Transposition of Native Chromatin for Personal Epigenomics

Abstract

Provided herein is a method for analyzing polynucleotides such as genomic DNA. In certain embodiments, the method comprises: (a) treating chromatin isolated from a population of cells with an insertional enzyme complex to produce tagged fragments of genomic DNA; (b) sequencing a portion of the tagged fragments to produce a plurality of sequence reads; and (c) making an epigenetic map of a region of the genome of the cells by mapping information obtained from the sequence reads to the region. A kit for performing the method is also provided.

1 .- 30 . (canceled) 
     
     
         31 . A composition comprising:
 an insertional enzyme complex comprising a transposase enzyme; and   a plurality of tagged nucleic acid fragments derived from one or more regions of open chromatin, wherein said insertional enzyme complex does not comprise an antibody specific to a protein that is part of said chromatin.   
     
     
         32 . The composition of  claim 31 , further comprising a plurality of divalent cations. 
     
     
         33 . The composition of  claim 32 , wherein the plurality of divalent cations are not chelated. 
     
     
         34 . The composition of  claim 32 , wherein the plurality of divalent cations are selected from the group consisting of: magnesium, manganese, or any combination thereof. 
     
     
         35 . The composition of  claim 31 , wherein the transposase is a Tn transposase. 
     
     
         36 . The composition of  claim 35 , wherein the Tn transposase is a Tn5 transposase. 
     
     
         37 . The composition of  claim 31 , wherein the plurality of tagged nucleic acid fragments correspond to two or more regions of a genome. 
     
     
         38 . The composition of  claim 31 , wherein the plurality of tagged nucleic acid fragments correspond to at least 1,000 regions of a genome. 
     
     
         39 . The composition of  claim 31 , wherein the plurality of tagged nucleic acid fragments correspond to genome-wide regions of open chromatin. 
     
     
         40 . The composition of  claim 31 , wherein the insertional enzyme complex is contained within a permeabilized cell nucleus. 
     
     
         41 . The composition of  claim 40 , wherein the permeabilized cell nucleus is isolated from a cell. 
     
     
         42 . The composition of  claim 40 , wherein the permeabilized cell nucleus is contained within a cell. 
     
     
         43 . A composition comprising:
 an insertional enzyme complex comprising a transposase enzyme; and   a plurality of tagged nucleic acid fragments derived from one or more regions of open chromatin, wherein the plurality of tagged nucleic acid fragments correspond to genome-wide regions of open chromatin.   
     
     
         44 . The composition of  claim 43 , further comprising a plurality of divalent cations. 
     
     
         45 . The composition of  claim 44 , wherein the plurality of divalent cations are not chelated. 
     
     
         46 . The composition of  claim 44 , wherein the plurality of divalent cations are selected from the group consisting of: magnesium, manganese, or any combination thereof. 
     
     
         47 . The composition of  claim 43 , wherein the transposase is a Tn transposase. 
     
     
         48 . The composition of  claim 47 , wherein the Tn transposase is a Tn5 transposase. 
     
     
         49 . The composition of  claim 43 , wherein the insertional enzyme complex is contained within a permeabilized cell nucleus. 
     
     
         50 . The composition of  claim 49 , wherein the permeabilized cell nucleus is isolated from a cell. 
     
     
         51 . The composition of  claim 49 , wherein the permeabilized cell nucleus is contained within a cell.