Methods of epigenetic analysis

Abstract

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 .- 10 . (canceled) 
     
     
         11 . A method, comprising:
 contacting a polynucleotide with an enzyme or a catalytically active fragment thereof that performs an oxidation on an epigenetic modification to form a contacted polynucleotide; and   sequencing the contacted polynucleotide.   
     
     
         12 . The method of  claim 11 , wherein the enzyme or the catalytically active fragment performs a conversion selected from the group consisting of:
 oxidizing 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC);   oxidizing 5mC to an acid beyond hydroxymethylation;   oxidizing 5mC to an aldehyde beyond hydroxymethylation;   oxidizing 5hmC to an acid beyond hydroxymethylation;   oxidizing 5hmC to an aldehyde beyond hydroxymethylation; and any combination thereof.   
     
     
         13 . The method of  claim 11 , further comprising isolating the polynucleotide from a sample. 
     
     
         14 . The method of  claim 11 , wherein the polynucleotide is isolated from an extracellular fluid. 
     
     
         15 . The method of  claim 11 , wherein the enzyme or the catalytically active fragment thereof is isolated prior to contacting. 
     
     
         16 . The method of  claim 11 , wherein the polynucleotide is contacted with the enzyme. 
     
     
         17 . The method of  claim 11 , wherein the polynucleotide is contacted with the catalytically active fragment of the enzyme. 
     
     
         18 . The method of  claim 11 , wherein the enzyme or the catalytically active fragment thereof comprises a catalytically active TET family enzyme or a functional fragment thereof. 
     
     
         19 . The method of  claim 11 , wherein the sequencing comprises determining a methylation state of the contacted polynucleotide. 
     
     
         20 . The method of  claim 11 , wherein the sequencing comprises an imaging. 
     
     
         21 . The method of  claim 11 , wherein the polynucleotide comprises 5mC and wherein the contacting converts at least in part the 5mC to 5hmC. 
     
     
         22 . The method of  claim 11 , wherein the polynucleotide comprises 5mC and wherein the contacting converts at least in part the 5mC to an acid beyond hydroxymethylation. 
     
     
         23 . The method of  claim 11 , wherein the polynucleotide comprises 5mC and wherein the contacting converts at least in part the 5mC to an aldehyde beyond hydroxymethylation. 
     
     
         24 . The method of  claim 11 , wherein the polynucleotide comprises 5hmC and wherein the contacting converts at least in part the 5hmC to an acid beyond hydroxymethylation. 
     
     
         25 . The method of  claim 11 , wherein the polynucleotide comprises 5hmC and wherein the contacting converts at least in part the 5hmC to an aldehyde beyond hydroxymethylation. 
     
     
         26 . The method of  claim 11 , wherein the enzyme comprises a TET1 enzyme or a catalytically active fragment thereof. 
     
     
         27 . The method of  claim 11 , wherein the enzyme comprises a TET2 enzyme or a catalytically active fragment thereof. 
     
     
         28 . The method of  claim 11 , wherein the enzyme comprises a TET3 enzyme or a catalytically active fragment thereof. 
     
     
         29 . The method of  claim 11 , wherein the enzyme comprises a CXXC4 enzyme or a catalytically active fragment thereof. 
     
     
         30 . The method of  claim 11 , further comprising identifying a 5mC. 
     
     
         31 . The method of  claim 11 , further comprising identifying a 5hmC.