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Figure 5. Differential methylation of a subset of NMIs.(A) All vertebrate genomes have a subset of NMIs that are subject to differential methylation as illustrated by a heat map of non-methylated DNA signal from testes and liver in human, mouse and zebrafish. In each case NMIs are ranked according to length and clustered as shared (upper) or unique (lower) between the two tissues. A 5-kb window centred at the NMI is shown and read density is indicated by colour intensity. (B) The overlap of NMIs identified in liver and testes is depicted by Venn diagrams for NMIs associated with protein-coding TSSs (upper) and for NMIs away from TSSs (lower). NMIs at TSSs are generally non-methylated in both tissues whereas differentially methylated NMIs tend to be found away from TSSs. (C) NMI length distribution plots for shared (Shared NMIs, solid line) or unique (Unique NMIs, dashed line) NMIs from testes (blue) or liver (red). Shared NMIs tend to be longer than tissue-specific unique NMIs. (D) CpG density distribution plots for shared (solid line) or unique (dashed line) NMIs from testes (blue) or liver (red). Shared NMIs tend to have higher CpG density than unique NMIs.DOI: http://dx.doi.org/10.7554/eLife.00348.008Figure 5—figure supplement 1. Validation of differentially methylated NMIs between liver and testes in mouse and zebrafish by bisulfite sequencing.(A, i–iv) Mouse NMIs unique to liver or testes were analysed by bisulfite sequencing to verify that the regions were indeed differentially methylated. Traces of non-methylated DNA are depicted for differentially methylated regions in mouse liver (red) and testes (blue) with NMIs depicted as bars under the traces. The y-axis depicts read density. Methylation status of the unique NMIs was confirmed using the indicated bisulfite PCR amplicon (BA, black rectangle). Empty and filled circles represent non-methylated and methylated CpG dinucleotides, respectively. (B, (i–iii) Zebrafish NMIs unique to liver or testes were validated by bisulfite sequencing as in (A).DOI: http://dx.doi.org/10.7554/eLife.00348.009 Image published in: Long HK et al. (2013) Copyright © 2013, Long et al. This image is reproduced with permission of the journal and the copyright holder. This is an open-access article distributed under the terms of the Creative Commons Attribution license Larger Image Printer Friendly View

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