This article is part of a special issue on epigenomics.

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Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax

John R Bracht1*, David H Perlman2 and Laura F Landweber1*

Author Affiliations

1 Ecology & Evolutionary Biology Department, Princeton University, Washington Rd., Princeton, NJ, 08544, USA

2 Collaborative Proteomics and Mass Spectrometry Center, Molecular Biology Department and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Rd., Princeton, NJ, 08544, USA

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Genome Biology 2012, 13:R99  doi:10.1186/gb-2012-13-10-r99

Published: 17 October 2012

Additional files

Additional file 1:

The methyl cohort. A list of chromosomes whose methylation was predicted by meDIP-seq and validated by bisulfite-PCR or qPCR. Columns labeled as 'signal' indicate the number of meDIP-seq reads at 46 h less the number of reads from vegetative DNA. For columns labeled 'bisulfite-qPCR' and '40 h dAza demethylated?', bold font denotes statistically significant effects relative to vegetative or untreated controls (Student's 1-tailed t-test for unequal variance, p < 0.05), while a 'yes' indicates an effect that was observed but did not reach statistical significance. 'n/a' indicates that the test was not performed.

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Additional file 2:

The CC motif cohort. A list of chromosomes containing three or more CC motifs and that overlap substantially with the methylation and hydroxymethylation cohorts (Additional files 1 and 3).

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Additional file 3:

The hydroxymethyl cohort. A list of chromosomes whose hydroxymethylation was predicted by meDIP-seq, with signal defined as in Additional file 1.

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Additional file 4:

Supplemental figure depicting bisulfite-PCR sequence analysis. (a) Contig4414.0 following bisulfite treatment of 40 h DNA and PCR with C-to-T converted primers, which are not methyl-specific. (b) Contig4414.0 following bisulfite treatment of 40 h DNA and PCR with cytosine-retaining (methyl-specific) primers. (c) The 170 bp satellite following bisulfite treatment of vegetative and PCR with C-to-T converted primers, which are not methyl-specific. (d) The 170 bp satellite following bisulfite treatment of 40 h DNA and PCR with cytosine-retaining (methyl-specific) primers. (e) The transposon TBE1 following bisulfite treatment of 40 h DNA and PCR with cytosine-retaining (methyl-specific) primers. TBE1, telomere bearing element 1.

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Additional file 5:

Supplemental figure depicting Southern analysis for retention of 170 bp repeat and TBE1 transposon in 72 h azacitidine-treated cells. (a) Southern hybridization. (b) quantification of (a).

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Additional file 6:

A table of primers used in this study. All primers used for bisulfite PCR, bisulfite qPCR and Southern blotting experiments.

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Additional file 7:

Sanger sequencing data (in FASTA format) for Figure 6b. Bisulfite-treated TEBPα PCR product, MAC isoforms (smaller) shown in lane 9. TEBPα, Telomere End-Binding Protein α. MAC, macronucleus.

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Additional file 8:

Sanger sequencing data (in FASTA format) for Figure 6b. Bisulfite-treated TEBPα PCR product, MIC isoforms (larger) shown in lane 9. TEBPα, Telomere End-Binding Protein α. MIC, micronucleus.

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Additional file 9:

Sanger sequencing data (in FASTA format) for Figure 6c. Contig4414 bisulfite sequences.

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Additional file 10:

Sanger sequencing data (in FASTA format) for Figure 6d. Bisulfite sequences of TEBPα aberrantly spliced products. TEBPα, Telomere End-Binding Protein α.

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Additional file 11:

Sanger sequencing data (in FASTA format) for Additional file 4a. Sequences for Contig4414.0 following bisulfite treatment of 40 h DNA and PCR with C-to-T converted primers.

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Additional file 12:

Sanger sequencing data (in FASTA format) for Additional file 4b. Sequences for Contig4414.0 following bisulfite treatment of 40 h DNA and PCR with cytosine-retaining (methyl-specific) primers.

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Additional file 13:

Sanger sequencing data (in FASTA format) for Additional file 4c. Sequences for the 170 bp satellite following bisulfite treatment of vegetative and PCR with C-to-T converted primers.

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Additional file 14:

Sanger sequencing data (in FASTA format) for Additional file 4d. Sequences for the 170 bp satellite following bisulfite treatment of 40 h DNA and PCR with cytosine-retaining (methyl-specific) primers.

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Additional file 15:

Sanger sequencing data (in FASTA format) for Additional file 4e. Sequences for the transposon TBE1 following bisulfite treatment of 40 h DNA and PCR with cytosine-retaining (methyl-specific) primers. TBE1, telomere bearing element 1.

Format: FASTA Size: 8KB Download file

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