Methods of Epigenetic Analysis
The present invention provides for methods of epigenetic analysis. In some cases, the methods may include obtaining a sample comprising a nucleic acid sequence. In some cases, the nucleic acid sequence may comprise one or more epigenetic marks. The methods may include performing a sequencing. The methods may include distinguishing a hydroxymethylated base from a methylated base.
1 - 96 . (canceled)
97 . A composition comprising a mixture of a methylcytosine dioxygenase, and nucleic acid comprising glucosylated 5-hydroxymethylcytosine.
98 . The composition of claim 97 , wherein said methylcytosine dioxygenase is a ten eleven translocation (TET) enzyme.
99 . The composition of claim 98 , wherein said TET enzyme comprises TET1, TET2, TET3, CXXC4, or a combination thereof.
100 . composition of claim 97 , wherein said mixture comprises a DNA methyltransferase.
101 . The composition of claim 100 , wherein said DNA methyltransferase is DNMT1.
102 . The composition of claim 97 , further comprising a glucose donor substrate.
103 . The composition of claim 102 , wherein said glucose donor substrate comprises uridine diphosphate glucose (UDPG).
104 . The composition of claim 97 , further comprising a buffer.
105 . The composition of claim 97 , further comprising 5-methylcytosine.
106 . The composition of claim 97 , further comprising a short interfering ribonucleic acid (siRNA).
107 . The composition of claim 106 , wherein the siRNA is selected from the group consisting of SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 70, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 86, SEQ ID NO: 98, and SEQ ID NO: 92.
108 . A method comprising using a methylcytosine dioxygenase to generate a 5-hydroxymethylcytosine.
109 . The method of claim 108 , wherein said methylcytosine dioxygenase is a ten eleven translocation (TET) enzyme.
110 . The method of claim 109 , wherein said TET enzyme comprises TET1, TET2, TET3, CXXC4, or a combination thereof.
111 . The method of claim 108 , further comprising using a DNA methyltransferase.
112 . The method of claim 111 , wherein said DNA methyltransferase is DNMT1.