES
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Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

Jun Liu, Choonkyun Jung, Jun Xu, Huan Wang, Shulin Deng, Lucia Bernad, Catalina Arenas-Huertero, Nam-Hai Chua
Jun Liu
Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065
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Choonkyun Jung
Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065
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Jun Xu
Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065
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Huan Wang
Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065
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Shulin Deng
Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065
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Lucia Bernad
Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065
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Catalina Arenas-Huertero
Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065
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Nam-Hai Chua
Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065
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  • For correspondence: chua@mail.rockefeller.edu

Published November 2012. DOI: https://doi.org/10.1105/tpc.112.102855

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    Figure 1.

    Flow Chart of RepTAS.

    [See online article for color version of this figure.]

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    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.

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    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.]

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    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.

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    Table 1. Summary of Intergenic TUs Identified by Various Approaches
    TU TypeOther RNAsESTTiling Array Analysis (Seedlings)Tiling Array Analysis (Seeds)RepTASRNA-seq
    lincRNAs363632616,480278
    GATUs5269369434*370
    TUCPs5000227
    RCTUs55831722376,728678
    OITUs1816*7
    Total intergenic TUs14919657473813,2301,340
    • *In our RepTAS analysis (Methods), GATUs and OITUs could not meet the identification criteria and therefore these TUs were filtered out.

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Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis
Jun Liu, Choonkyun Jung, Jun Xu, Huan Wang, Shulin Deng, Lucia Bernad, Catalina Arenas-Huertero, Nam-Hai Chua
The Plant Cell Nov 2012, 24 (11) 4333-4345; DOI: 10.1105/tpc.112.102855

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Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis
Jun Liu, Choonkyun Jung, Jun Xu, Huan Wang, Shulin Deng, Lucia Bernad, Catalina Arenas-Huertero, Nam-Hai Chua
The Plant Cell Nov 2012, 24 (11) 4333-4345; DOI: 10.1105/tpc.112.102855
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The Plant Cell Online: 24 (11)
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Vol. 24, Issue 11
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