METHODS AND KITS FOR DETECTION OF METHYLATION STATUS
First Claim
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1. A process for detecting 5-methylated and/or other modified cytosine residues in a nucleic acid sample comprising:
- a) replicating said nucleic acid sample under conditions such that 5-methylated cytosine residues are maintained and said other modified cytosine residues are diluted;
b) treating said replicated nucleic acid sample to convert unmodified cytosine residues to a uracil or thymidine residues; and
c) reading the sequence of said replicated nucleic acid sample wherein 5-hydroxymethylated cytosine residues are identified as residues that are read by sequencing as a thymidine or uracil residue in said replicated nucleic acid sample.
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Abstract
The present invention relates to methods and kits for the detection of 5-hydroxymethylcytosine (5hmC) and/or 5-methylcytosine (5meC). In some embodiments, the present invention relates to methods and kits for detection of 5hmC and/or 5meC in nucleic acid (e.g., DNA, RNA). In some embodiments, the present invention relates to detection of 5hmC in genomic DNA, e.g., mammalian genomic DNA
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Citations
42 Claims
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1. A process for detecting 5-methylated and/or other modified cytosine residues in a nucleic acid sample comprising:
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a) replicating said nucleic acid sample under conditions such that 5-methylated cytosine residues are maintained and said other modified cytosine residues are diluted; b) treating said replicated nucleic acid sample to convert unmodified cytosine residues to a uracil or thymidine residues; and c) reading the sequence of said replicated nucleic acid sample wherein 5-hydroxymethylated cytosine residues are identified as residues that are read by sequencing as a thymidine or uracil residue in said replicated nucleic acid sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 40, 41, 42)
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26. A process for detecting methylated and hydroxymethylated cytosine residues in a nucleic acid sample comprising:
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a) dividing said sample into at least first and second untreated portions; b) replicating said first portion with a tagged primer and a polymerase to provide parent and tagged replicated nucleic acid; c) treating said parent and said tagged replicated nucleic acid strands with a DNA methyltransferase to provide tagged 5-methylcytosine-modified replicated nucleic acid; d) isolating said tagged 5-methylcytosine-modified replicated nucleic acid; e) treating said isolated tagged 5-methylcytosine-modified replicated nucleic acid with bisulfite to convert unmodified cytosine residues to uracil residues; f) replicating said isolated tagged bisulfite-treated nucleic acid with a polymerase to provide a first bisulfite treated nucleic acid portion; g) sequencing said first bisulfite treated nucleic acid portion; h) treating said second portion with bisulfite to convert unmodified cytosine residues to uracil residues; i) replicating said bisulfite-treated nucleic acid with a polymerase to provide a second bisulfite treated nucleic acid portion; j) sequencing said second bisulfite treated nucleic acid portion; and k) comparing the sequence of said first bisulfite treated nucleic acid portion with the sequence of said second bisulfite treated portion, wherein 5-hydroxymethylated cytosine residues are identified as residues that are read by sequencing as a uracil or thymidine residue in said first bisulfite treated nucleic acid portion and as a cytosine residue at the corresponding position in said second bisulfite treated nucleic acid portion and wherein 5-methylated cytosine residues are identified as residues that are read as cytosine residues in said first and second bisulfite treated portions.
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27-39. -39. (canceled)
Specification