Selective oxidation of 5-methylcytosine by tet-family proteins

Abstract

The present invention provides for novel methods for regulating and detecting the cytosine methylation status of DNA. The invention is based upon identification of a novel and surprising catalytic activity for the family of TET proteins, namely TET1, TET2, TET3, and CXXC4. The novel activity is related to the enzymes being capable of converting the cytosine nucleotide 5-methylcytosine into 5-hydroxymethylcytosine by hydroxylation.

1 .- 10 . (canceled) 
     
     
         11 . A method comprising:
 high throughput sequencing a nucleic acid sequence; and   detecting a methylation state of a site in said nucleic acid sequence, wherein said nucleic acid sequence comprises a hydroxymethylated base.   
     
     
         12 . The method of  claim 11 , wherein said nucleic acid sequence is a mammalian nucleic acid sequence. 
     
     
         13 . The method of  claim 11 , wherein said nucleic acid sequence is obtained from a eukaryotic organism 
     
     
         14 . The method of  claim 11 , wherein said nucleic acid sequence is not obtained from a bacteriophage. 
     
     
         15 . The method of  claim 11 , wherein said nucleic acid sequence is of an extracellular fluid sample. 
     
     
         16 . The method of  claim 11 , further comprising isolating said nucleic acid sequence from a sample. 
     
     
         17 . The method of  claim 11 , further comprising obtaining said nucleic acid sequence. 
     
     
         18 . The method of  claim 11 , further comprising associating a label with said site. 
     
     
         19 . The method of  claim 11 , wherein said site comprises a genomic region. 
     
     
         20 . The method of  claim 11 , wherein said nucleic acid sequence is from a subject in need thereof. 
     
     
         21 . The method of  claim 11 , wherein said nucleic acid sequence is from a subject having or suspected of having cancer.