Methods for phrasing epigenetic modifications of genomes

Abstract

Provided herein are methods and compositions for analyzing epigenetic modifications of genomes. The methods and compositions are suited for complete epigenome sequencing of any modification for which an antibody or an affinity binding agent has been developed.

1 . A method for analyzing an epigenetic modification comprising:
 (a) stretching a deoxynucleic acid (DNA comprising an epigenetic modification, and capturing the DNA on a spatially barcoded surface, wherein the spatially barcoded surface comprises oligonucleotides, each oligonucleotide comprising a positional barcode sequence indicative of a location of the oligonucleotide on the surface;   (b) constructing a spatially barcoded library of the DNA, the spatially barcoded library comprises a spatially barcoded sequence comprising the epigenetic modification; and   (c) labeling the epigenetic modification in the spatially barcoded sequence with an affinity agent that binds to the epigenetic modification.   
     
     
         2 . The method of  claim 1 , wherein the affinity agent comprises an antibody. 
     
     
         3 . The method of  claim 1 , wherein the affinity agent comprises biotin. 
     
     
         4 . (canceled) 
     
     
         5 . The method of  claim 1 , wherein the constructing the spatially barcoded library comprises using in vitro transposition. 
     
     
         6 . The method of  claim 1 , wherein the positional barcode sequence is indicative of the oligonucleotide on the spatially barcoded surface to within 0.1 μm, 0.2 μm, 0.5 μm, 1 μm, or 2 μm. 
     
     
         7 .- 10 . (canceled) 
     
     
         11 . The method of  claim 1 , further comprising sequencing the spatially barcoded library to generate sequence reads, and assembling the sequence reads with the aid of the positional barcode sequence. 
     
     
         12 . The method of  claim 1 , wherein the stretching the DNA comprises combing. 
     
     
         13 . The method of  claim 1 , wherein the DNA is from a genome, and wherein the stretching the DNA results in the DNA being stretched on the spatially barcoded surface at a density of at least about 20 genomes per square centimeter. 
     
     
         14 . The method of  claim 1 , wherein the DNA is from a genome, and wherein the stretching the DNA results in the DNA being stretched on the spatially barcoded surface at a density of at least about 30× diploid genome coverage. 
     
     
         15 . (canceled) 
     
     
         16 . (canceled) 
     
     
         17 . The method of  claim 1 , wherein the DNA comprises genomic DNA. 
     
     
         18 . The method of  claim 1 , wherein the DNA is at least 1 megabase (Mb) in length. 
     
     
         19 .- 39 . (canceled) 
     
     
         40 . The method of  claim 1 , wherein the spatially barcoded surface is an oligonucleotide array. 
     
     
         41 . The method of  claim 1 , wherein the spatially barcoded surface is a chip. 
     
     
         42 . The method of  claim 1 , wherein the spatially barcoded surface is a gel. 
     
     
         43 . The method of  claim 1 , further comprising: providing a phased map of the epigenomic modification across the DNA. 
     
     
         44 . The method of  claim 1 , wherein the DNA comprises at least two, three, four, or five different epigenetic modifications of the DNA with reference to the spatially barcoded surface. 
     
     
         45 . The method of  claim 44 , further comprising: providing a phased map of the at least two, three, four, or five different epigenomic modifications across the DNA. 
     
     
         46 . The method of  claim 44 , further comprising: determining relative positions between the at least two, three, four, or five different epigenetic modifications of the DNA, thereby phasing the at least two, three, four, or five different epigenetic modifications of the DNA. 
     
     
         47 . The method of  claim 1 , wherein capturing the DNA on the spatially barcoded surface comprises capturing ends of the DNA on the spatially barcoded surface. 
     
     
         48 . The method of  claim 47 , further comprising: determining the epigenomic modification between the captured ends of the DNA on the spatially barcoded surface.