Methods and compositions for amplification and sequencing of genome and epigenome
AssigneeBoard of Regents, The University of Texas System
InventorsKaile Wang, Nicholas Navin, Yun Yan, Heba Elgamal, Yiyun Lin, Junke Wang
Life of this patent
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Abstract
The present disclosure relates to methods and compositions for the approximately simultaneous amplification of closed chromatin region DNA and open chromatin region DNA. The present disclosure further provides methods of producing a DNA library for analysis of open chromatin region DNA and closed chromatin region DNA approximately simultaneously and methods of identifying a DNA sequence variation or an epigenetic modification in a sample. Aspects of the present disclosure further relate to a DNA library produced by the methods of the present disclosure.
Claims50
A method of producing a DNA library for analysis of open chromatin region DNA and closed chromatin region DNA approximately simultaneously, the method comprising:
- a) obtaining a sample comprising chromosomal DNA;
- b) performing a first labeling reaction on said chromosomal DNA to label at least a first portion of open chromatin region DNA comprised within said chromosomal DNA with a first label;
- c) disrupting the structure of said chromosomal DNA to expose at least a first portion of closed chromatin region DNA comprised within said chromosomal DNA;
- d) performing a second labeling reaction on said chromosomal DNA to label:
- i) at least said first portion of said exposed closed chromatin region DNA with a second label;
- and
- ii) at least said first portion, or a second portion, of open chromatin region DNA with the second label;
- and
- e) performing an amplification reaction to amplify said first labeled open chromatin region DNA, said second labeled exposed closed chromatin region DNA, and said second labeled open chromatin region DNA comprised within said chromosomal DNA.
A method of producing a DNA library for analysis of open chromatin region DNA and closed chromatin region DNA approximately simultaneously, the method comprising:
- a) obtaining a plurality of samples comprising chromosomal DNA;
- b) performing a first labeling reaction on said chromosomal DNA of each sample to label at least a first portion of open chromatin region DNA comprised within said chromosomal DNA with a first label;
- c) disrupting the structure of said chromosomal DNA of each sample to expose at least a first portion of closed chromatin region DNA comprised within said chromosomal DNA;
- d) performing a second labeling reaction to label:
- i) at least said first portion of said exposed closed chromatin region DNA with a second label;
- and
- ii) at least said first portion, or a second portion, of open chromatin region DNA with the second label;
- e) combining the first labeled open chromatin region DNA, the second labeled exposed closed chromatin region DNA, and the second labeled open chromatin region DNA from each sample of the plurality of samples;
- and
- f) performing an amplification reaction to amplify the first labeled open chromatin region DNA, the second labeled exposed closed chromatin region DNA, and the second labeled open chromatin region DNA comprised within said chromosomal DNA.
A method of identifying a DNA sequence variation or an epigenetic modification in a sample, the method comprising:
- a) obtaining a sample comprising chromosomal DNA;
- b) performing a first labeling reaction on said chromosomal DNA to label at least a first portion of open chromatin region DNA comprised within said chromosomal DNA with a first label;
- c) disrupting the structure of said chromosomal DNA to expose at least a first portion of closed chromatin region DNA comprised within said chromosomal DNA;
- d) performing a second labeling reaction to label:
- i) at least said first portion of said exposed closed chromatin region DNA with a second label;
- and
- ii) at least said first portion, or a second portion, of open chromatin region DNA with the second label;
- e) performing an amplification reaction to amplify the first labeled open chromatin region DNA, the second labeled exposed closed chromatin region DNA, and the second labeled open chromatin region DNA comprised within said chromosomal DNA;
- f) performing a DNA sequencing reaction to obtain the DNA sequence of the first labeled open chromatin region DNA, the second labeled exposed closed chromatin region DNA, or the second labeled open chromatin region DNA comprised within said chromosomal DNA;
- and
- g) identifying said DNA sequence variation or said epigenetic modification in said sample.
A kit comprising:
- a) a first transposase;
- b) a first adaptor molecule for labeling open chromatin region DNA;
- c) a second adaptor molecule for labeling closed chromatin region DNA and open chromatin region DNA;
- and
- d) a chromatin disruption agent for disrupting the chromatin structure of chromosomal DNA.
Dependencies are inferred from the claim text.