Compositions and methods for identifying hydroxymethylcytosine in a DNA
Provided herein in some embodiments is a non-naturally occurring variant of a wild type restriction enzyme defined by SEQ ID NO: 20, wherein the variant has at least a 2 fold increase in cleavage at 5-β glucosylhydroxymethylcytosine (5βghmC) compared with methylcytosine relative to the wild type enzyme. Methods for examining hydroxymethylation of a DNA sample using the variant enzyme are also provided.
1. A non-naturally occurring variant having at least 90% sequence identity to the corresponding wild type restriction enzyme in a family of related restriction endonucleases characterized by a consensus sequence of SEQ ID NO:21, wherein the variant has a mutation at one or more positions selected from positions corresponding to V72, T152 and R282 in SEQ ID NO: 11, and wherein the variant has at least a 2 fold increase in cleavage at 5-β glucosylhydroxymethylcytosine (5βghmC) compared with 5 methyl C (5mC) relative to the wild type enzyme.
2. The variant of claim 1 , wherein the variant has an amino acid substitution at a position corresponding to R282 of SEQ ID NO:11.
3. The variant of claim 2 , wherein the position corresponding to R282 of SEQ ID NO:11 is substituted with any amino acid except for F, Y, I, and V.
4. The variant of claim 2 , wherein the position corresponding to R282 of SEQ ID NO:11 is substituted with K, T, Q, L, S, M, C, N, G or A.
5. The variant of claim 2 , wherein the position corresponding to R282 of SEQ ID NO:11 is substituted with a G or A.
6. A method, comprising:
reacting a variant restriction enzyme of claim 1 with a DNA comprising one or more nucleotides selected from the group consisting of 5-β glucosylhydroxymethylcytosine (5βghmC) and hydroxymethylcytosine (hmC), for cleaving the DNA.
7. The method of claim 6 , further comprising:
determining at least one of the location of and the amount of 5hmC or 5βghmC in the DNA.
8. The method of claim 6 , wherein the method further comprises:
reacting the DNA with β glucosyltransferase (βGT) prior to reacting the variant enzyme with the DNA, thereby converting any hmC in the DNA to 5 βghmC.
9. The method of claim 6 , further comprising:
sequencing the DNA to create a hydroxymethylome map of the DNA.
10. The method of claim 6 , wherein the DNA is part or all of a genome.
11. The method of claim 6 , wherein the method comprises determining the presence or absence of 5hmC or 5βghmC at a predetermined position in the DNA.
12. A method, comprising:
a. obtaining a library of non-naturally occurring variants having at least 90% sequence identity to the corresponding wild type restriction enzyme in a family of related restriction endonucleases characterized by a consensus sequence of SEQ ID NO:21, wherein the variant has a mutation at one or more positions selected from positions corresponding to V72, T152 and R282 in SEQ ID NO: 11, and wherein the variant has at least a 2 fold increase in cleavage at 5βghmC compared with 5mC relative to the wild type enzyme
b. assaying for cleavage specificity of the variant enzymes for 5βghmC and for 5mC; and
c. selecting a variant having at least 2 fold increase in selectivity for 5βghmC versus 5mC compared to the wild type restriction enzyme.