1. DNA Damage-Induced Transcription of Transposable Elements and Long Non-coding RNAs in Arabidopsis Is Rare and ATM-Dependent 
Zhenxing Wang, Rainer Schwacke, Reinhard Kunze 
Molecular Plant 
Volume 9, Issue 8, Pages (August 2016)
DOI: /j.molp
Copyright © 2016 The Author Terms and Conditions

2. Figure 1
Phenotypic and Transcriptional Consequences of X-Ray Treatment of Arabidopsis WT and atm Mutant Seedlings.
(A) Seven days after irradiation with 80 Gy X-rays, root growth and true leaf appearance are retarded in WT seedlings, whereas development of atm mutant seedlings has stopped.
(B) 30 days after X-ray treatment, WT Arabidopsis plants are slightly smaller than non-irradiated control plants, whereas atm mutants are dead.
(C) The Venn diagram shows the numbers of transcriptionally ≥2-fold upregulated (green) and ≥2-fold downregulated (pink) genes in WT seedlings (left circle) and atm mutant seedlings (right circle). The two gene groups crossing the green-pink border are upregulated in WT and downregulated in atm (14 genes) or downregulated in WT and upregulated in atm (18 genes).
Molecular Plant 2016 9, DOI: ( /j.molp )
Copyright © 2016 The Author Terms and Conditions

3. Figure 2
Transcriptionally Regulated TEs after X-Ray Treatment in Arabidopsis Seedlings.
(A) Numbers of upregulated (red) and downregulated TEs (blue) from different retrotransposon (top half) and DNA transposon superfamilies (bottom half) in Arabidopsis Col-0 WT seedlings.
(B) Depicted are the 43 upregulated and 33 downregulated TEs in WT and the single up- and downregulated TEs in atm mutant seedlings. The color scale indicates the log2-fold changes.
Molecular Plant 2016 9, DOI: ( /j.molp )
Copyright © 2016 The Author Terms and Conditions

4. Figure 3
Transcriptionally Regulated lncRNAs after X-Ray Treatment in Arabidopsis.
(A) In column WT, the 56 upregulated and 32 downregulated lncRNAs in Arabidopsis Col-0 seedlings are shown. Column atm shows the four upregulated and three downregulated lncRNAs in Arabidopsis atm mutant seedlings. The color scale indicates the log2-fold changes.
(B) In WT seedlings, 46 of 86 regulated lncRNAs are derived from TEs. In atm mutant seedlings, six of seven regulated lncRNAs are derived from TEs. Five of the six lncRNAs with altered expression after X-ray treatment both in WT and atm mutant plants are derived from TEs/repeats.
Molecular Plant 2016 9, DOI: ( /j.molp )
Copyright © 2016 The Author Terms and Conditions

5. Figure 4 Intersection of Arabidopsis TEs and lncRNAs
Green bars, 5583 of 14 719 lncRNAs (38%) overlap with at least one TE; blue bars, 5067 of 23 609 TEs (21%) overlap with at least one lncRNA.
Molecular Plant 2016 9, DOI: ( /j.molp )
Copyright © 2016 The Author Terms and Conditions

6. Figure 5
Genes Coexpressed with Flanking X-Ray-Responsive lncRNAs in Arabidopsis Seedlings.
(A) Heatmap showing the X-ray-responsive lncRNAs (column R) with flanking coexpressed protein-coding genes (column G). The color scale indicates the log2-fold changes.
(B) The 28 genes coexpressed with flanking lncRNAs after X-ray treatment of Arabidopsis thaliana Col-0 and the single coexpressed gene in atm mutant seedlings (marked with an asterisk) are distributed on all five chromosomes. Open triangles indicate the centromere positions.
Molecular Plant 2016 9, DOI: ( /j.molp )
Copyright © 2016 The Author Terms and Conditions

7. Figure 6
Coexpression of Closely Spaced Genes, lncRNAs, and TEs on Chromosome 1.
Coexpression of closely spaced genes, lncRNAs, and TEs on the chromosome 1 region from positions 111 776 600 to 111 785 600.
(A) RNA-seq reads from untreated (0 Gy) and X-ray treated (80 Gy) WT and mutant (atm) seedlings were mapped to the Arabidopsis genome sequence using the Integrated Genome Browser (Nicol et al., 2009).
(B) Location of genes and lncRNAs (track Locus), TEs (track Natural transposons), and gene structures (track Protein Coding Genes), displayed by PLncDBG/Browse ( Arrowheads beneath loci indicate the positions of qRT–PCR primers.
(C) Relative expression levels of protein-coding genes AT1G32580 and AT1G32580, lncRNAs At1NC and At1NC043010, TE AT1TE38195 determined by qRT–PCR. Relative expression levels in untreated WT seedlings were set to 1 (0 Gy WT). Error bars indicate the SD. Significant differences (Student's t-test) between untreated and irradiated plants with *p < 0.05, **p < 0.01, and ***p <
Molecular Plant 2016 9, DOI: ( /j.molp )
Copyright © 2016 The Author Terms and Conditions

8. Figure 7
Transcriptional Response to DNA Damage of DNA Repair and Epigenetic Genes Downstream of ATM.
Relative expression levels of BRCA1, DRM1, JMJ30, AGO2, and AGO4 in untreated (–) and X-ray treated (+) WT and atm seedlings determined by qRT–PCR. Error bars indicate the SD. Significant differences (Student's t-test) between untreated and irradiated plants with *p < 0.05, **p < 0.01, and ***p <
Molecular Plant 2016 9, DOI: ( /j.molp )
Copyright © 2016 The Author Terms and Conditions

9. Figure 8
DNA Damage-Induced Transcriptional Regulation of TEs and lncRNAs Depends on DNA Repair and Epigenetic Genes Downstream of ATM.
(A–D) Relative expression levels of (A) the MULE/MuDR-related TE AT1TE04710, (B) the Helitron-related TE AT1TE69990, (C) the AtCopia95-derived TE ATCOPEG1 (AT2G04460), and (D) the lncRNA RLFS_ in untreated (–) and X-ray treated (+) WT and mutant (atm, brca1, drm1, jmj30, ago2, ago4) seedlings determined by qRT–PCR. Error bars indicate the SD. Significant differences (Student's t-test) between untreated and irradiated plants with *p < 0.05, **p < 0.01, and ***p <
Molecular Plant 2016 9, DOI: ( /j.molp )
Copyright © 2016 The Author Terms and Conditions