Method for detecting methylated CpG islands
First Claim
1. A method of detecting methylated CpG islands which comprises:
- (a) purifying genomic DNA from a sample;
(b) incubating a methylated CpG island binding protein, a binding partner for the binding protein, and the purified genomic DNA to produce bound DNA, wherein the bound DNA comprises genomic DNA having methylated CpG islands bound to the said binding protein, having bound the binding partner;
(c) isolating the bound DNA; and
(d) amplifying the bound DNA to detect methylated CpG islands.
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Abstract
The present invention provides new and improved assay for detection of genomic methylated CpG islands. This new method is termed the methylated-CpG island recovery assay (MIRA). In accordance with one embodiment, MIRA comprises the steps of: (a) incubating genomic DNA fragments with a methylated CpG island binding protein in the presence of a binding partner for the binding protein to produce bound DNA containing methylated CpG islands, (b) isolating the bound DNA, and (c) detecting CpG island methylation by gene-specific amplification reactions. In accordance with a preferred embodiment, MIRA comprises the steps of: (a) incubating sonicated genomic DNA with a matrix containing a fusion protein of glutathione S-transferase (GST) and MBD2b (GST-MBD2b) in the presence of MBD3L1 to produce bound DNA containing methylated CpG islands, (b) eluting bound DNA from the matrix, and (c) detecting CpG island methylation by gene-specific amplification reactions.
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Citations
38 Claims
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1. A method of detecting methylated CpG islands which comprises:
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(a) purifying genomic DNA from a sample; (b) incubating a methylated CpG island binding protein, a binding partner for the binding protein, and the purified genomic DNA to produce bound DNA, wherein the bound DNA comprises genomic DNA having methylated CpG islands bound to the said binding protein, having bound the binding partner; (c) isolating the bound DNA; and (d) amplifying the bound DNA to detect methylated CpG islands. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16)
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17. A method of detecting methylated CpG islands which comprises:
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(a) isolating genomic DNA from a sample; (b) incubating MBD2b or a fusion protein comprising MBD2b, MBD3L1 and genomic DNA to produce bound DNA, wherein the bound DNA comprises genomic DNA containing methylated CpG islands bound to the MBD2b or the fusion protein comprising MBD2b and wherein the MBD2b or the fusion protein comprising MBD2b is bound to a solid phase; (c) eluting the bound DNA from the solid phase; and (d) amplifying the bound DNA to detect methylated CpG islands. - View Dependent Claims (18, 19, 20, 21, 22, 23, 24, 25, 26)
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27. A method of detecting methylated CpG islands which comprises:
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(a) isolating genomic DNA from a sample; (b) fragmenting the genomic DNA by sonication or restriction endonuclease; (c) incubating a solid phase containing MBD2b or a fusion protein comprising MBD2b with MBD3L1 such that MBD3L1 binds to the MBD2b or the fusion protein; (d) incubating the fragmented genomic DNA and the MBD2b having bound MBD3L1 or the fusion protein comprising MBD2b having bound MBD3L1 to produce bound DNA, wherein the bound DNA comprises the fragmented genomic DNA containing methylated CpG islands bound to the MBD2b having bound MBD3L1 or the fusion protein comprising MBD2b having bound MBD3L1; (e) eluting the bound DNA from the solid phase; and (f) gene-specific amplifying the bound DNA to detect methylated CpG islands. - View Dependent Claims (28, 29, 30, 31)
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32. A method of determining genome-wide methylation patterns which comprises:
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(a) isolating genomic DNA from a sample; (b) incubating a solid phase containing MBD2b or a fusion protein comprising MBD2b with MBD3L1 such that MBD3L1 binds to the MBD2b or the fusion protein comprising MBD2b; (c) incubating the isolated genomic DNA and the MBD2b having bound MBD3L1 or the fusion protein comprising MBD2b having bound MBD3L1 to produce bound DNA, wherein the bound DNA comprises the genomic DNA containing methylated CpG islands bound to the MBD2b having bound MBD3L1 or the fusion protein comprising MBD2b having bound MBD3L1; (d) eluting the bound DNA from the solid phase; (e) amplifying the bound DNA; (f) labeling the amplified bound DNA and input DNA; (g) hybridizing the labeled amplified bound DNA and labeled input DNA to a CpG island-containing microarray; and (h) analyzing the microarray to determine DNA methylation pattern. - View Dependent Claims (33, 34, 35, 36, 37, 38)
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Specification