Detection and quantification of hydroxymethylated nucleotides in a polynucleotide preparation
First Claim
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1. A method of quantifying the amount of a hydroxymethylated nucleotide (hmN) in a polynucleotide preparation, comprising:
- (a) obtaining a preparation of polynucleotides;
(b) modifying any hmN in the polynucleotides of a first portion of the preparation to produce modified hmN (mhmN), wherein the modifying is done using a DNA glucosyltransferase; and
(c) quantifying the amount of hmN in the preparation by;
(i) reacting the polynucleotides from (b) with a site-specific endonuclease selected from BccI, BciVI, BspHI, BspQI, BstEII, BstNI, BstYI, BstCI, CviAII, CviQI, DpnI, EcoRI, HinfI, Hpy188I, Hpy188III, MboII, MfeI, MlyI, NsiI, RsaI, ScaI, SfcI, SmlI, Tsp45I, XbaI, BsaWI, BsoBI, BspEI, BssI, BtgZI, EciI, MspI, NmeAII, PspXI, TliI, XhoI, and XmaI; and
(ii) comparing the amount of an uncleaved polynucleotide that would otherwise be cleaved but for the modified hmN with the amount of uncleaved polynucleotide produced by digesting a control sample by the site-specific endonuclease, wherein the control sample is a second portion of the preparation that has not been modified to produce mhmN.
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Abstract
Methods and compositions are described for detecting hydroxymethylated nucleotides (hmNs) in a polynucleotide preparation with a view to mapping the location of hmNs in a genome, quantifying the occurrence of hmNs at selected loci and correlating the occurrence of hmNs with gene expression and phenotypic traits. Embodiments describe the use of modifying enzymes together with site-specific endonucleases to detect the hmNs.
33 Citations
14 Claims
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1. A method of quantifying the amount of a hydroxymethylated nucleotide (hmN) in a polynucleotide preparation, comprising:
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(a) obtaining a preparation of polynucleotides; (b) modifying any hmN in the polynucleotides of a first portion of the preparation to produce modified hmN (mhmN), wherein the modifying is done using a DNA glucosyltransferase; and (c) quantifying the amount of hmN in the preparation by; (i) reacting the polynucleotides from (b) with a site-specific endonuclease selected from BccI, BciVI, BspHI, BspQI, BstEII, BstNI, BstYI, BstCI, CviAII, CviQI, DpnI, EcoRI, HinfI, Hpy188I, Hpy188III, MboII, MfeI, MlyI, NsiI, RsaI, ScaI, SfcI, SmlI, Tsp45I, XbaI, BsaWI, BsoBI, BspEI, BssI, BtgZI, EciI, MspI, NmeAII, PspXI, TliI, XhoI, and XmaI; and (ii) comparing the amount of an uncleaved polynucleotide that would otherwise be cleaved but for the modified hmN with the amount of uncleaved polynucleotide produced by digesting a control sample by the site-specific endonuclease, wherein the control sample is a second portion of the preparation that has not been modified to produce mhmN. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
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14. A method of quantifying the amount of a hydroxymethylated cytosine (hmC) in a polynucleotide preparation, comprising:
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(a) obtaining a preparation of polynucleotides; (b) modifying any hmC in the polynucleotides of a first portion of the preparation to produce modified hmC (mhmC), wherein the modifying is done using a DNA glucosyltransferase; and (c) quantifying the amount of hmC in the preparation by; (i) reacting the polynucleotides from (b) with MspI; and (ii) comparing the amount of an uncleaved polynucleotide that would otherwise be cleaved but for the mhmC with the amount of uncleaved polynucleotide produced by digesting a control sample by MspI, wherein the control sample is a second portion of the preparation that has not been modified to produce mhmC.
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Specification