This article is part of a special issue on epigenomics.

Open Access Research

The landscape of DNA repeat elements in human heart failure

Syed Haider1, Lina Cordeddu2, Emma Robinson2, Mehregan Movassagh2, Lee Siggens2, Ana Vujic2, Mun-Kit Choy2, Martin Goddard3, Pietro Lio1 and Roger Foo245*

Author Affiliations

1 Computer Laboratory, William Gates Building, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0FD

2 Division of Cardiovascular Medicine, University of Cambridge, Addenbrooke's Centre for Clinical Investigation, Level 6, Hills Road, Cambridge, CB2 0QQ

3 Department of Histopathology, Papworth Hospital, Papworth Everard, Cambridge, UK

4 Cardiovascular Research Institute, National University Health System, Singapore

5 Genome Institute of Singapore, Singapore 138672, Singapore

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Genome Biology 2012, 13:R90  doi:10.1186/gb-2012-13-10-r90

Published: 3 October 2012

Additional files

Additional file 1:

Figure S1 - schematic view of the analysis workflow. (a) Methylated DNA immunoprecipitation (MeDIP) was conducted to isolate methylated DNA fragments across four end-stage cardiomyopathic (EsCM 1 to 4) and four normal healthy control (CTRL A to D) hearts as listed in Additional file 2 and as published [10]. (b) MeDIP samples were sequenced using an Illumina genome analyzer (GIIx). (a) Short single-end reads from high-throughput sequencing were aligned against the human reference genome assembly (Hg18) and repeats database (Repbase). (d) Number of unique reads was normalized with reference to the respective total number of reads generated for each sample, and used as a proxy for the level of methylation for all repeat sequences. (e) Differential methylation between each of EsCM and CTRL samples was compared using Fisher's exact test statistic as well as unpaired Welch's t-test. (f) Differentially methylated repeat elements (DMReps) were selected for downstream analysis.

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Additional file 2:

Table S1 - number of sequencing reads from LV samples.

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Additional file 3:

Figure S2 - fully annotated large-scale version of Figure 1.

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Additional file 4:

List of all annotated repeat elements in the human genome.

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Additional file 5:

Figure S3. (a) All EsCM LV samples (EsCM 1 to 4) were compared against each of the CTRL samples (CTRL 1 to 4) using Fisher's exact test (P < 0.05 in at least 14 comparisons). Green color indicates hypomethylation in EsCM compared to the corresponding CTRL and red color indicates the converse, hypermethylation in EsCM. The color bar on the vertical axis represents families of repeat elements. A consistent pattern of hypomethylation was found only in satellite (SAT) family repeats in EsCM (arrow labels). (b) A bar chart representing the number of repeat sequences per family, following the elimination of repeats that were not differentially methylated between the two groups of samples.

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Additional file 6:

Figure S4 - fully annotated version of Additional file 5.

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Additional file 7:

CTRL versus EsCM comparison of each repeat element's methylation using unpaired Welch's t-test.

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Additional file 8:

Figure S5 - count data of repeat sequences merged into respective families. All EsCM LV samples (EsCM 1 to 4) were compared against each of the CTRL samples (CTRL 1 to 4) using Fisher's exact test (P < 0.05 in at least 14 comparisons). Green color indicates hypomethylation in EsCM compared to the corresponding CTRL and red color indicates the converse, hypermethylation in EsCM. The color bar on the vertical axis represents families of repeat elements. A consistent pattern of hypomethylation was found only in satellite (SAT) family repeats in EsCM.

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Additional file 9:

Figure S6 - the count data of repeat sequences merged into respective classes. All EsCM LV samples (EsCM 1 to 4) were compared against each of the CTRL samples (CTRL 1 to 4) using Fisher's exact test (P < 0.05 in at least 14 comparisons). Green color indicates hypomethylation in EsCM compared to the corresponding CTRL and red color indicates the converse, hypermethylation in EsCM. The color bar on the vertical axis represents families of repeat elements. A consistent pattern of hypomethylation was found only in satellite (SAT) family repeats in EsCM.

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Additional file 10:

List of all ALR, ALR_ and ALRb elements and coordinates in the human genome according to Hg18.

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Additional file 11:

Figure S7. (a-c) Average density plot for the methylation of ALR (a), ALR_ (b) and ALRb (c) comparing between EsCM (red) and CTRL (blue). Methylation density was consistently reduced in EsCM within the global coordinates of each repeat element (represented collectively here as 0.0 to 1.0 on the X-axis) as well as extending to the flanks (+3.0 and -3.0 kb) of the repeat elements. Light blue- and cream-colored error bars represent Bayesian credible intervals for CTRL and EsCM, respectively. See Movassagh et al. and Down et al. for detailed methods of methylation density analysis [10,39].

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Additional file 12:

Figure S8 - quantitative PCR using genomic DNA for the copy number abundance of SAT family repeat sequences (ALR, ALR_ and ALRb). (a-c) Quantification of copy number abundance for ALR (a), ALR_ (b) and ALRb (c) repeat elements was performed for EsCM and CTRL LV samples (EsCM A to H and CTRL 1 to 16), and normalized to the copy number for a control genomic locus (promoter region of OXT). A similar result was obtained when normalized to a second control genome locus (promoter region of GAPDH). The significance of difference between the two groups was computed using unpaired Wilcoxon rank-sum test, and a significance of P < 0.05 was detected only for ALRb.

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Additional file 13:

Table S2 - list of LV sample details.

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Additional file 14:

Figure S9. (a-c) Average density plot for the H3K36me3 ChIP-seq enrichment of ALR (a), ALR_ (b) and ALRb (c) comparing between EsCM (red) and CTRL (blue), similar to Additional file 11. H3K36me3 demarcates genomic regions that are actively transcribed. An enrichment of H3K36me3 mark in all three repeat elements in EsCM is consistent with increased transcriptional activity at these sites in EsCM.

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Additional file 15:

Table S3 - genes related to SAT elements.

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Additional file 16:

Table S4 - primers used for quantification PCR for SAT repeat elements.

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